cirRNA DAQ updates

[kopardev]

• [x] add min_reads to bam generation
• [x] remove BSJ based on this criteria:
  • 150 min 5kb max for virus
  • 150 min no max for human
• [x] #49

[kopardev]

• [x] update read extraction scripts (linear and spliced reads)
• [x] update same scripts for SE FYI, types of BSJ in PE data:

Type of linear reads:

[kopardev]

Finally settling on

[kopardev]

Testing c2debce in /gpfs/gsfs8/users/CBLCCBR/kopardevn_tmp/issue57_testing_6

[kopardev]

Error in rule ciri:

+ cd /gpfs/gsfs8/users/CBLCCBR/kopardevn_tmp/issue57_testing_6/results/GI1_N/ciri
+ '[' PE == PE ']'
+ bwa mem -t 56 -T 19 /gpfs/gsfs8/users/CBLCCBR/kopardevn_tmp/issue57_testing_6/ref/ref /gpfs/gsfs8/users/CBLCCBR/kopardevn_tmp/issue57_testing_6/results/GI1_N/trim/GI1_N.R1.trim.fastq.gz /gpfs/gsfs8/users/CBLCCBR/kopardevn_tmp/issue57_testing_6/results/GI1_N/trim/GI1_N.R2.trim.fastq.gz
+ perl /data/Ziegelbauer_lab/tools/CIRI_v2.0.6/CIRI2.pl -I GI1_N.bwa.sam -O /gpfs/gsfs8/users/CBLCCBR/kopardevn_tmp/issue57_testing_6/results/GI1_N/ciri/GI1_N.ciri.out -F /gpfs/gsfs8/users/CBLCCBR/kopardevn_tmp/issue57_testing_6/ref/ref.fa -A /gpfs/gsfs8/users/CBLCCBR/kopardevn_tmp/issue57_testing_6/ref/ref.fixed.gtf -G /gpfs/gsfs8/users/CBLCCBR/kopardevn_tmp/issue57_testing_6/results/GI1_N/ciri/GI1_N.ciri.log -T 56
+ samtools view -@56 -T /gpfs/gsfs8/users/CBLCCBR/kopardevn_tmp/issue57_testing_6/ref/ref.fa -CS GI1_N.bwa.sam
+ samtools sort -l 9 -T /lscratch/62298969/c24ed023-21e9-4cd4-bfff-dd82c2d5146c --write-index -@56 -O CRAM -o /gpfs/gsfs8/users/CBLCCBR/kopardevn_tmp/issue57_testing_6/results/GI1_N/ciri/GI1_N.ciri.cram -
[E::cram_populate_ref] Mismatching md5sum for downloaded reference
[E::cram_get_ref] Failed to populate reference for id 20
[E::cram_decode_slice] Unable to fetch reference #20:8390288-29065090

[E::cram_populate_ref] Mismatching md5sum for downloaded reference
[E::cram_get_ref] Failed to populate reference for id 169
[E::cram_decode_slice] Unable to fetch reference #169:135317-135413

[E::cram_next_slice] Slice decode failure
samtools sort: truncated file. Aborting

This could be related to the filesystem sluggishness of biowulf offlate ... need to add retry options to the pipeline!