https://bioinformaticsonline.com/snippets/view/37913/test-bp-assembly? https://bioinformaticsonline.com/snippets/view/37913/test-bp-assembly Wed, 10 Oct 2018 06:10:30 -0500 https://bioinformaticsonline.com/snippets/view/37913/test-bp-assembly (denovo_asm) [jnarayan@hmem00 ~]$ git clone https://github.com/cdunn2001/git-sym.git fatal: destination path 'git-sym' already exists and is not an empty directory. (denovo_asm) [jnarayan@hmem00 ~]$ git clone https://github.com/pb-cdunn/FALCON-examples.git Initialized empty Git repository in /home/users/j/n/jnarayan/FALCON-examples/.git/ remote: Enumerating objects: 6, done. remote: Counting objects: 100% (6/6), done. remote: Compressing objects: 100% (6/6), done. remote: Total 680 (delta 0), reused 1 (delta 0), pack-reused 674 Receiving objects: 100% (680/680), 82.78 KiB, done. Resolving deltas: 100% (398/398), done. (denovo_asm) [jnarayan@hmem00 ~]$ cd FALCON-examples/ (denovo_asm) [jnarayan@hmem00 FALCON-examples]$ ../git-sym/git-sym update run/greg200k-sv2/ mkdir -p /home/users/j/n/jnarayan/FALCON-examples/.git/git-sym-local/links os.symlink('.git/git-sym-local/links', '/home/users/j/n/jnarayan/FALCON-examples/.git-sym') git: 'check-ignore' is not a git command. See 'git --help'. mkdir -p /home/users/j/n/jnarayan/FALCON-examples/.git/git-sym-local/cache -> in dir 'run/greg200k-sv2/' <- back to dir '/home/users/j/n/jnarayan/FALCON-examples' symlink: 'run/greg200k-sv2/data/greg200k-sv2' 'run/greg200k-sv2/data/greg200k-sv2' -> '../../../.git-sym/greg200k-sv2.2' does not exist -> in dir '/home/users/j/n/jnarayan/FALCON-examples/.git/git-sym-local/links' -> in dir '/home/users/j/n/jnarayan/FALCON-examples/.git/git-sym-local/cache' make -j -f /home/users/j/n/jnarayan/FALCON-examples/git-sym.makefile 'greg200k-sv2.2' curl -L https://downloads.pacbcloud.com/public/data/git-sym/greg200k-sv2.2.tar | tar xvf - % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0greg200k-sv2.2/ greg200k-sv2.2/orig.links/ greg200k-sv2.2/orig.links/000000F_005_580044-780233.fasta greg200k-sv2.2/orig.links/000000F_005_580044-780233_SV.fasta greg200k-sv2.2/orig.links/000000F_2769948-2970164.fasta greg200k-sv2.2/orig.links/000000F_2769948-2970164_SV.fasta greg200k-sv2.2/orig.links/orig1.fasta greg200k-sv2.2/orig.links/orig2.fasta greg200k-sv2.2/orig.links/sv1.fasta greg200k-sv2.2/orig.links/sv2.fasta greg200k-sv2.2/orig/ greg200k-sv2.2/orig/orig1.fasta.gz 0 18.6M 0 32768 0 0 18778 0 0:17:22 0:00:01 0:17:21 18767greg200k-sv2.2/orig/orig2.fasta.gz greg200k-sv2.2/orig/sv1.fasta.gz greg200k-sv2.2/orig/sv2.fasta.gz 1 18.6M 1 256k 0 0 94979 0 0:03:26 0:00:02 0:03:24 94945greg200k-sv2.2/README.txt greg200k-sv2.2/SAM.txt greg200k-sv2.2/makefile greg200k-sv2.2/ref1.fasta greg200k-sv2.2/ref2.fasta greg200k-sv2.2/subreads1.bam 12 18.6M 12 2480k 0 0 517k 0 0:00:36 0:00:04 