[Announcement] do not have to run bcftools call

[sr320]

see https://github.com/course-fish546-2023/assistance-public/issues/9#issuecomment-1535606240

[hailaschultz]

I am also getting errors for this step:

/home/shared/bcftools-1.14/bcftools mpileup --threads 4 --no-BAQ \
--fasta-ref ../data/cgigas_uk_roslin_v1_genomic-mito.fa \
../output/F143_cgigas_sorted.bam > ../output/F143_mpileup_output.txt

[W::bam_hdr_read] EOF marker is absent. The input is probably truncated [mpileup] 1 samples in 1 input files [mpileup] maximum number of reads per input file set to -d 250 [flush_bcf_records] Error: failed to write the record to standard output

I have a F143_mpile.vcf.gz file in my output, but it is 0 B

[sr320]

assuming you are working on raven - use this location for your sorted bam ~/home/shared/8TB_HDD_01/sr320/github/steven-crabby-duck/F143_cgigas_sorted.bam~

[sr320]

sorry actual path is

/home/shared/8TB_HDD_01/sr320/github/steven-crabby-duck/output/F143_cgigas_sorted.bam

[hailaschultz]

Is there a url to this bam file for use with IGV?

[sr320]

Where is your repo on raven?

[hailaschultz]

/home/shared/8TB_HDD_02/schulh2/GitHub/haila-coursework/assignments/output

[sr320]

see https://d.pr/i/9hCjDT

https://gannet.fish.washington.edu/seashell/bu-546/schulh2/GitHub/haila-coursework/assignments/output/F143_cgigas_sorted.bam

[hailaschultz]

that worked thanks!