https://bioinformaticsonline.com/snippets?offset=320 https://bioinformaticsonline.com/snippets/view/37263/running-trinity-on-rna-seq Mon, 09 Jul 2018 06:05:43 -0500 https://bioinformaticsonline.com/snippets/view/37263/running-trinity-on-rna-seq ➜ trinityrnaseq-Trinity-v2.6.6 git:(master) ✗ ./Trinity --seqType fq --max_memory 250G --left /media/urbe/MyPassport/rnaseq_boris/AIG_AAAOSW_8_1_C1CBGACXX.IND11_noribo_clean.fastq --right /media/urbe/MyPassport/rnaseq_boris/AIG_AAAOSW_8_2_C1CBGACXX.IND11_noribo_clean.fastq --CPU 40 ______ ____ ____ ____ ____ ______ __ __ | || \ | || \ | || || | | | || D ) | | | _ | | | | || | | |_| |_|| / | | | | | | | |_| |_|| ~ | | | | \ | | | | | | | | | |___, | | | | . \ | | | | | | | | | | | |__| |__|\_||____||__|__||____| |__| |____/ Left read files: $VAR1 = [ '/media/urbe/MyPassport/rnaseq_boris/AIG_AAAOSW_8_1_C1CBGACXX.IND11_noribo_clean.fastq' ]; Right read files: $VAR1 = [ '/media/urbe/MyPassport/rnaseq_boris/AIG_AAAOSW_8_2_C1CBGACXX.IND11_noribo_clean.fastq' ]; Trinity version: Trinity-v2.6.6 ** NOTE: Latest version of Trinity is Trinity-v2.7.0-PRERELEASE, and can be obtained at: https://github.com/trinityrnaseq/trinityrnaseq/releases Monday, July 9, 2018: 10:35:42 CMD: java -Xmx64m -XX:ParallelGCThreads=2 -jar /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/util/support_scripts/ExitTester.jar 0 Monday, July 9, 2018: 10:35:42 CMD: java -Xmx64m -XX:ParallelGCThreads=2 -jar /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/util/support_scripts/ExitTester.jar 1 Monday, July 9, 2018: 10:35:42 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir Monday, July 9, 2018: 10:35:42 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/chrysalis ---------------------------------------------------------------------------------- -------------- Trinity Phase 1: Clustering of RNA-Seq Reads --------------------- ---------------------------------------------------------------------------------- --------------------------------------------------------------- ------------ In silico Read Normalization --------------------- -- (Removing Excess Reads Beyond 50 Coverage -- --------------------------------------------------------------- # running normalization on reads: $VAR1 = [ [ '/media/urbe/MyPassport/rnaseq_boris/AIG_AAAOSW_8_1_C1CBGACXX.IND11_noribo_clean.fastq' ], [ '/media/urbe/MyPassport/rnaseq_boris/AIG_AAAOSW_8_2_C1CBGACXX.IND11_noribo_clean.fastq' ] ]; Monday, July 9, 2018: 10:35:42 CMD: /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/util/insilico_read_normalization.pl --seqType fq --JM 250G --max_cov 50 --min_cov 1 --CPU 40 --output /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/insilico_read_normalization --max_pct_stdev 10000 --left /media/urbe/MyPassport/rnaseq_boris/AIG_AAAOSW_8_1_C1CBGACXX.IND11_noribo_clean.fastq --right /media/urbe/MyPassport/rnaseq_boris/AIG_AAAOSW_8_2_C1CBGACXX.IND11_noribo_clean.fastq --pairs_together --PARALLEL_STATS Converting input files. (both directions in parallel)CMD: seqtk-trinity seq -A /media/urbe/MyPassport/rnaseq_boris/AIG_AAAOSW_8_1_C1CBGACXX.IND11_noribo_clean.fastq >> left.fa CMD: seqtk-trinity seq -A /media/urbe/MyPassport/rnaseq_boris/AIG_AAAOSW_8_2_C1CBGACXX.IND11_noribo_clean.fastq >> right.fa CMD finished (128 seconds) CMD finished (129 seconds) CMD: touch left.fa.ok CMD finished (0 seconds) CMD: touch right.fa.ok CMD finished (0 seconds) Done converting input files.CMD: cat left.fa right.fa > both.fa CMD finished (5 seconds) CMD: touch both.fa.ok CMD finished (0 seconds) ------------------------------------------- ----------- Jellyfish -------------------- -- (building a k-mer catalog from reads) -- ------------------------------------------- CMD: jellyfish count -t 40 -m 25 -s 100000000 --canonical both.fa CMD finished (33 seconds) CMD: jellyfish histo -t 40 -o jellyfish.K25.min2.kmers.fa.histo mer_counts.jf CMD finished (6 seconds) CMD: jellyfish dump -L 2 mer_counts.jf > jellyfish.K25.min2.kmers.fa CMD finished (16 seconds) CMD: touch jellyfish.K25.min2.kmers.fa.success CMD finished (0 seconds) CMD: /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/util/..//Inchworm/bin/fastaToKmerCoverageStats --reads left.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25 --num_threads 20 --DS > left.fa.K25.stats CMD: /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/util/..//Inchworm/bin/fastaToKmerCoverageStats --reads right.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25 --num_threads 20 --DS > right.fa.K25.stats -reading Kmer occurrences...-reading Kmer occurrences... done parsing 59324464 Kmers, 59324464 added, taking 99 seconds. done parsing 59324464 Kmers, 59324464 added, taking 113 seconds. STATS_GENERATION_TIME: 252 seconds. CMD finished (378 seconds) STATS_GENERATION_TIME: 299 seconds. CMD finished (411 seconds) CMD: touch left.fa.K25.stats.ok CMD finished (0 seconds) CMD: touch right.fa.K25.stats.ok CMD finished (0 seconds) -sorting each stats file by read name. CMD: /usr/bin/sort --parallel=40 -k5,5 -T . -S 125G left.fa.K25.stats > left.fa.K25.stats.sort CMD: /usr/bin/sort --parallel=40 -k5,5 -T . -S 125G right.fa.K25.stats > right.fa.K25.stats.sort CMD finished (9 seconds) CMD finished (9 seconds) CMD: touch left.fa.K25.stats.sort.ok CMD finished (0 seconds) CMD: touch right.fa.K25.stats.sort.ok CMD finished (0 seconds) CMD: /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/util/..//util/support_scripts//nbkc_merge_left_right_stats.pl --left left.fa.K25.stats.sort --right right.fa.K25.stats.sort --sorted > pairs.K25.stats -opening left.fa.K25.stats.sort -opening right.fa.K25.stats.sort -done opening files. CMD finished (85 seconds) CMD: touch pairs.K25.stats.ok CMD finished (0 seconds) CMD: /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/util/..//util/support_scripts//nbkc_normalize.pl --stats_file pairs.K25.stats --max_cov 50 --min_cov 1 --max_pct_stdev 10000 > pairs.K25.stats.C50.pctSD10000.accs 6275795 / 16641634 = 37.71% reads selected during normalization. 0 / 16641634 = 0.00% reads discarded as likely aberrant based on coverage profiles. 0 / 16641634 = 0.00% reads missing kmer coverage (N chars included?). 0 / 16641634 = 0.00% reads discarded as below minimum coverage threshold=1 CMD finished (25 seconds) CMD: touch pairs.K25.stats.C50.pctSD10000.accs.ok CMD finished (0 seconds) CMD: touch /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/insilico_read_normalization/AIG_AAAOSW_8_1_C1CBGACXX.IND11_noribo_clean.fastq.normalized_K25_maxC50_minC1_pctSD10000.fq.ok CMD finished (0 seconds) CMD: touch /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/insilico_read_normalization/AIG_AAAOSW_8_2_C1CBGACXX.IND11_noribo_clean.fastq.normalized_K25_maxC50_minC1_pctSD10000.fq.ok CMD finished (0 seconds) CMD: ln -sf /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/insilico_read_normalization/AIG_AAAOSW_8_1_C1CBGACXX.IND11_noribo_clean.fastq.normalized_K25_maxC50_minC1_pctSD10000.fq left.norm.fq CMD finished (0 seconds) CMD: ln -sf /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/insilico_read_normalization/AIG_AAAOSW_8_2_C1CBGACXX.IND11_noribo_clean.fastq.normalized_K25_maxC50_minC1_pctSD10000.fq right.norm.fq CMD finished (0 seconds) -removing tmp dir /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/insilico_read_normalization/tmp_normalized_reads Normalization complete. See outputs: /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/insilico_read_normalization/AIG_AAAOSW_8_1_C1CBGACXX.IND11_noribo_clean.fastq.normalized_K25_maxC50_minC1_pctSD10000.fq /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/insilico_read_normalization/AIG_AAAOSW_8_2_C1CBGACXX.IND11_noribo_clean.fastq.normalized_K25_maxC50_minC1_pctSD10000.fq Monday, July 9, 2018: 10:51:26 CMD: touch /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/insilico_read_normalization/normalization.ok Converting input files. (in parallel)Monday, July 9, 2018: 10:51:26 CMD: cat /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/insilico_read_normalization/left.norm.fq | seqtk-trinity seq -A - >> left.fa Monday, July 9, 2018: 10:51:26 CMD: cat /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/insilico_read_normalization/right.norm.fq | seqtk-trinity seq -A - >> right.fa Monday, July 9, 2018: 10:51:30 CMD: touch left.fa.ok Monday, July 9, 2018: 10:51:30 CMD: touch right.fa.ok Monday, July 9, 2018: 10:51:30 CMD: touch left.fa.ok right.fa.ok Monday, July 9, 2018: 10:51:30 CMD: cat left.fa right.fa > /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/both.fa Monday, July 9, 2018: 10:51:32 CMD: touch /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/both.fa.ok ------------------------------------------- ----------- Jellyfish -------------------- -- (building a k-mer catalog from reads) -- ------------------------------------------- * Running CMD: jellyfish count -t 40 -m 25 -s 100000000 --canonical /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/both.fa * Running CMD: jellyfish dump -L 1 mer_counts.jf > jellyfish.kmers.fa * Running CMD: jellyfish histo -t 40 -o jellyfish.kmers.fa.histo mer_counts.jf ---------------------------------------------- --------------- Inchworm --------------------- -- (Linear contig construction from k-mers) -- ---------------------------------------------- * Running CMD: /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/Inchworm/bin//inchworm --kmers jellyfish.kmers.fa --run_inchworm -K 25 -L 25 --monitor 1 --DS --num_threads 6 --PARALLEL_IWORM > /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/inchworm.K25.L25.DS.fa.tmp * Running CMD: mv /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/inchworm.K25.L25.DS.fa.tmp /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/inchworm.K25.L25.DS.fa Monday, July 9, 2018: 11:00:35 CMD: touch /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/inchworm.K25.L25.DS.fa.finished -------------------------------------------------------- -------------------- Chrysalis ------------------------- -- (Contig Clustering & de Bruijn Graph Construction) -- -------------------------------------------------------- inchworm_target: /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/both.fa bowite_reads_fa: /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/both.fa chrysalis_reads_fa: /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/both.fa * Running CMD: /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/util/support_scripts/filter_iworm_by_min_length_or_cov.pl /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/inchworm.K25.L25.DS.fa 100 10 > /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/chrysalis/inchworm.K25.L25.DS.fa.min100 * Running CMD: /home/urbe/anaconda3/bin/bowtie2-build --threads 40 -o 3 /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/chrysalis/inchworm.K25.L25.DS.fa.min100 /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/chrysalis/inchworm.K25.L25.DS.fa.min100 1>/dev/null * Running CMD: bash -c " set -o pipefail;/home/urbe/anaconda3/bin/bowtie2 --local -k 2 --no-unal --threads 40 -f --score-min G,20,4 -x /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/chrysalis/inchworm.K25.L25.DS.fa.min100 /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/both.fa | samtools view -@ 40 -F4 -Sb - | samtools sort -m 3355443200 -@ 40 -no - - > /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/chrysalis/iworm.bowtie.nameSorted.bam" * Running CMD: /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/util/support_scripts/scaffold_iworm_contigs.pl /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/chrysalis/iworm.bowtie.nameSorted.bam /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/inchworm.K25.L25.DS.fa > /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/chrysalis/iworm_scaffolds.txt * Running CMD: /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/Chrysalis/GraphFromFasta -i /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/inchworm.K25.L25.DS.fa -r /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/both.fa -min_contig_length 200 -min_glue 2 -glue_factor 0.05 -min_iso_ratio 0.05 -t 40 -k 24 -kk 48 -scaffolding /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/chrysalis/iworm_scaffolds.txt > /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/chrysalis/iworm_cluster_welds_graph.txt * Running CMD: /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/Chrysalis/BubbleUpClustering -i /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/inchworm.K25.L25.DS.fa -weld_graph /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/chrysalis/iworm_cluster_welds_graph.txt -min_contig_length 200 > /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/chrysalis/GraphFromIwormFasta.out * Running CMD: /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/Chrysalis/CreateIwormFastaBundle -i /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/chrysalis/GraphFromIwormFasta.out -o /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/chrysalis/bundled_iworm_contigs.fasta -min 200 * Running CMD: /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/Chrysalis/ReadsToTranscripts -i /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/both.fa -f /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/chrysalis/bundled_iworm_contigs.fasta -o /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/chrysalis/readsToComponents.out -t 40 -max_mem_reads 50000000 * Running CMD: /usr/bin/sort --parallel=40 -T . -S 250G -k 1,1n /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/chrysalis/readsToComponents.out > /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/chrysalis/readsToComponents.out.sort Monday, July 9, 2018: 11:17:32 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_0 Monday, July 9, 2018: 11:17:32 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_1 Monday, July 9, 2018: 11:17:32 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_2 Monday, July 9, 2018: 11:17:33 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_3 Monday, July 9, 2018: 11:17:33 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_4 Monday, July 9, 2018: 11:17:33 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_5 Monday, July 9, 2018: 11:17:33 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_6 Monday, July 9, 2018: 11:17:33 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_7 Monday, July 9, 2018: 11:17:33 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_8 Monday, July 9, 2018: 11:17:34 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_9 Monday, July 9, 2018: 11:17:34 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_10 Monday, July 9, 2018: 11:17:34 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_11 Monday, July 9, 2018: 11:17:34 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_12 Monday, July 9, 2018: 11:17:34 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_13 Monday, July 9, 2018: 11:17:35 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_14 Monday, July 9, 2018: 11:17:35 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_15 Monday, July 9, 2018: 11:17:35 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_16 Monday, July 9, 2018: 11:17:35 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_17 Monday, July 9, 2018: 11:17:35 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_18 Monday, July 9, 2018: 11:17:36 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_19 Monday, July 9, 2018: 11:17:36 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_20 Monday, July 9, 2018: 11:17:36 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_21 Monday, July 9, 2018: 11:17:36 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_22 Monday, July 9, 2018: 11:17:36 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_23 Monday, July 9, 2018: 11:17:37 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_24 Monday, July 9, 2018: 11:17:37 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_25 Monday, July 9, 2018: 11:17:37 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_26 Monday, July 9, 2018: 11:17:37 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_27 