question about “--sams=bam.list”

[Henry-Ding]

hi,

I am using the genotype_sv function of V2.7.x, my bamlist is shown in the picture, but it will report an error, is my bamlist format wrong? When I use "--sam" to give a separate bam file program can run.
bamlist:

err.log:

looking forward your reply
best wishes
ding

[Henry-Ding]

This is my command.

thanks

[hannespetur]

Hi, the bamlist format looks right to me. Can you check if those are the the correct read paths, there are no whitespaces/tabs in the bamlist, and that you have permissions to read the data by using i.e. samtools

samtools view /data/..../2.bam/I1.bam Chr1:1-1200000 | less -S

Best,
Hannes

[Henry-Ding]

Thanks for your reply.
I tried the following command as you suggested, these results do not seem to be problematic:

[hannespetur]

The newline style needs to be UNIX (\n) but it looks you have the DOS style (\r\n) from your cat -A output. You can convert to UNIX style with

sed $'s/\r$//' tst.bam.list > unix.tst.bam.list
cat -A unix.tst.bam.list # Should not print the ^M in output

and use unix.tst.bam.list in graphtyper

[Henry-Ding]

Damn, I didn't catch the formatting problem, thanks for your careful answer. The program is running.

One more small question, how many samples does the program support at a time? I have 5,000 samples

[Henry-Ding]

I ran graphtyper with my samples and got this error.

[hannespetur]

alright, well that error message doesn't explain much. Only that some std::map had an access problem, somewhere. Is there really nothing else helpful in your logs?

And it would help me a lot if you could demonstrate your problem in a way for me to reproduce it

[Henry-Ding]

graphtyper genotype_sv ${reference_fasta} 5k.svimmer.vcf.gz --sams=5k.bam.list --region=Chr${1}
--threads=52 --vverbose --log=5k.Chr${1}.log --output=5k.graphtyper.SV
5k.Chr12.log
0_graphtyper_4481436.log
Hi, this is my command line and all the logs I can get. I hope this can help.