lh3/fermi

Option -n non-existent in samtools bam2fq -n

Closed this issue · 6 comments

aldeluis commented

Hi,
I'm having problems running this new version because run-fermi.pl generates a make file that calls to samtools bam2fq -n file.bam.

Seems that there's no option -n in "samtools bam2fq".

Your work is great, thank you!

lh3 commented

What is your command line? Are you feeding a BAM as input?

aldeluis commented

Yes, I'm feeding BAM as input.

run-fermi.pl -t24 ../unmapped.bam > fmdef.mak
make -f ./fmdef.mak -j24 > log 2>&1

(samtools bam2fq -n ../unmapped.bam) | fermi ropebwt -a bcr -v3 -btNf fmdef.raw.tmp - > fmdef.raw.fmd 2> fmdef.raw.fmd.log
open: No such file or directory

After editing fmdef.mak, deleting the option -n in samtools bam2fq -n, all runs flawlessly.

lh3 commented

It is not recommended to use BAM as input, unless you know what samtools/fermi is doing. If you want to use BAM anyway, you need "-n" at least for some versions of fermi (not sure now). The option is available in the latest samtools.

Also, your BAM must be name sorted and both ends in each pair are present; otherwise you can only get contigs without using read pairs.

aldeluis commented

Right, then I need the latest samtools.

I'm trying samtools 0.1.18-dev (r982:313) from your sourceforge svn repository (is this the primary source?). Seems that hasn't the -n option.

samtools bam2fq -n unmapped.bam | head -10
open: No such file or directory

samtools bam2fq unmapped.bam | head -10
@HWUSI-EAS1829:0:1:1:1301:945:1
NACGCCAACAGGCTCTTTCTGCTCTATGAATGAATCCGCCTTTTTTGCCGGACAAATACACTCCATTGTAACTGTCAGGTTTCTCTAGAGGGGGGTGAGNN
+
#####################################################################################################
@HWUSI-EAS1829:0:1:61:12257:16153:1
GGAAGAACCCTTCTGAGAAAGGGCCCAAACTAGCTGCCTTCCTGCAACGTGGCTTGCTGCCCGCTTCTAGTAAGTCGGTGACGAATCTGGCCCACAGCGGG
+
#####################################################################################################
@HWUSI-EAS1829:0:1:1:1564:937:1
NTCCAGCATTTCTACCTGTTGGTCTCAGATGTCTTGAAGCTGTTTCTGCTCAGGTTGAGGAACCACTGGAAGCGCTTGAACTCACTGTGTATGTCCCNNNN

lh3 commented

Samtools has been moved to samtools/samtools for a year or so.

aldeluis commented

Oh, sorry, I didn't realize.

Now all is working with version 0.1.18-r580

Thank you!