Monday, July 9, 2018: 11:17:37 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_28 Monday, July 9, 2018: 11:17:38 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_29 Monday, July 9, 2018: 11:17:38 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_30 Monday, July 9, 2018: 11:17:38 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_31 Monday, July 9, 2018: 11:17:38 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_32 Monday, July 9, 2018: 11:17:38 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_33 Monday, July 9, 2018: 11:17:39 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_34 Monday, July 9, 2018: 11:17:39 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_35 Monday, July 9, 2018: 11:17:39 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_36 Monday, July 9, 2018: 11:17:39 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_37 Monday, July 9, 2018: 11:17:39 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_38 Monday, July 9, 2018: 11:17:40 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_39 Monday, July 9, 2018: 11:17:40 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_40 Monday, July 9, 2018: 11:17:40 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_41 Monday, July 9, 2018: 11:17:40 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_42 Monday, July 9, 2018: 11:17:40 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_43 Monday, July 9, 2018: 11:17:41 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_44 Monday, July 9, 2018: 11:17:41 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_45 Monday, July 9, 2018: 11:17:41 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_46 Monday, July 9, 2018: 11:17:41 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_47 Monday, July 9, 2018: 11:17:41 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_48 Monday, July 9, 2018: 11:17:42 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_49 Monday, July 9, 2018: 11:17:42 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_50 Monday, July 9, 2018: 11:17:42 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_51 Monday, July 9, 2018: 11:17:42 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_52 Monday, July 9, 2018: 11:17:42 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_53 Monday, July 9, 2018: 11:17:42 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_54 Monday, July 9, 2018: 11:17:43 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_55 Monday, July 9, 2018: 11:17:43 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_56 Monday, July 9, 2018: 11:17:43 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_57 Monday, July 9, 2018: 11:17:43 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_58 Monday, July 9, 2018: 11:17:43 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_59 Monday, July 9, 2018: 11:17:44 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_60 Monday, July 9, 2018: 11:17:44 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_61 Monday, July 9, 2018: 11:17:44 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_62 Monday, July 9, 2018: 11:17:44 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_63 Monday, July 9, 2018: 11:17:44 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_64 Monday, July 9, 2018: 11:17:45 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_65 Monday, July 9, 2018: 11:17:45 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_66 Monday, July 9, 2018: 11:17:45 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_67 Monday, July 9, 2018: 11:17:45 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_68 Monday, July 9, 2018: 11:17:46 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_69 Monday, July 9, 2018: 11:17:46 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_70 Monday, July 9, 2018: 11:17:46 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_71 Monday, July 9, 2018: 11:17:46 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_72 Monday, July 9, 2018: 11:17:47 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_73 Monday, July 9, 2018: 11:17:47 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_74 Monday, July 9, 2018: 11:17:47 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_75 Monday, July 9, 2018: 11:17:47 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_76 Monday, July 9, 2018: 11:17:48 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_77 Monday, July 9, 2018: 11:17:48 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_78 Monday, July 9, 2018: 11:17:48 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_79 Monday, July 9, 2018: 11:17:48 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_80 Monday, July 9, 2018: 11:17:49 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_81 Monday, July 9, 2018: 11:17:49 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_82 Monday, July 9, 2018: 11:17:49 CMD: mkdir -p 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/home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_139 Monday, July 9, 2018: 11:18:08 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_140 Monday, July 9, 2018: 11:18:08 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_141 Monday, July 9, 2018: 11:18:09 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_142 Monday, July 9, 2018: 11:18:09 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_143 Monday, July 9, 2018: 11:18:10 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_144 Monday, July 9, 2018: 11:18:10 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_145 Monday, July 9, 2018: 11:18:11 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_146 Monday, July 9, 2018: 11:18:12 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_147 Monday, July 9, 2018: 11:18:12 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_148 Monday, July 9, 2018: 11:18:13 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_149 Monday, July 9, 2018: 11:18:14 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_150 Monday, July 9, 2018: 11:18:14 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_151 Monday, July 9, 2018: 11:18:15 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_152 Monday, July 9, 2018: 11:18:16 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_153 Monday, July 9, 2018: 11:18:17 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_154 Monday, July 9, 2018: 11:18:17 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_155 Monday, July 9, 2018: 11:18:18 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_156 Monday, July 9, 2018: 11:18:19 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_157 Monday, July 9, 2018: 11:18:20 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_158 Monday, July 9, 2018: 11:18:20 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_159 Monday, July 9, 2018: 11:18:21 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_160 Monday, July 9, 2018: 11:18:22 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_161 Monday, July 9, 2018: 11:18:22 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_162 Monday, July 9, 2018: 11:18:22 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_163 Monday, July 9, 2018: 11:18:22 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_164 Monday, July 9, 2018: 11:18:23 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_165 Monday, July 9, 2018: 11:18:23 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_166 Monday, July 9, 2018: 11:18:23 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_167 Monday, July 9, 2018: 11:18:23 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_168 Monday, July 9, 2018: 11:18:23 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_169 Monday, July 9, 2018: 11:18:24 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_170 Monday, July 9, 2018: 11:18:24 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_171 Monday, July 9, 2018: 11:18:24 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_172 Monday, July 9, 2018: 11:18:24 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_173 