I'm running "OPERA-LG_v2.0.5/bin/preprocess_reads.pl" and have the following error:

fail to open file './temporarySam'

[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 70778880 sequences have been processed.
[bwa_aln_core] calculate SA coordinate... 161.35 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 70989574 sequences have been processed.
[main] Version: 0.7.15-r1140
[main] CMD: bwa aln -t 30 all_p_ctg.fa -
[main] Real time: 2402.523 sec; CPU: 53429.488 sec
[E::hts_open_format] Failed to open file temporarySam
samtools sort: can't open "temporarySam": No such file or directory
[bwa_aln_core] convert to sequence coordinate... 1.00 sec
[bwa_aln_core] refine gapped alignments... 6.07 sec
[bwa_aln_core] print alignments... PREPROCESS:
Fastq format is recognized
[Thu Jun 14 18:16:47 2018] Building bwa index...
bwa index -p all_p_ctg.fa /home/urbe/Tools/OPERA-LG_v2.0.6/all_p_ctg.fa
[Thu Jun 14 18:18:35 2018] Finding the SA coordinates of the reads using BWA aln...
[Thu Jun 14 18:58:37 2018] Generate alignments of reads using bwa sampe...
bwa samse -n 1 all_p_ctg.fa read.sai - | grep '\(^@\|XT:A:U\)' | /usr/local/bin/samtools view -S -h -b -F 0x4 - | /usr/local/bin/samtools sort -@ 20 -no - temporarySam > FALCON-Unzip-Scaff.bam
Mapping long-reads using blasr...
/home/urbe/Tools/SSpace/SSPACE-LongRead_v1-1/blasr -nproc 40 -m 1 -minMatch 5 -bestn 10 -noSplitSubreads -advanceExactMatches 1 -nCandidates 1 -maxAnchorsPerPosition 1 -sdpTupleSize 7 /media/urbe/MyDDrive/ONTdata/allONT/allONT.fasta /home/urbe/Tools/OPERA-LG_v2.0.6/all_p_ctg.fa | cut -d ' ' -f1-5,7-12 | sed 's/ /\t/g' > FALCON-Unzip-Scaff.map
sh: 1: /home/urbe/Tools/SSpace/SSPACE-LongRead_v1-1/blasr: Permission denied
Sorting mapping results...
sort -k1,1 -k9,9g FALCON-Unzip-Scaff.map > FALCON-Unzip-Scaff.map.sort
Analyzing sorted results...
Extracting linking information...
i3 2000 5000
i2 1000 2000
i4 5000 15000
i0 -200 300
i5 15000 40000
i1 300 1000
Repeat detection...
/home/urbe/Tools/OPERA-LG_v2.0.6/bin//filter_conflicting_edge.pl pairedEdges_i0 contig_length.dat 100 2
Illegal division by zero at /home/urbe/Tools/OPERA-LG_v2.0.6/bin//filter_conflicting_edge.pl line 93.
readline() on closed filehandle FILE at bin/OPERA-long-read.pl line 250.
rm anchor_contig_info.dat contig_length.dat filtered_edges.dat filtered_edges_cov.dat *.sai
rm: cannot remove 'anchor_contig_info.dat': No such file or directory
mv FALCON-Unzip-Scaff.bam FALCON-Unzip-Scaff-with-repeat.bam
/home/urbe/Tools/OPERA-LG_v2.0.6/bin//filter_repeat.pl FALCON-Unzip-Scaff-with-repeat.bam repeat.dat | /usr/local/bin/samtools view - -h -S -b > FALCON-Unzip-Scaff.bam
rm FALCON-Unzip-Scaff-with-repeat.bam
/home/urbe/Tools/OPERA-LG_v2.0.6/bin/OPERA-LG config > log
Analyzing 1 library: FALCON-Unzip-Scaff.bam
min library mean : 0
minimum contig length is 500
Current library: 1 out of 7
Analyzing file: pairedEdges_no_repeat_i0
Analyzing file: pairedEdges_no_repeat_i1
Analyzing file: pairedEdges_no_repeat_i2
Analyzing file: pairedEdges_no_repeat_i3
Analyzing file: pairedEdges_no_repeat_i4
Analyzing file: pairedEdges_no_repeat_i5
ln -s results/scaffoldSeq.fasta scaffoldSeq.fasta

To resolve this, try downloading blasr version 1.3 above and re-run :)

(Deemed University)

Hamdard Nagar, New Delhi – 110 062

R E C R U I T M E N T

(Advertisement No. 5/2014)

Applications on prescribed form are invited for filling up the following teaching positions in the Department of Biotechnology, Faculty of Science in the university. Eligible candidates may apply on or before 30.09.2014.

