STAR v2.4.0f1 bash problem?

[René Böttcher]

Dear Alex,

Thank you for STAR, I am becoming a real fan of your program and am currently using it for alignment of my RNA-seq samples.

My latest try to use STAR unfortunately did not finish well, as it seems that the program is getting stuck. The settings I use are the following:

STAR
--genomeDir /home/rboettcher/bin/STAR-STAR_2.4.0f1/genomes/hg19/
--readFilesIn sample_1P.fastq.gz sample_2P.fastq.gz
--runThreadN 12
--chimSegmentMin 15
--outReadsUnmapped Fastx
--readFilesCommand zcat
--outSAMtype BAM SortedByCoordinate;

and the only output I get is:

sh: 1: Syntax error: Bad fd number

after which I have no other notifications are printed and I have to cancel the run. The system I am running STAR on is a Dell workstation with Ubuntu 12.04 (Kernel 3.2.0-70) 2 Xeon hexacores and 128GB RAM. I used the same STAR version to index hg19 which worked fine, and I am using Trimmomatic for adapter removal prior to alignment.

When Googling the error I came across some posts mentioning that the shebang before some bash code might be set to !#/bin/sh instead of !#bin/bash, which could cause Ubuntu to use the standard dash instead of bash. Maybe this helps to tackle this issue.

Best,

René

[René Böttcher]

Hi Alex,

Sorry for double posting, but I think I tracked down the error to the --readFilesCommand zcat option, as the following substitute code works fine:

mkfifo fileR1.fifo;
mkfifo fileR2.fifo;
zcat sample_1P.fastq.gz > fileR1.fifo &
zcat sample_2P.fastq.gz > fileR2.fifo &
STAR --genomeDir /home/rboettcher/bin/STAR-STAR_2.4.0f1/genomes/hg19/ --runThreadN 12 \
     --chimSegmentMin 15 --outReadsUnmapped Fastx --outSAMtype BAM SortedByCoordinate \
     --readFilesIn fileR1.fifo fileR2.fifo;

Cheers,
René

[Alexander Dobin]

Hi René 

thanks for tracking this problem. I have pushed an update to GitHub master https://github.com/alexdobin/STAR
that contains --sysShell option, where you can specify your path to bash, for example --sysShell /bin/bash

Please let me know if it solves the problem.

Cheers

Alex

[Tobias Meißner]

Hi Alex,

I just run into the same issue as Rene did, using STAR 2.4.0g version and the new --sysShell option. I think this might be more of an Ubuntu issue and I could solve the problem by:

sudo mv /bin/sh /bin/sh.orig
sudo ln -s /bin/bash /bin/sh

as Ubuntu (at least 12.04 which I am using) links /bin/sh to /bin/dash instead /bin/bash

With those changes STAR runs fine again with the zcat option and no need for the --sysShell option.

Cheers,

Tobias

[Jason Byars]

I'm using the --sysShell fix without issue, but that is a good point about the /bin/sh symlink. Thanks!

[Alexander Dobin]

Hi Tobias,

Thanks for this work-around. I think I have finally fixed the problem in the 2.4.0h release. I have tested it on Amazon's Ubuntu server, and it run without errors even without changing the deault shell.

Cheers

Alex