fq2dna quits unexpectedly during the second polish

Hi, I was unable to successfully run the fq2dna without modifying the script at line 1053, where I added the -f option to allow samtools merge to overwrite the existing file (though I am unsure if this modification is appropriate).

The modified line is as follows: else runcmd $SAMTOOLS_MERGE --threads $NTHREADS -o $TMP_DIR/aln.bam $infiles -f &>/dev/null ; rm -f $infiles ;

After making this change, the results I obtained were inconsistent with the ones you provided, specifically, the results of the second polish changed ([dna] Nseq=30 Nres=3099386 NG50=532745 auGN=431354). I suspect there may be an issue with my modification, but I am unsure where the problem lies.

I have attached the log information for your reference.log.txt

Dear Xu Dong,

Thank you very much for your interest to fq2dna.

I have run fq2dna v24.02 using both samtools v1.18 and samtools v1.21, but I was never able to reproduce your problem. Maybe you have used an alternative version of samtools? Or another dependency version (e.g. bwa-mem2)?

However, I have slightly modified the code to take into account your suggestion, i.e. rm $TMP_DIR/aln.bam before running $SAMTOOLS_MERGE. This updated code is available from this gitlab repository: tag version 25.01.

To compare your results with the ones reported in the Example section, please make sure that you are using the same versions for the different dependencies (specified into the file example/program.versions.txt); this can be easily checked by running fq2dna.sh -d

Best regards,

-- Alexis --

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