So I've been using Freebayes for a while now to do my variant calling with usually around 100-200 samples and I've never had a problem running it before. I usually make a text file with my list of bam files (everything is in the same directory and my bam files are indexed). I've actually used this same samples in the past calling variants with Freebayes, but now I cannot get Freebayes to run on these samples to save my life! I keep getting the following error:
[E::hts_open_format] Failed to open file 2012EL-1410.bam ERROR(freebayes): Could not open input BAM file: 2012EL-1410.bam
2012EL-1410.bam is just the name of the bam file that is first on my list. I've changed the read groups and everything for my samples. Like I said, I did the same exact pipeline I did before and never had a problem with running Freebayes and now I can't get it to run. I'm wondering if there was an updated and I need to do something differently but I can't find any info about what to do. Here is my Freebayes command:
freebayes -L $FILE1 -f $REF -v $FILE2 -T 0.001 -p 1 -i -X -n 0 -E 3 --min-repeat-size 5 -m 1 -q 20 -R 0 -Y 0 -e 1000 -F 0.5 -C 2 -3 0 -G 1 -! 0 -d
I do not believe there is a problem with my text file, its formatted with each bam file listed on one line, then the next bam file on the next line, one after the other.
Now just to test it out, I ran Freebayes with a list of 2 samples and it started running! So I'm not sure if something has changed in regards to the number of samples you can run with Freebayes now, because I ran it not that long ago with over 250 bam files with no problem and now I can't get it to run with 100 bam files.
The version of Freebayes I'm using is v1.1.0-20170823. Has anyone else had this problem and could help me out?? I would be appreciate it so much!!