Monday, July 9, 2018: 11:18:24 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_174 Monday, July 9, 2018: 11:18:24 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_175 Monday, July 9, 2018: 11:18:25 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_176 Monday, July 9, 2018: 11:18:25 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_177 Monday, July 9, 2018: 11:18:25 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_178 Monday, July 9, 2018: 11:18:25 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_179 Monday, July 9, 2018: 11:18:25 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_180 Monday, July 9, 2018: 11:18:26 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_181 Monday, July 9, 2018: 11:18:26 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_182 Monday, July 9, 2018: 11:18:26 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_183 Monday, July 9, 2018: 11:18:26 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_184 Monday, July 9, 2018: 11:18:26 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_185 Monday, July 9, 2018: 11:18:27 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_186 Monday, July 9, 2018: 11:18:27 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_187 Monday, July 9, 2018: 11:18:27 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_188 Monday, July 9, 2018: 11:18:27 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_189 Monday, July 9, 2018: 11:18:27 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_190 Monday, July 9, 2018: 11:18:27 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_191 Monday, July 9, 2018: 11:18:28 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_192 Monday, July 9, 2018: 11:18:28 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_193 Monday, July 9, 2018: 11:18:28 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_194 Monday, July 9, 2018: 11:18:28 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_195 Monday, July 9, 2018: 11:18:28 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_196 Monday, July 9, 2018: 11:18:29 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_197 Monday, July 9, 2018: 11:18:29 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_198 Monday, July 9, 2018: 11:18:29 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_199 Monday, July 9, 2018: 11:18:29 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_200 Monday, July 9, 2018: 11:18:29 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_201 Monday, July 9, 2018: 11:18:30 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_202 Monday, July 9, 2018: 11:18:30 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_203 Monday, July 9, 2018: 11:18:30 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_204 Monday, July 9, 2018: 11:18:30 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_205 Monday, July 9, 2018: 11:18:30 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_206 Monday, July 9, 2018: 11:18:31 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_207 Monday, July 9, 2018: 11:18:31 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_208 Monday, July 9, 2018: 11:18:31 CMD: mkdir -p 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/home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_251 Monday, July 9, 2018: 11:18:40 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_252 Monday, July 9, 2018: 11:18:40 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_253 Monday, July 9, 2018: 11:18:41 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_254 Monday, July 9, 2018: 11:18:41 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_255 Monday, July 9, 2018: 11:18:41 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_256 Monday, July 9, 2018: 11:18:41 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_257 Monday, July 9, 2018: 11:18:41 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_258 Monday, July 9, 2018: 11:18:42 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_259 Monday, July 9, 2018: 11:18:42 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_260 Monday, July 9, 2018: 11:18:42 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_261 Monday, July 9, 2018: 11:18:42 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_262 Monday, July 9, 2018: 11:18:42 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_263 Monday, July 9, 2018: 11:18:42 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_264 Monday, July 9, 2018: 11:18:43 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_265 Monday, July 9, 2018: 11:18:43 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_266 Monday, July 9, 2018: 11:18:43 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_267 Monday, July 9, 2018: 11:18:43 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_268 Monday, July 9, 2018: 11:18:43 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_269 Monday, July 9, 2018: 11:18:44 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_270 Monday, July 9, 2018: 11:18:44 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_271 Monday, July 9, 2018: 11:18:44 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_272 Monday, July 9, 2018: 11:18:44 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_273 Monday, July 9, 2018: 11:18:44 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_274 Monday, July 9, 2018: 11:18:44 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_275 Monday, July 9, 2018: 11:18:45 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_276 Monday, July 9, 2018: 11:18:45 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_277 Monday, July 9, 2018: 11:18:45 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_278 Monday, July 9, 2018: 11:18:46 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_279 Monday, July 9, 2018: 11:18:46 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_280 Monday, July 9, 2018: 11:18:46 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_281 Monday, July 9, 2018: 11:18:46 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_282 Monday, July 9, 2018: 11:18:46 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_283 Monday, July 9, 2018: 11:18:47 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_284 Monday, July 9, 2018: 11:18:47 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_285 Monday, July 9, 2018: 11:18:47 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_286 Monday, July 9, 2018: 11:18:47 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_287 Monday, July 9, 2018: 11:18:47 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_288 Monday, July 9, 2018: 11:18:48 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_289 Monday, July 9, 2018: 11:18:48 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_290 Monday, July 9, 2018: 11:18:48 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_291 Monday, July 9, 2018: 11:18:48 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_292 Monday, July 9, 2018: 11:18:48 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_293 Monday, July 9, 2018: 11:18:48 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_294 Monday, July 9, 2018: 11:18:49 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_295 Monday, July 9, 2018: 11:18:49 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_296 Monday, July 9, 2018: 11:18:49 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_297 Monday, July 9, 2018: 11:18:49 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_298 Monday, July 9, 2018: 11:18:49 CMD: touch /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/partitioned_reads.files.list.ok Monday, July 9, 2018: 11:18:49 CMD: /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/util/support_scripts/write_partitioned_trinity_cmds.pl --reads_list_file /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/partitioned_reads.files.list --CPU 1 --max_memory 1G --run_as_paired --seqType fa --trinity_complete --full_cleanup > recursive_trinity.cmds Monday, July 9, 2018: 11:18:50 CMD: touch recursive_trinity.cmds.ok