Sorting Issue With SQuIRE Map

[Sesukai]

Hello,

I have been having encountering an error running the SQuIRE Map command on my Fastqs.

Traceback (most recent call last): File "/gs/gsfs0/users/skattapong/.conda/envs/squire/bin/squire", line 11, in load_entry_point('SQuIRE', 'console_scripts', 'squire')() File "/gs/gsfs0/users/skattapong/SQuIRE/squire/cli.py", line 156, in main subargs.func(args = subargs) File "/gs/gsfs0/users/skattapong/SQuIRE/squire/Map.py", line 387, in main align_paired(read1,read2,pthreads,trim3,index,outfile,gtf,gzip,prefix, read_length,extra_fapath) File "/gs/gsfs0/users/skattapong/SQuIRE/squire/Map.py", line 138, in align_paired sp.check_call(["/bin/sh", "-c", sortcommand]) File "/gs/gsfs0/users/skattapong/.conda/envs/squire/lib/python2.7/subprocess.py", line 186, in check_call raise CalledProcessError(retcode, cmd) subprocess.CalledProcessError: Command '['/bin/sh', '-c', 'samtools sort -@ 48 squire_map/SRR9127453Aligned.out.bam squire_map/SRR9127453']' returned non-zero exit status 1

I see that there is an issue with the samtools sort command here, so I was wondering if there was a way to manually sort the Aligned.out.bam files.

I attached the script I used here: Squire_Map.txt

Thank you, Seth

[jakewendt]

I just had the same error. It is because the format of the samtools sort command format is from an older version. Either downgrade your samtools to around version 0.1.18 or modify Map.py.

[jamesc99]

Hi,

May I ask how I can downgrade the samtools/modify Map.py? Thanks so much!

Sincerely, Ryan

[jakewendt]

Either install an older version of samtools. 0.1.18 would work.

Or edit squire/Map.py around line 136 and change the sort command

# samtools version 0.1.18 sort format
sortcommand_list = ["samtools", "sort", "-@",str(pthreads), STAR_output, prefix]

# samtools version 1.9 sort format
sortcommand_list = ["samtools", "sort", "-@",str(pthreads), "-o",outfile, STAR_output]