1. Professor/Associate Professor - One in Pay Band of Rs. 37400-67000+ AGP Rs.10000/9000

2. Assistant Professor - Two in Pay Band of Rs. 15600-39100+ AGP Rs. 6000/-

ASSISTANT PROFESSOR – 02 (including 01 SFS)

Specialization : Bioinformatics

Qualification and Experience :

Ph.D. in Biotechnology or an allied discipline with M.Sc. in Biotechnology/ Biochemistry in the First division or equivalent grade from a recognized University/ Institute.

NET in Life Science or allied discipline in addition to the above qualification.

Experience : At least two years of Post-doctoral teaching and/or research experience in Bioinformatics or relevant field in a UGC recognized Institution of repute or international research institute/ University. Proof of research to be evidenced by publications in SCI-indexed journals of high impact factor as the first or corresponding author.

Note : University may consider exempting candidates from NET, who has been awarded Ph.D. degree from ‘A’ Grade accredited University following the procedure as notified by the UGC in its Regulations of 2009 and adopted by Jamia Hamdard.

For more information: http://www.jamiahamdard.ac.in/PDF/Online%20application%20form%20_Teaching_1.pdf
http://www.jamiahamdard.ac.in/PDF/PBAS.pdf

Functional and Comparative Genomics

http://jp.senescence.info/
http://www.senescence.info/
http://www.liv.ac.uk/integrative-biology/staff/joao-de-magalhaes/

This script has been modified by others to convert InDels as well, e.g. this by David Eccles

./vcf2fq.pl -f <input.fasta> <all-site.vcf> > <output.fastq>

https://github.com/gringer/bioinfscripts/blob/master/vcf2fq.pl

https://github.com/lh3/samtools/blob/master/bcftools/vcfutils.pl

Extent of employment: 30 Hours per Week
Duration of employment: 1st of October 2015 to 30th of September 2019
Gross monthly salary and pay grade in terms of collective agreement for university staff (payable 14 times per year): B1, € 1.997,20

Responsibilities
The successful candidate (f/m) will pursue a Ph.D. project related to the interpretation of plant genome and transcriptome sequencing data from next-generation sequencing (NGS) platforms. In particular, the candidate will characterize the unexplored genome of quinoa, a crop plant of long-standing tradition in Latin America. We collaborate with research partners in Austria and abroad, and the candidate’s project will be of central importance in the context of this research network.

Required skills and qualifications
We are looking for a graduate student (f/m) with a Master’s degree in bioinformatics or in a related field, solid programming skills (e.g. developing sequence analysis tools), experience with the analysis of NGS data sets, understanding of lab methods and knowledge of genomics/transcriptomics. The group has successfully performed several projects using NGS technology. We have recently published the reference genome sequence of sugar beet (Dohm et al., Nature, 2014), a crop plant closely related to quinoa (same family, but different genus). Not yet published is a quinoa genome assembly that we have generated, and which will serve as the starting point of the candidate’s project. We are a multidisciplinary team and offer work in a lively and friendly atmosphere, and state-of-the-art computing infrastructure. We are looking forward to expanding our team by a dedicated and strongly motivated person with a distinct interest in the challenges of plant genomics.

Applications can be submitted until: 16th of August 2015

University of Natural Resources and Life Sciences Vienna seeks to increase the number of its female faculty and staff members. Therefore qualified women are strongly encouraged to apply. In case of equal qualification, female candidates will be given preference unless reasons specific to an individual male candidate tilt the balance in his favour.