Monday, July 9, 2018: 11:18:50 CMD: touch recursive_trinity.cmds.ok -------------------------------------------------------------------------------- ------------ Trinity Phase 2: Assembling Clusters of Reads --------------------- -------------------------------------------------------------------------------- Monday, July 9, 2018: 11:18:50 CMD: /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity-plugins/BIN/ParaFly -c recursive_trinity.cmds -CPU 40 -v -shuffle Number of Commands: 29867 succeeded(29867) 100% completed. All commands completed successfully. :-) ** Harvesting all assembled transcripts into a single multi-fasta file... Monday, July 9, 2018: 12:52:14 CMD: find /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partitions/ -name '*inity.fasta' | /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/util/support_scripts/partitioned_trinity_aggregator.pl TRINITY_DN > /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/Trinity.fasta.tmp -relocating /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/Trinity.fasta.tmp to /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/Trinity.fasta Monday, July 9, 2018: 12:52:15 CMD: mv /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/Trinity.fasta.tmp /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/Trinity.fasta ################################################################### Trinity assemblies are written to /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/Trinity.fasta ################################################################### Monday, July 9, 2018: 12:52:15 CMD: /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/util/support_scripts/get_Trinity_gene_to_trans_map.pl /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/Trinity.fasta > /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/Trinity.fasta.gene_trans_map]]> Jit https://bioinformaticsonline.com/snippets/view/37227/perl-subroutine-to-read-genomereads-fasta-file Tue, 03 Jul 2018 04:56:15 -0500 https://bioinformaticsonline.com/snippets/view/37227/perl-subroutine-to-read-genomereads-fasta-file sub readSeqFromFasta{ my $file = $_[0]; my (%map,$id,$seq); open(IN,$file) or die("Cannot open file for reading $file:$!\n"); while(<IN>){ chomp; if($_ =~ /^>/){ if(defined $id && defined $seq){ $map{$id} = $seq; $seq=""; } ($id) = split(' ',$_); $id=~s/>//; } else { $seq=$seq.$_; } } $map{$id} = $seq; close(IN); return \%map; }]]> Rahul Nayak https://bioinformaticsonline.com/snippets/view/37209/bash-script-to-run-busco2 Fri, 29 Jun 2018 05:34:08 -0500 https://bioinformaticsonline.com/snippets/view/37209/bash-script-to-run-busco2 #!/bin/bash #set the path export PATH=$PATH:/home/urbe/Tools/augustus-3.2.3/bin export PATH=$PATH:/home/urbe/Tools/augustus-3.2.3/scripts export AUGUSTUS_CONFIG_PATH=/home/urbe/Tools/augustus-3.2.3/config #run BUSCO python BUSCO.py -i /media/urbe/MyDDrive/longMIRA_canuCorrect_sspaceLong/GRAAL_Haploid/adineta_p_lvl6/genome_CORRECTED2.fasta -c 30 -l metazoa_odb9 -o GRAALHaploid_BUSCO -m genome -f #Plot BUSCO python BUSCO_plot.py -wd GRAALHaploid_BUSCO]]> Jit https://bioinformaticsonline.com/snippets/view/37189/perl-script-to-convert-gff-2-fasta Wed, 27 Jun 2018 09:58:20 -0500 https://bioinformaticsonline.com/snippets/view/37189/perl-script-to-convert-gff-2-fasta #!/usr/bin/perl use strict; use warnings; use Bio::Seq; use Bio::SeqIO; use Bio::DB::Fasta; $| = 1; # Flush output my $outfile_cds = Bio::SeqIO->new( -format => 'fasta', -file => ">$ARGV[2].cds.fasta" ); my $outfile_pep = Bio::SeqIO->new( -format => 'fasta', -file => ">$ARGV[2].pep.fasta" ); my $outfile_cdna = Bio::SeqIO->new( -format => 'fasta', -file => ">$ARGV[2].cdna.fasta" ); my $outfile_gene = Bio::SeqIO->new( -format => 'fasta', -file => ">$ARGV[2].gene.fasta" ); my $outfile_upstream3000 = Bio::SeqIO->new( -format => 'fasta', -file => ">$ARGV[2].upstream3000.fasta" ); ###### Output type description ###### # cds - translated sequence (starting with ATG and ending with a stop codon included) # cdna - transcribed sequence (devoid of introns, but containing untranslated exons) # protein - cds translated (includes a * as the stop codon) # gene - the entire gene sequence (including UTRs and introns) # upstream3000 - the 3000 upstream region of the gene (likely including the promoter) ### First, index the genome my $file_fasta = $ARGV[0]; my $db = Bio::DB::Fasta->new($file_fasta); print ("Genome fasta parsed\n"); ### Second, parse the GFF3 my %CDS; my %CDNA; my $mRNA_name; my $frame; open GFF, "<$ARGV[1]" or die $!; while ( my $line = <GFF> ) { chomp $line; my @array = split( "\t", $line ); my $type = $array[2]; if ($type eq 'gene') { my @attrs = split( ";", $array[8] ); $attrs[0] =~ s/ID=//; my $gene_name = $attrs[0]; my $gene_start = $array[3]; my $gene_end = $array[4]; my $gene_seq = $db->seq( $array[0], $gene_start, $gene_end ); my $output_gene = Bio::Seq->new( -seq => $gene_seq, -id => $gene_name, -display_id => $gene_name, -alphabet => 'dna', ); # The upstream 3000 my $upstream_start; my $upstream_end; if($array[6] eq '+') { $upstream_start=$gene_start-3000; $upstream_end=$gene_start-1; } elsif ($array[6] eq '-') { $upstream_start=$gene_end+1; $upstream_end=$gene_end+3000; } my $upstream_seq = $db->seq( $array[0], $upstream_start, $upstream_end ); my $output_upstream3000 = Bio::Seq->new( -seq => $upstream_seq, -id => $gene_name."_upstream3000", -display_id => $gene_name."_upstream3000", -alphabet => 'dna', ); # Reverse Complement if the frame is minus if($array[6] eq '+') { } elsif ($array[6] eq '-') { $output_gene = $output_gene->revcom(); $output_upstream3000 = $output_upstream3000->revcom(); } else { die "Unknown frame! At line $. of the GFF\n"; } $outfile_gene->write_seq($output_gene); $outfile_upstream3000->write_seq($output_upstream3000); } if ( ( $type eq 'mRNA' ) and ( $. > 2 ) ) { # CDS: Collect CDSs and extract sequence of the previous mRNA my $mergedCDS_seq; # WARNING we must sort by $cds_coord[1] foreach my $key (sort {$a <=> $b} keys %CDS) { # Ascending numeric sort of the starting coordinate my $coord = $CDS{$key}; my @cds_coord = split( " ", $coord ); my $cds_seq = $db->seq( $cds_coord[0], $cds_coord[1], $cds_coord[2] ); $mergedCDS_seq .= $cds_seq; } my $output_cds = Bio::Seq->new( -seq => $mergedCDS_seq, -id => $mRNA_name, -display_id => $mRNA_name, -alphabet => 'dna', ); if ($frame eq '-') { $output_cds = $output_cds->revcom(); } my $output_pep = $output_cds->translate(); $outfile_cds->write_seq($output_cds); $outfile_pep->write_seq($output_pep); # CDNA: Collect UTRs and CDSs and extract sequence of the previous mRNA my $mergedCDNA_seq; foreach my $key (sort {$a <=> $b} keys %CDNA) { # Ascending numeric sort of the starting coordinate my $coord = $CDNA{$key}; my @cds_coord = split( " ", $coord ); my $cds_seq = $db->seq( $cds_coord[0], $cds_coord[1], $cds_coord[2] ); $mergedCDNA_seq .= $cds_seq; } my $output_cdna = Bio::Seq->new( -seq => $mergedCDNA_seq, -id => $mRNA_name, -display_id => $mRNA_name, -alphabet => 'dna', ); if ($frame eq '-') { $output_cdna = $output_cdna->revcom(); } $outfile_cdna->write_seq($output_cdna); # Now initialize the next mRNA my @attrs = split( ";", $array[8] ); $attrs[0] =~ s/ID=//; $mRNA_name = $attrs[0]; $frame=$array[6]; %CDS = (); %CDNA = (); # Empty the chunk arrays } elsif ( $type eq 'mRNA' ) { # First mRNA my @attrs = split( ";", $array[8] ); $attrs[0] =~ s/ID=//; $mRNA_name = $attrs[0]; $frame=$array[6]; } elsif ( $type eq 'CDS' ) { my $cds_coord = $array[0] . " " . $array[3] . " " . $array[4]; $CDS{$array[3]}=$cds_coord; $CDNA{$array[3]}=$cds_coord; } elsif ($type eq 'UTR' ) { my $utr_coord = $array[0] . " " . $array[3] . " " . $array[4]; $CDNA{$array[3]}=$utr_coord; } } close GFF; __END__ jitendra@jitendra-UNLOCK-INSTALL[telomeX&] perl gff2fasta.pl Adineta_vaga_v2.0.scaffolds.fa Adineta_vaga.v2.gff3 Avaga]]> Jit https://bioinformaticsonline.com/snippets/view/37054/perl-script-to-run-satsuma-in-loop Tue, 26 Jun 2018 04:56:08 -0500 https://bioinformaticsonline.com/snippets/view/37054/perl-script-to-run-satsuma-in-loop #!