0:00:32 517kgreg200k-sv2.2/subreads1.bam.pbi greg200k-sv2.2/subreads1.dexta greg200k-sv2.2/subreads1.fasta 30 18.6M 30 5840k 0 0 1005k 0 0:00:19 0:00:05 0:00:14 1166kgreg200k-sv2.2/subreads2.bam greg200k-sv2.2/subreads2.bam.pbi greg200k-sv2.2/subreads2.dexta greg200k-sv2.2/subreads2.fasta 100 18.6M 100 18.6M 0 0 2730k 0 0:00:07 0:00:07 --:--:-- 4447k <- back to dir '/home/users/j/n/jnarayan/FALCON-examples/.git/git-sym-local/links' os.symlink('../cache/greg200k-sv2.2', 'greg200k-sv2.2') <- back to dir '/home/users/j/n/jnarayan/FALCON-examples' (denovo_asm) [jnarayan@hmem00 FALCON-examples]$ cd run/greg200k-sv2/ (denovo_asm) [jnarayan@hmem00 greg200k-sv2]$ ls data fc_run.cfg fc_unzip.cfg input_bam.fofn input.fofn makefile README.md (denovo_asm) [jnarayan@hmem00 greg200k-sv2]$ ls -lh total 24K drwxrwxr-x 2 jnarayan jnarayan 25 10. Okt 13:08 data -rwxrwxr-x 1 jnarayan jnarayan 1,7K 10. Okt 13:08 fc_run.cfg -rw-rw-r-- 1 jnarayan jnarayan 1,1K 10. Okt 13:08 fc_unzip.cfg -rw-rw-r-- 1 jnarayan jnarayan 64 10. Okt 13:08 input_bam.fofn -rw-rw-r-- 1 jnarayan jnarayan 68 10. Okt 13:08 input.fofn -rw-rw-r-- 1 jnarayan jnarayan 339 10. Okt 13:08 makefile -rw-rw-r-- 1 jnarayan jnarayan 102 10. Okt 13:08 README.md (denovo_asm) [jnarayan@hmem00 greg200k-sv2]$ fc_run fc_run.cfg (denovo_asm) [jnarayan@hmem00 greg200k-sv2]$ ls 0-rawreads 1-preads_ovl 2-asm-falcon all.log config.json data fc_run.cfg fc_unzip.cfg General_config.json input_bam.fofn input.fofn makefile README.md (denovo_asm) [jnarayan@hmem00 greg200k-sv2]$ ls -lh total 956K drwxrwxr-x 27 jnarayan jnarayan 4,0K 10. Okt 13:17 0-rawreads drwxrwxr-x 14 jnarayan jnarayan 4,0K 10. Okt 13:16 1-preads_ovl drwxrwxr-x 2 jnarayan jnarayan 4,0K 10. Okt 13:17 2-asm-falcon -rw-rw-r-- 1 jnarayan jnarayan 911K 10. Okt 13:17 all.log -rw-rw-r-- 1 jnarayan jnarayan 1,6K 10. Okt 13:10 config.json drwxrwxr-x 2 jnarayan jnarayan 25 10. Okt 13:08 data -rwxrwxr-x 1 jnarayan jnarayan 1,7K 10. Okt 13:08 fc_run.cfg -rw-rw-r-- 1 jnarayan jnarayan 1,1K 10. Okt 13:08 fc_unzip.cfg -rw-rw-r-- 1 jnarayan jnarayan 1,1K 10. Okt 13:10 General_config.json -rw-rw-r-- 1 jnarayan jnarayan 64 10. Okt 13:08 input_bam.fofn -rw-rw-r-- 1 jnarayan jnarayan 68 10. Okt 13:08 input.fofn -rw-rw-r-- 1 jnarayan jnarayan 339 10. Okt 13:08 makefile -rw-rw-r-- 1 jnarayan jnarayan 102 10. Okt 13:08 README.md (denovo_asm) [jnarayan@hmem00 greg200k-sv2]$ fc_unzip.py fc_unzip.cfg (denovo_asm) [jnarayan@hmem00 greg200k-sv2]$ ls -lh total 356K drwxrwxr-x 27 jnarayan jnarayan 4,0K 10. Okt 13:17 0-rawreads drwxrwxr-x 14 jnarayan jnarayan 4,0K 10. Okt 13:16 1-preads_ovl drwxrwxr-x 2 jnarayan jnarayan 4,0K 10. Okt 13:17 2-asm-falcon drwxrwxr-x 6 jnarayan jnarayan 4,0K 10. Okt 13:19 3-unzip drwxrwxr-x 15 jnarayan jnarayan 4,0K 10. Okt 13:23 4-polish lrwxrwxrwx 1 jnarayan jnarayan 8 10. Okt 13:18 