tmp

[slsevilla]

Summary

• Project failure at three rules for all samples.
• Choose one sample to review issue: DGE0_CD3_Wk4_BCG.
• Rules failing:
  • Error in rule atac_fld:
  • Error in rule atac_genrich_peakcalling:
  • Error in rule atac_macs_peakcalling:

Project location

/data/NCI_VB/franchini/ccrvb19_Max_covid_ATACseq_KCG/ASAP_221215_subset20

Rule code for atac_fld

cat /data/NCI_VB/franchini/ccrvb19_Max_covid_ATACseq_KCG/ASAP_221215_subset20/logs/54331095.54336662.atac_fld.replicate=DGE0_CD3_Wk4_BCG.err

python /gpfs/gsfs10/users/NCI_VB/franchini/ccrvb19_Max_covid_ATACseq_KCG/ASAP_221215_subset20/scripts/ccbr_atac_bam2FLD.py -i /gpfs/gsfs10/users/NCI_VB/franchini/ccrvb19_Max_covid_ATACseq_KCG/ASAP_221215_subset20/results/dedupBam/DGE0_CD3_Wk4_BCG.dedup.bam -o /gpfs/gsfs10/users/NCI_VB/franchini/ccrvb19_Max_covid_ATACseq_KCG/ASAP_221215_subset20/results/QC/fld/DGE0_CD3_Wk4_BCG.fld.txt

Review input; no reads found

samtools view /gpfs/gsfs10/users/NCI_VB/franchini/ccrvb19_Max_covid_ATACseq_KCG/ASAP_221215_subset20/results/dedupBam/DGP4_CD3_Wk4_BCG.dedup.bam

Review QC for bam file

cat DGE0_CD3_Wk4_BCG.bowtie2.bam.flagstat
67647231 + 0 in total (QC-passed reads + QC-failed reads)
16561337 + 0 secondary
0 + 0 supplementary
0 + 0 duplicates
66637105 + 0 mapped (98.51% : N/A)
51085894 + 0 paired in sequencing
25542947 + 0 read1
25542947 + 0 read2
48207136 + 0 properly paired (94.36% : N/A)
49686192 + 0 with itself and mate mapped
389576 + 0 singletons (0.76% : N/A)
92274 + 0 with mate mapped to a different chr
38075 + 0 with mate mapped to a different chr (mapQ>=5)