/usr/bin/perl -w use strict; use File::Temp qw(tempfile); # Usage perl 1by1.pl for SATSUMA analysis # User need to set the reference multifasta file name here my $seqfile=""; my $queryfile = "genome.fasta"; # Ur query genome my $tarfile = "renamedAdinetaV2.fa"; #Ur target file my $satsumaLoc="/home/urbe/Tools/SATSUMA/satsuma-code-0"; # Location of ur SATSUMA my $maxSize = 5000; my $resolution = 5000; my $dotsize = 1; my $cpu=40; my @ids; #Store the ids if ($ARGV[1] eq "ids") { my $idFile="palindrome_ids.txt"; open my $handle, '<', $idFile; chomp(@ids = <$handle>); close $handle; } my %params = map { $_ => 1 } @ids; #foreach (sort keys %params) { print "$_ : $params{$_}\n"; } if ($ARGV[0] eq "flip") {$seqfile = $tarfile;} else { $seqfile = $queryfile;} local $/ = "\n>"; # read by FASTA record open FASTA, $seqfile; while (<FASTA>) { chomp; my $seq = $_; my ($id) = $seq =~ /^>*(\S+)/; # parse ID as first word in FASTA header $seq =~ s/^>*.+\n//; # remove FASTA header $seq =~ s/\n//g; # remove endlines next if length($seq) < $maxSize; # Size check if ($ARGV[1] eq "ids") { if (exists($params{$id})) { print "$id Working on it\n"; } else { next; } } # remove the file when the reference goes away with the UNLINK option my $tmp_fh = new File::Temp( UNLINK => 1 ); print $tmp_fh ">$id\n$seq\n"; if ($ARGV[0] eq "flip") { #FLIPPED #print "$id\n$seq\n"; my $mySS="$satsumaLoc/SatsumaSynteny -q $tmp_fh -t $queryfile -o RESULT_OUT_FLIP_$id -m 32 -ni 10 -n $cpu -chain_only"; system ("$mySS"); #let me sleep -- I am doing this because it messed up with other running processes print "Sorry guy m tired let me sleep a while :)\n"; sleep(600); #plot blocksynteny file my $myBDS="$satsumaLoc/BlockDisplaySatsuma -i RESULT_OUT_FLIP_$id/satsuma_summary.chained.out -t $queryfile -q $tmp_fh > RESULT_OUT_FLIP_$id/$id-out.synteny"; system ("$myBDS"); #chromosome paint print "Painting chromosomes\n"; my $myCP="$satsumaLoc/ChromosomePaint -i RESULT_OUT_FLIP_$id/$id-out.synteny -o RESULT_OUT_FLIP_$id/$id-out.cpaint -s 5000 -d 5000"; system ("$myCP"); } else { #NORMAL #print "$id\n$seq\n"; my $mySS="$satsumaLoc/SatsumaSynteny -q $tmp_fh -t $tarfile -o RESULT_OUT_NORMAL_$id -m 32 -ni 10 -n $cpu -chain_only"; system ("$mySS"); #let me sleep -- I am doing this because it messed up with other running processes print "Sorry guy m tired let me sleep a while :)\n"; sleep(600); #plot blocksynteny file my $myBDS="$satsumaLoc/BlockDisplaySatsuma -i RESULT_OUT_NORMAL_$id/satsuma_summary.chained.out -t $tarfile -q $tmp_fh > RESULT_OUT_NORMAL_$id/$id-out.synteny"; system ("$myBDS"); #chromosome paint print "Painting chromosomes\n"; my $myCP="$satsumaLoc/ChromosomePaint -i RESULT_OUT_NORMAL_$id/$id-out.synteny -o RESULT_OUT_NORMAL_$id/$id-out.cpaint -s 5000 -d 5000"; system ("$myCP"); } } close FASTA; __END__ SatsumaSynteny ################################################################## # -q : query fasta sequence # -t : target fasta sequence # -o : output directory # -l : minimum alignment length (def=0) # -t_chunk : target chunk size (def=4096) # -q_chunk : query chunk size (def=4096) # -t_chunk_seed : target chunk size (seed) (def=8192) # -q_chunk_seed : query chunk size (seed) (def=8192) # -n : number of CPUs (def=1) # -ni : number of initial search blocks (def=-1) # -lsf : submit jobs to LSF (def=0) # -nosubmit : do not run jobs (def=0) # -nowait : do not wait for jobs (def=0) # -chain_only : only chain the matches (def=0) # -refine_only : only refine the matches (def=0) # -min_prob : minimum probability to keep match (def=0.99999) # -proteins : align in protein space (def=0) # -cutoff : signal cutoff (def=1.8) # -cutoff : signal cutoff (seed) (def=3) # -m : number of jobs per block (def=8) # -resume : resumes w/ the output of a previous run (xcorr*data) (def=) # -seed : loads seeds and runs from there (xcorr*data) (def=) #-pixel : number of blocks per pixel (def=24) # -nofilter : do not pre-filter seeds (slower runtime) (def=0) # –dups : allow for duplications in the query sequence (def=0) #####################################################################################################################################]]> Jit https://bioinformaticsonline.com/snippets/view/37053/perl-script-to-find-the-distance-beetween-all-the-contigs-and-scaffolds Tue, 26 Jun 2018 04:40:48 -0500 https://bioinformaticsonline.com/snippets/view/37053/perl-script-to-find-the-distance-beetween-all-the-contigs-and-scaffolds #!/usr/bin/perl use strict; use warnings; use Bio::SeqIO; $| = 1; #Script to see the distance beetween all the contigs and scaffolds #Usage: perl clustalReads.pl genome.fa > HammingDist.txt #Dependancy: MAFFT my ($refSeq, $SeqIds) = fastafile2hash($ARGV[0]); my $tmpFile="tmpOutfile"; foreach my $chr (@$SeqIds) { my $cnt=0; my $value=scalar(@$SeqIds); do{{ $value=$value-1; my $ofh = write_fh($tmpFile); next if $chr eq @$SeqIds[$cnt]; print "$chr\t@$SeqIds[$cnt]\t"; print $ofh ">$chr\n$refSeq->{$chr}{seq}\n>@$SeqIds[$cnt]\n$refSeq->{@$SeqIds[$cnt]}{seq}\n"; close $ofh or die "Could not close file '$tmpFile' $!"; $cnt++; system ("mafft --retree 1 --maxiterate 0 --thread 40 $tmpFile > MAFFT_out"); #usage: perl clustalRead.pl MAFFT_out my ($seqRef, $ids) = fastafile2hash('MAFFT_out'); my ($fval, $sval) = trimMSA($seqRef->{$ids->[0]}{seq}, $seqRef->{$ids->[1]}{seq}); my $seq1 = substr $seqRef->{$ids->[0]}{seq}, $fval, ($seqRef->{$ids->[0]}{len}-$sval)-$fval; my $seq2 = substr $seqRef->{$ids->[1]}{seq}, $fval, ($seqRef->{$ids->[1]}{len}-$sval)-$fval; my $val = hammingDist($seq1, $seq2); print "$val\n"; }} until($value<=0); } #calculate the hamming distance sub hammingDist { return ($_[0] ^ $_[1]) =~ tr/\001-\255//; } #Remove '-' from both end sub trimMSA { my ($seq1, $seq2) = @_; my ($substring1) = $seq1 =~ /^.{0}(.*?)[a-zA-Z_]/s; my ($substring2) = $seq2 =~ /^.{0}(.*?)[a-zA-Z_]/s; my $trimLen1=length($substring1); my $trimLen2=length($substring2); my $val; #print "$trimLen1 <= $trimLen2\n"; if ($trimLen1 >= $trimLen2) {$val = $trimLen1; } elsif ($trimLen1 <= $trimLen2) {$val = $trimLen2; } my $seq1_rev = reverse $seq1; my $seq2_rev = reverse $seq2; my ($substring1_rev) = $seq1_rev =~ /^.{0}(.*?)[a-zA-Z_]/s; my ($substring2_rev) = $seq2_rev =~ /^.{0}(.*?)[a-zA-Z_]/s; my $trimLen1_rev=length($substring1_rev); my $trimLen2_rev=length($substring2_rev); my $val_rev; if ($trimLen1_rev >= $trimLen2_rev) {$val_rev = $trimLen1_rev; } elsif ($trimLen1_rev <= $trimLen2_rev) {$val_rev = $trimLen2_rev; } return $val, $val_rev; } #Store fasta file to hash sub fastafile2hash { my $fastafile = shift @_; my %sequences; my $fh = &read_fh($fastafile); my $seqid; my @allIds; while (my $line = <$fh>) { if ($line =~ /^>(\S+)(.*)/) { $seqid = $1; $sequences{$seqid}{desc} = $2; push @allIds, $seqid; } else { chomp $line; $sequences{$seqid}{seq} .= $line; $sequences{$seqid}{len} += length $line; $sequences{$seqid}{gc} += ($line =~ tr/gcGC/gcGC/); $line =~ s/[^atgc]/N/ig; $sequences{$seqid}{nonatgc} += ($line =~ tr/N/N/); } } close $fh; return \%sequences, \@allIds; } sub read_fh { my $filename = shift @_; my $filehandle; if ($filename =~ /gz$/) { open $filehandle, "gunzip -dc $filename |" or die $!; } else { open $filehandle, "<$filename" or die $!; } return $filehandle; } sub write_fh { my $filename = shift @_; my $filehandle; open $filehandle, ">$filename" or die $!; return $filehandle; }]]> Jit https://bioinformaticsonline.com/snippets/view/37031/perl-subroutine-for-reading-multifasta-file Fri, 22 Jun 2018 05:51:19 -0500 https://bioinformaticsonline.com/snippets/view/37031/perl-subroutine-for-reading-multifasta-file sub readfasta { (my $file)=@_; my %sequence; my $header; my $temp_seq; #suppose fasta files contains multiple sequences; open (IN, "<$file") or die "couldn't open the file $file $!"; while (<IN>) { chop; next if /^\s*$/; #skip empty line if ($_ =~ /^>/) #when see head line { $header= $_; if ($sequence{$header}){print colored("#CAUTION: SAME FASTA HAS BEEN READ MULTIPLE TIMES.