samtools-1.3 sort bug

[sidiropoulos]

Hi,

I had an error while running the pipeline during the bamfile pairing step. More specifically got the "Forward and reverse reads not paired. Check that BAM files are sorted." error from mergeSam.py file.

Tracking it down I realised that the 'samtools sort' output was never stored. In bowtie_combine.sh samtools sort is called by:

cmd="${SAMTOOLS_PATH}/samtools sort -@ ${N_CPU} -n ${BOWTIE2_FINAL_OUTPUT_DIR}/${prefix}.bwt2merged.bam ${BOWTIE2_FINAL_OUTPUT_DIR}/${prefix}.bwt2merged.sorted"

In samtools 1.3, "The obsolete samtools sort in.bam out.prefix usage has been removed. If you are still using ‑f, ‑o, or out.prefix, convert to use -T PREFIX and/or -o FILE instead."

Consider switching the sort call by specifying the output name with the -o flag.

Thank you for a great pipeline. :-)

Regards,
Nikos

[nservant]

Hi Nikos,
Thank you for reporting this. If I understand correctly, using the -o option should work will all versions ?
I will fix that as soon as possible.
N

[sidiropoulos]

Hi Nicolas,

Yes that would work, but make sure you don't just specify the output suffix but use the full output file name. It will work with all samtools >1.0 versions which is already a prerequisite for HiC-Pro.

Bests,
Nikos

[nservant]

Hi Nikos,
I made a few tests. It seems that -o option cannot be used without -T option.
Can you confirm this ? Thanks. N

[sidiropoulos]

Hi Nicolas,

Sorry for the delay.

You are right. In samtools-1.2 (also 1.0 and 1.1) the option -T or -O has to be supplied if -o is used.
In samtools-1.3 the -T or -O requirement is removed.

I would suggest to keep both -o and -T to cover all cases.

Bests,
Nikos

[nservant]

Fixed in current master (v2.7.3b). Thank you again Nikos !