Please send your job application (incl. letter of motivation, CV, summary of Master’s thesis and contact details for two referees) to Personnel department, University of Natural Resources and Life Sciences, 1190 Vienna, Peter-Jordan-Straße 70; E-Mail: kerstin.buchmueller@boku.ac.at. (Reference code: 59)

We regret that we cannot reimburse applicants travel and lodging expenses incurred as part of the selection and hiring process.

www.boku.ac.at

• Updated human gene set (GENCODE 21)
• Updated rat gene set including manual annotation from HAVANA
• New species: Vervet-African green monkey
• Imported Transcript Support Levels (TSLs) from UCSC for human and mouse
• Imported APPRIS flag for human and mouse
• Updated Amazon molly gene set

Find more at http://www.ensembl.info/blog/2014/10/02/ensembl-77-has-been-released/

Address of the bookmark: https://github.com/rhysf/Synima

Qualified and interested candidates can send their curriculum vitae by e-mail to hr@drils.org on or before 27th October 2014 mention in the subject line of the mail the following code: AMPK-Biology.

Selected candidates will be called for a personal interview to Dr. Reddy’s Institute of Life Sciences, University of Hyderabad Campus, Gachibowli, Hyderabad. The selected candidate is expected to report within two weeks from the date of selection to start work on the project.

Junior Research Fellowship (Molecular Modeling/Biology) for two years and Senior Research fellowship for one year

Junior Research Fellowship: Rs. 15,600/- (consolidated) per month for first two years.
Senior Research Fellowship: Rs. 18,200/-(consolidated) per month for the 3rd year.

Duration: The duration of the fellowship is for three years. However, the performance of the candidate will be reviewed after the completion of every year and the fellowship will be renewed only upon satisfactory performance.

Responsibilities:

1) Literature search.
2) Design, plan and execute experiments under the supervision of the scientist.
3) Provide scientific support to the scientist in his/her research activities.
4) Book keeping and maintenance of stocks and consumables.

Essential Qualifications:

Required: M.Sc. in Microbiology/Biotechnology/Bioinformatics or any other related branch of basic Sciences from a recognized university/institute with a consistent academic record of minimum 60% aggregate in all qualifying examinations. The candidate should be NET qualified for lectureship. The candidate should be motivated to work with dedication.

Desirable: expertise/experience in both Molecular Modeling and Molecular Biology.

Experience: 0-2 years in the areas of Molecular Modeling and/or Molecular Biology and cell biology and Biochemistry.

Preferable: Relevant research experience as evident from thesis/dissertation/project work.

Advertisement: http://www.ilsresearch.org/userfiles/Junior%20REsearch%20Fellowship%20-%20AMPK(Biology).pdf

https://academic.oup.com/database/article/doi/10.1093/database/baw084/2630454

Address of the bookmark: http://ani.mypathogen.cn/

Faculty Positions
The Central University of Punjab (CUP), Bathinda will be having the Schools and Departments as given in Table-I. The University invites applications from eligible candidates for the posts of Professors (Pay Band Rs. 37400-67000 with AGP of Rs. 10, 000/-), Associate Professors (Pay Band Rs.37400-67000 with AGP of Rs. 9,000/-) and Assistant Professors (Pay Band Rs.15600-39100 with AGP of Rs. 6,000/-)

POSITION AVAILABLE IN THE AREA OF SPECIALIZTION

3. Bioinformatics,

Procedure to apply: Application forms along with API form complete in all respect along with necessary documents and application fee of Rs. 750/-. (Rs. 250/- for Scheduled Caste/Scheduled Tribe/Person with disabilities) should be sent to:

Registrar (Officiating)
Central University of Punjab
City Campus, Mansa Road
Bathinda-151 001

Application forms from the prospective candidates are accepted upto November 10, 2014.

Based on the qualification of the candidates and the need of the university, the applications received will be processed through appropriately constituted selection committees shortly. Minimum qualification can be relaxed in case of exceptionally outstanding candidate. For further details visit www.cup.ac.in; www.centralunipunjab.com; www.cup.edu.in

The candidate should download the application form available at website www.cup.ac.in;
www.centralunipunjab.com; and submit it complete in all respects on or before 10th November 2014.

Those who have applied earlier need to submit Academic Performance Index (API) form, 5 copies of Summary of the Application Form (available at: www.cup.ac.in; www.centralunipunjab.com and Updated CV if not updated recently (without application fee).

http://cup.edu.in/Faculty_details_and_general_instructions.pdf

http://cup.edu.in/Final%20Application%20and%20summary%20Sheet%20and%20Api%20form.pdf