resuming the run - Githubissues

Hi I am running pepper for ont samples and encountering the following error. I would like to do the next step by resuming and using the VCF files already generated on the deduplicated bam file. How can I do that? Thanks!


> Polishing 99% complete (30292/30567, 4h 37m).  Estimated time remaining: 2m 48s
> Starting merge
Expected three tokens in header line, got 2
This usually means you have multiple primary alignments with the same read ID.
You can identify whether this is the case with this command:

        samtools view -F 0x904 YOUR.bam | cut -f 1 | sort | uniq -c | awk '$1 > 1'

real    367m9.645s
user    840m17.342s
sys     26m43.772s
[E::hts_open_format] Failed to open file "/tier2/nanopore/OXN-026/snp_pepper/intermediate_files/PHASED.PEPPER_MARGIN.haplotagged.bam" : No such file or directory
samtools index: failed to open "/tier2/nanopore/OXN-026/snp_pepper/intermediate_files/PHASED.PEPPER_MARGIN.haplotagged.bam": No such file or directory
[05-20-2023 02:47:38] ERROR: None]
[05-20-2023 02:47:38] THE FOLLOWING COMMAND FAILED: time margin phase /tier2/nanopore/OXN-026/OXN-026.sorted.bam /analysis/programmes/test_cnv_output/hg19.fa /tier2/nanopore/OXN-026/snp_pepper/intermediate_files/PEPPER_VARIANT_FULL.vcf.gz /opt/margin_dir/params/phase/allParams.haplotag.ont-r94g507.snp.json -t 45 -V -o /tier2/nanopore/OXN-026/snp_pepper/intermediate_files/PHASED.PEPPER_MARGIN 2>&1 | tee /tier2/nanopore/OXN-026/snp_pepper/logs/2_margin_haplotag.log;
samtools index -@45 /tier2/nanopore/OXN-026/snp_pepper/intermediate_files/PHASED.PEPPER_MARGIN.haplotagged.bam]
Processing OXN-027
phased variant calling using pepper-margin deepvariant...
[05-20-2023 02:47:39] INFO: VARIANT CALLING MODULE SELECTED
[05-20-2023 02:47:39] INFO: [1/10] RUNNING THE FOLLOWING COMMAND

kishwarshafin / pepper

resuming the run #189