\n#CAUTION: PLEASE CHECK FASTA SEQUENCE:$header\n","red")}; if ($temp_seq) {$temp_seq=""} # If there is alreay sequence in temp_seq, empty the sequence file } else # when see the sequence line { s/\s+//g; $temp_seq .= $_; $sequence{$header}=$temp_seq; #update the contents } } return \%sequence; }]]> Aaryan Lokwani https://bioinformaticsonline.com/snippets/view/37016/perl-script-to-count-number-of-ns-in-a-multifasta-file Fri, 22 Jun 2018 05:43:04 -0500 https://bioinformaticsonline.com/snippets/view/37016/perl-script-to-count-number-of-ns-in-a-multifasta-file #!/usr/bin/perl my ($h, $n, $l); open(I,$ARGV[0]) or die($!); while(<I>){ chomp; next if /^$/; if(/^>/){ $h=substr($_,1); }else{ $n=($_=~tr/nN/nN/); $l=length($_); print $h,"\t",$l,"\t",$n,"\t",$n/($l-$n),"\n"; } } close(I); __END__ Note: Convert sequences in oneline first perl -pe '/^>/ ? print "\n" : chomp' scaffolds_backup.fasta > out.fasta perl countN.pl scaff.fa Result ➜ SSPACED_P2 perl countN.pl out.fasta scaffold1_size15575755 15575755 71824 0.00463263155647429 scaffold2_size10632363 10632363 64900 0.00614149299600103 scaffold3_size10490233 10490233 14872 0.0014197124089566 scaffold4_size8615068 8615068 28079 0.00326994712582024 scaffold5_size7253348 7253348 0 0 scaffold6_size5859599 5859599 51144 0.00880509533085821 scaffold7_size5312044 5312044 144 2.71089440689772e-05 scaffold8_size4790259 4790259 167678 0.0362736748150005 scaffold9_size2901530 2901530 4652 0.001605866729631 scaffold10_size2523421 2523421 142217 0.0597248282801474 scaffold11_size2396892 2396892 6066 0.00253719844104088 scaffold12_size2309371 2309371 240122 0.11604306683246 scaffold13_size2240539 2240539 48209 0.0219898464191066 scaffold14_size2236206 2236206 132012 0.0627375612704912 scaffold15_size2184218 2184218 29144 0.0135234335340689 scaffold16_size2020193 2020193 11868 0.00590940211370172 scaffold17_size1776796 1776796 132882 0.0808326956276302 scaffold18_size1445477 1445477 50836 0.0364509576299564 scaffold19_size1287487 1287487 102593 0.0865841163850944 scaffold20_size1287226 1287226 23771 0.0188142830571726 scaffold21_size1176376 1176376 18339 0.0158362815695872 scaffold22_size1164766 1164766 82205 0.075935674756434 scaffold23_size1108643 1108643 36256 0.0338086903328742 scaffold24_size1010466 1010466 93216 0.10162551103843 scaffold25_size1009266 1009266 51939 0.0542541890075178 scaffold26_size990651 990651 75286 0.082246972519159 scaffold27_size971184 971184 55725 0.0608711040035654 scaffold28_size898523 898523 92917 0.115338018833028 scaffold29_size889417 889417 33420 0.0390421929048817 scaffold30_size864014 864014 80076 0.10214583296128 scaffold31_size790135 790135 0 0 scaffold32_size767454 767454 42932 0.0592556195671077 scaffold33_size711456 711456 0 0 scaffold34_size672622 672622 0 0 scaffold35_size649832 649832 0 0 scaffold36_size583465 583465 10815 0.0188858814284467 scaffold37_size532901 532901 19453 0.0378869914772285 scaffold38_size462550 462550 16583 0.0371843656593425 scaffold39_size413010 413010 29289 0.0763288952129281 scaffold40_size395146 395146 72775 0.225749214414448 scaffold41_size385263 385263 0 0 scaffold42_size378415 378415 0 0 scaffold43_size374696 374696 0 0 scaffold44_size369872 369872 0 0 scaffold45_size357218 357218 0 0 scaffold46_size308025 308025 25709 0.0910646226214596 scaffold47_size306566 306566 16299 0.056151749940572 scaffold48_size288610 288610 59285 0.258519568298267 scaffold49_size269035 269035 0 0 scaffold50_size267296 267296 0 0 scaffold51_size239237 239237 0 0 scaffold52_size229546 229546 81 0.000352995010132264 scaffold53_size228017 228017 3283 0.0146083814643089 scaffold54_size218690 218690 9299 0.0444097406287758 scaffold55_size205658 205658 0 0 scaffold56_size203300 203300 0 0 scaffold57_size189523 189523 54248 0.401020144150804 scaffold58_size164988 164988 0 0 scaffold59_size158628 158628 0 0 scaffold60_size158343 158343 29807 0.231896122487085 scaffold61_size148599 148599 0 0 scaffold62_size137911 137911 19923 0.168856154863206 scaffold63_size129836 129836 0 0 scaffold64_size127140 127140 2695 0.0216561533207441 scaffold65_size121401 121401 0 0 scaffold66_size119540 119540 7247 0.0645365249837479 scaffold67_size114479 114479 11483 0.111489766592877 scaffold68_size111283 111283 0 0 scaffold69_size106201 106201 0 0 scaffold70_size102444 102444 7907 0.0836392100447444 scaffold71_size97059 97059 9770 0.11192704693604 scaffold72_size94628 94628 14575 0.182066880691542 scaffold73_size86984 86984 0 0 scaffold74_size80782 80782 0 0 scaffold75_size68265 68265 0 0 scaffold76_size67964 67964 0 0 scaffold77_size56495 56495 0 0 scaffold78_size51859 51859 0 0 scaffold79_size46742 46742 0 0 scaffold80_size44222 44222 0 0 scaffold81_size39139 39139 0 0 scaffold82_size36951 36951 0 0 scaffold83_size35745 35745 0 0 scaffold84_size34131 34131 0 0 scaffold85_size33753 33753 0 0 scaffold86_size33604 33604 0 0 scaffold87_size32653 32653 0 0 scaffold88_size32281 32281 0 0 scaffold89_size32217 32217 0 0 scaffold90_size29934 29934 0 0 scaffold91_size29230 29230 0 0 scaffold92_size22007 22007 0 0 scaffold93_size20584 20584 0 0]]> Aaryan Lokwani https://bioinformaticsonline.com/snippets/view/37015/install-perl-locally Fri, 22 Jun 2018 05:26:42 -0500 https://bioinformaticsonline.com/snippets/view/37015/install-perl-locally # To follow these instructions, we'll assume your system admins have already installed these essentials: # Debian/Ubuntu system admins should run: sudo apt-get install -y build-essential libexpat1-dev libssl-dev libmysqlclient-dev libxml2-dev # RHEL/CentOS system admins should run: sudo yum groupinstall -y 'Development Tools' sudo yum install -y expat-devel openssl-devel mysql-devel libxml2-devel # Create a folder where you want to install different Perls, and cd into it: # Note that it doesn't need to be your home folder. Put it wherever you want to maintain such software: export PERL_BASE="$HOME/perl" mkdir -p $PERL_BASE cd $PERL_BASE # Download source tarball into a subfolder named src, and untar: curl --create-dirs -L -o src/perl-5.24.1.tar.gz http://www.cpan.org/src/5.0/perl-5.24.1.tar.gz cd src tar -zxf perl-5.24.1.tar.gz # Configure and build, making sure that this non-standard location is baked into the perl binary: cd perl-5.24.1 ./Configure -des -Dprefix=$PERL_BASE/perl-5.24.1 -Dotherlibdirs=$PERL_BASE/perl-5.24.1/lib/perl5 make make install # Install dependencies for Ensembl API, VEP, OncoKB, and other tools we use here at MSKCC: curl -sL https://cpanmin.us | $PERL_BASE/perl-5.24.1/bin/perl - --notest -l $PERL_BASE/perl-5.24.1 App::cpanminus JSON::Parse XML::Parser XML::Simple LWP LWP::Simple LWP::Protocol::https Archive::Extract Archive::Tar Archive::Zip CGI DBI Time::HiRes DBD::mysql Encode File::Copy::Recursive Perl::OSType Module::Metadata Statistics::Lite Tie::Autotie Tie::IxHash Log::Log4perl FindBin::Real Getopt::Long Catalyst::Runtime Catalyst::Devel List::Util Test::XML::Simple Test::XPath IO::String Bio::Perl version # Set $PERL5LIB to find these libraries, and set $PATH to use this Perl instead of the system Perl: export PERL5LIB="$PERL_BASE/perl-5.24.1/lib/perl5:$PERL_BASE/perl-5.24.1/lib/perl5/x86_64-linux:$PERL5LIB" export PATH="$PERL_BASE/perl-5.24.1/bin:$PATH" # You can add those 2 lines to the end of your `~/.bashrc` to make it persistent. # But be sure to define `$PERL_BASE` in your `~/.bashrc` too.]]