Questions tagged [bash]

Use this tag to refer to the questions related to the Linux and Unix shell abbreviated as bash (Bourne Again SHell).

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4 votes
0 answers
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Write a bash script to run gatk, fix errors with input, and rerun until completion

I have a bam file that I want to run through GATK's SplitNCigarReads tool. Because of the way the bam file was generated, the program will often fail, with an error message stating: ...
kylep's user avatar
  • 41
2 votes
0 answers
40 views

Racon: empty overlap set!

Not sure if anyone can help me with a Racon issue as the developers are not very responsive on GitHub. I am trying to assemble a genome without a reference. I first did basecalling using dorado, then ...
Setshaba's user avatar
2 votes
1 answer
113 views

Error Registering Job Definition AWS

I am in the process of creating a bioinformatics pipeline and I am currently trying to setup the AWS infrastructure for which it will run. The script I am running to setup the AWS batch job looks like ...
Joe_G's user avatar
  • 101
2 votes
0 answers
53 views

Is there a way antiSMASH can be used to screen a large number of genomes just for one type of biosynthetic gene cluster?

When we use antismash command with the genome sequence file as follows: antismash GCA_002095535.1_ASM209553v1_genomic.gbff it screens the genome for all the ...
snap_v's user avatar
  • 21
2 votes
0 answers
717 views

Cannot blast against specific NCBI databases

I am having issues with some prokaryote reference genome databases (exact names : ref_prok_rep_genomes.*), that I downloaded from the NCBI website : https://ftp.ncbi.nlm.nih.gov/blast/db/. Files in ...
Olivier Coen's user avatar
1 vote
1 answer
14 views

Salmon Multiple File SCRIPT giving error

Hi I am using Salmon quantitation for multiple fastq paired files using following code ...
Malik Saad's user avatar
1 vote
0 answers
45 views

tabix to subset each VCF by the coordinates given

I have a vcf file like below ...
Zizogolu's user avatar
  • 2,132
1 vote
0 answers
21 views

Nucleotide Frequency - HOMER?

I'm trying to find the frequency of UA dinucleotide in a bed file. I want to convert the bed file to FASTA, count all the UA dinucleotides up, then divide by the total length of the FASTA file. Also, ...
Kyle Stangline's user avatar
1 vote
0 answers
49 views

How to calculate GenePy score for vcf files in all subdirectories?

In a parent directory, I have several sub-directories, each of them contain one .vcf.gz file on which analysis should be performed. I want to run following commands on all .vcf.gz files in all ...
B.Germ's user avatar
  • 11
0 votes
1 answer
24 views

How to debug a bash script

Please somebody debug my code In sub-folders there are 500000 vcf files from which I only need 500 vcf files listed in ...
Zizogolu's user avatar
  • 2,132
0 votes
0 answers
75 views

Old program make error ProtDeform

Im trying to run ProtDeform on ubuntu 20.04 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3125161/ I need scoring function :/ to my project But error occurs: ...
MTG's user avatar
  • 147
0 votes
0 answers
190 views

Issues with AutoDock Vina

I am trying to use AutoDock Vina to do docking however I am getting this error. I would really appreciate any help as I have not been able to resolve this error despite trying numerous times.
ibio_rep1's user avatar
0 votes
1 answer
149 views

How to use extractfeat?

I am working on a script on bash linux to get the CDS (coding sequence) of a gene using extractfeat by EMBOSS. It gives me the error: Warning: No sequences written to output file I am unsure if my ...
KA97's user avatar
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