4-quiver -> 4-polish -rw-rw-r-- 1 jnarayan jnarayan 304K 10. Okt 13:23 all.log -rw-rw-r-- 1 jnarayan jnarayan 1,6K 10. Okt 13:10 config.json drwxrwxr-x 2 jnarayan jnarayan 25 10. Okt 13:08 data -rwxrwxr-x 1 jnarayan jnarayan 1,7K 10. Okt 13:08 fc_run.cfg -rw-rw-r-- 1 jnarayan jnarayan 1,1K 10. Okt 13:08 fc_unzip.cfg -rw-rw-r-- 1 jnarayan jnarayan 1,1K 10. Okt 13:10 General_config.json -rw-rw-r-- 1 jnarayan jnarayan 64 10. Okt 13:08 input_bam.fofn -rw-rw-r-- 1 jnarayan jnarayan 68 10. Okt 13:08 input.fofn -rw-rw-r-- 1 jnarayan jnarayan 339 10. Okt 13:08 makefile -rw-rw-r-- 1 jnarayan jnarayan 102 10. Okt 13:08 README.md (denovo_asm) [jnarayan@hmem00 greg200k-sv2]$ cd 4-polish/ (denovo_asm) [jnarayan@hmem00 4-polish]$ ls cns-gather cns-output merge-reads quiver-chunks quiver-run quiver-split segregate-chunks segregated-bam segregate-gathered segregate-run segregate-split select-reads track-reads (denovo_asm) [jnarayan@hmem00 4-polish]$ ls -lh total 36K drwxrwxr-x 3 jnarayan jnarayan 4,0K 10. Okt 13:23 cns-gather drwxrwxr-x 2 jnarayan jnarayan 4,0K 10. Okt 13:23 cns-output drwxrwxr-x 4 jnarayan jnarayan 4,0K 10. Okt 13:19 merge-reads drwxrwxr-x 4 jnarayan jnarayan 38 10. Okt 13:19 quiver-chunks drwxrwxr-x 4 jnarayan jnarayan 38 10. Okt 13:19 quiver-run drwxrwxr-x 3 jnarayan jnarayan 4,0K 10. Okt 13:19 quiver-split drwxrwxr-x 4 jnarayan jnarayan 34 10. Okt 13:19 segregate-chunks drwxrwxr-x 2 jnarayan jnarayan 4,0K 10. Okt 13:19 segregated-bam drwxrwxr-x 2 jnarayan jnarayan 4,0K 10. Okt 13:19 segregate-gathered drwxrwxr-x 4 jnarayan jnarayan 34 10. Okt 13:19 segregate-run drwxrwxr-x 2 jnarayan jnarayan 4,0K 10. Okt 13:19 segregate-split drwxrwxr-x 2 jnarayan jnarayan 4,0K 10. Okt 13:19 select-reads drwxrwxr-x 2 jnarayan jnarayan 4,0K 10. Okt 13:19 track-reads (denovo_asm) [jnarayan@hmem00 4-polish]$ cd cns-output/ (denovo_asm) [jnarayan@hmem00 cns-output]$ ls -lh total 1,2M -rw-rw-r-- 1 jnarayan jnarayan 188K 10. Okt 13:23 cns_h_ctg.fasta -rw-rw-r-- 1 jnarayan jnarayan 369K 10. Okt 13:23 cns_h_ctg.fastq -rw-rw-r-- 1 jnarayan jnarayan 202K 10. Okt 13:23 cns_p_ctg.fasta -rw-rw-r-- 1 jnarayan jnarayan 397K 10. Okt 13:23 cns_p_ctg.fastq -rw-rw-r-- 1 jnarayan jnarayan 0 10. Okt 13:23 job_done -rwxrwxr-x 1 jnarayan jnarayan 269 10. Okt 13:23 run-P3e4a88125c3657.bash -rw-rw-r-- 1 jnarayan jnarayan 6,6K 10. Okt 13:23 run-P3e4a88125c3657.bash.stderr -rw-rw-r-- 1 jnarayan jnarayan 5,7K 10. Okt 13:23 run-P3e4a88125c3657.bash.stdout -rw-rw-r-- 1 jnarayan jnarayan 237 10. Okt 13:23 run.sh -rw-rw-r-- 1 jnarayan jnarayan 0 10. Okt 13:23 run.sh.done -rw-rw-r-- 1 jnarayan jnarayan 479 10. Okt 13:23 task.json -rw-rw-r-- 1 jnarayan jnarayan 596 10. Okt 13:23 task.sh -rw-rw-r-- 1 jnarayan jnarayan 365 10. Okt 13:23 template.sh -rw-rw-r-- 1 jnarayan jnarayan 386 10. Okt 13:23 user_script.sh]]> Jit