> Aaryan Lokwani https://bioinformaticsonline.com/snippets/view/36949/bloomfilter Fri, 15 Jun 2018 03:49:39 -0500 https://bioinformaticsonline.com/snippets/view/36949/bloomfilter ➜ Tools git:(master) ✗ git clone git://github.com/bcgsc/bloomfilter.git Cloning into 'bloomfilter'... remote: Counting objects: 867, done. remote: Compressing objects: 100% (11/11), done. remote: Total 867 (delta 7), reused 12 (delta 4), pack-reused 852 Receiving objects: 100% (867/867), 330.70 KiB | 0 bytes/s, done. Resolving deltas: 100% (512/512), done. Checking connectivity... done. ➜ Tools git:(master) ✗ cd bloomfilter ➜ bloomfilter git:(master) ls AUTHORS COPYING ntHashIterator.hpp autogen.sh CountingBloomFilter.hpp pythonInterface BloomFilter.hpp Examples README BloomFilterUtil.h KmerBloomFilter.hpp README.md BloomMap.hpp Makefile.am swig ChangeLog NEWS Tests configure.ac nthash.hpp ➜ bloomfilter git:(master) swig -Wall -c++ -perl5 BloomFilter.i Unable to find file 'BloomFilter.i'. ➜ bloomfilter git:(master) git submodule update --init ➜ bloomfilter git:(master) ./autogen.sh + aclocal + autoconf + autoheader + automake -a configure.ac:19: installing './compile' configure.ac:6: installing './config.guess' configure.ac:6: installing './config.sub' configure.ac:8: installing './install-sh' configure.ac:8: installing './missing' Makefile.am: installing './INSTALL' Tests/AdHoc/Makefile.am: installing './depcomp' parallel-tests: installing './test-driver' ➜ bloomfilter git:(master) ✗ ./configure && make checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking target system type... x86_64-pc-linux-gnu checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking for ranlib... ranlib checking for g++... g++ checking whether the C++ compiler works... yes checking for C++ compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking for style of include used by make... GNU checking dependency style of g++... gcc3 checking for gcc... gcc checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking whether gcc understands -c and -o together... yes checking dependency style of gcc... gcc3 checking how to run the C preprocessor... gcc -E checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for size_t... yes checking for g++ option to support OpenMP... -fopenmp checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating Tests/Unit/Makefile config.status: creating Tests/AdHoc/Makefile config.status: creating config.h config.status: executing depfiles commands make all-recursive make[1]: Entering directory '/home/urbe/Tools/bloomfilter' Making all in Tests/AdHoc make[2]: Entering directory '/home/urbe/Tools/bloomfilter/Tests/AdHoc' make[2]: Nothing to be done for 'all'. make[2]: Leaving directory '/home/urbe/Tools/bloomfilter/Tests/AdHoc' Making all in Tests/Unit make[2]: Entering directory '/home/urbe/Tools/bloomfilter/Tests/Unit' make[2]: Nothing to be done for 'all'. make[2]: Leaving directory '/home/urbe/Tools/bloomfilter/Tests/Unit' make[2]: Entering directory '/home/urbe/Tools/bloomfilter' make[2]: Leaving directory '/home/urbe/Tools/bloomfilter' make[1]: Leaving directory '/home/urbe/Tools/bloomfilter' ➜ bloomfilter git:(master) ✗ pwd /home/urbe/Tools/bloomfilter ➜ bloomfilter git:(master) ✗ ./configure --prefix=/home/urbe/Tools/bloomfilter && make install zsh: correct 'install' to 'INSTALL' [nyae]? n checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking target system type... x86_64-pc-linux-gnu checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking for ranlib... ranlib checking for g++... g++ checking whether the C++ compiler works... yes checking for C++ compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking for style of include used by make... GNU checking dependency style of g++... gcc3 checking for gcc... gcc checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking whether gcc understands -c and -o together... yes checking dependency style of gcc... gcc3 checking how to run the C preprocessor... gcc -E checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for size_t... yes checking for g++ option to support OpenMP... -fopenmp checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating Tests/Unit/Makefile config.status: creating Tests/AdHoc/Makefile config.status: creating config.h config.status: config.h is unchanged config.status: executing depfiles commands Making install in Tests/AdHoc make[1]: Entering directory '/home/urbe/Tools/bloomfilter/Tests/AdHoc' make[2]: Entering directory '/home/urbe/Tools/bloomfilter/Tests/AdHoc' make[2]: Nothing to be done for 'install-exec-am'. make[2]: Nothing to be done for 'install-data-am'. make[2]: Leaving directory '/home/urbe/Tools/bloomfilter/Tests/AdHoc' make[1]: Leaving directory '/home/urbe/Tools/bloomfilter/Tests/AdHoc' Making install in Tests/Unit make[1]: Entering directory '/home/urbe/Tools/bloomfilter/Tests/Unit' make[2]: Entering directory '/home/urbe/Tools/bloomfilter/Tests/Unit' make[2]: Nothing to be done for 'install-exec-am'. make[2]: Nothing to be done for 'install-data-am'. make[2]: Leaving directory '/home/urbe/Tools/bloomfilter/Tests/Unit' make[1]: Leaving directory '/home/urbe/Tools/bloomfilter/Tests/Unit' make[1]: Entering directory '/home/urbe/Tools/bloomfilter' make[2]: Entering directory '/home/urbe/Tools/bloomfilter' make[2]: Nothing to be done for 'install-exec-am'. /bin/mkdir -p '/home/urbe/Tools/bloomfilter/share/doc/bloomfilter' /usr/bin/install -c -m 644 README.md '/home/urbe/Tools/bloomfilter/share/doc/bloomfilter' make[2]: Leaving directory '/home/urbe/Tools/bloomfilter' make[1]: Leaving directory '/home/urbe/Tools/bloomfilter' ➜ bloomfilter git:(master) ✗ pwd /home/urbe/Tools/bloomfilter ➜ bloomfilter git:(master) ✗ ./configure --with-boost=/boost/path --prefix=/home/urbe/Tools/bloomfilter && make install zsh: correct 'install' to 'INSTALL' [nyae]? n configure: WARNING: unrecognized options: --with-boost checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking target system type... x86_64-pc-linux-gnu checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking for ranlib... ranlib checking for g++... g++ checking whether the C++ compiler works... yes checking for C++ compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking for style of include used by make... GNU checking dependency style of g++... gcc3 checking for gcc... gcc checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking whether gcc understands -c and -o together... yes checking dependency style of gcc... gcc3 checking how to run the C preprocessor... gcc -E checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for size_t... yes checking for g++ option to support OpenMP... -fopenmp checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating Tests/Unit/Makefile config.status: creating Tests/AdHoc/Makefile config.status: creating config.h config.status: config.h is unchanged config.status: executing depfiles commands configure: WARNING: unrecognized options: --with-boost Making install in Tests/AdHoc make[1]: Entering directory '/home/urbe/Tools/bloomfilter/Tests/AdHoc' make[2]: Entering directory '/home/urbe/Tools/bloomfilter/Tests/AdHoc' make[2]: Nothing to be done for 'install-exec-am'. make[2]: Nothing to be done for 'install-data-am'. make[2]: Leaving directory '/home/urbe/Tools/bloomfilter/Tests/AdHoc' make[1]: Leaving directory '/home/urbe/Tools/bloomfilter/Tests/AdHoc' Making install in Tests/Unit make[1]: Entering directory '/home/urbe/Tools/bloomfilter/Tests/Unit' make[2]: Entering directory '/home/urbe/Tools/bloomfilter/Tests/Unit' make[2]: Nothing to be done for 'install-exec-am'. make[2]: Nothing to be done for 'install-data-am'. make[2]: Leaving directory '/home/urbe/Tools/bloomfilter/Tests/Unit' make[1]: Leaving directory '/home/urbe/Tools/bloomfilter/Tests/Unit' make[1]: Entering directory '/home/urbe/Tools/bloomfilter' make[2]: Entering directory '/home/urbe/Tools/bloomfilter' make[2]: Nothing to be done for 'install-exec-am'. /bin/mkdir -p '/home/urbe/Tools/bloomfilter/share/doc/bloomfilter' /usr/bin/install -c -m 644 README.md '/home/urbe/Tools/bloomfilter/share/doc/bloomfilter' make[2]: Leaving directory '/home/urbe/Tools/bloomfilter' make[1]: Leaving directory '/home/urbe/Tools/bloomfilter' ➜ bloomfilter git:(master) ✗ ls aclocal.m4 config.status Makefile.in AUTHORS config.sub missing autogen.sh configure NEWS autom4te.cache configure.ac nthash.hpp BloomFilter.hpp COPYING ntHashIterator.hpp BloomFilterUtil.h CountingBloomFilter.hpp pythonInterface BloomMap.hpp depcomp README ChangeLog Examples README.md compile INSTALL share config.guess install-sh stamp-h1 config.h KmerBloomFilter.hpp swig config.h.in Makefile test-driver config.log Makefile.am Tests ➜ bloomfilter git:(master) ✗]]> Jit