rule medaka_consensus failed to read bam file
bsiranosian opened this issue · comments
Using TensorFlow backend.
[14:28:55 - Predict] Processing region(s): tig00004723:0-4256
[14:28:55 - Predict] Setting tensorflow threads to 1.
[14:28:55 - Predict] Processing 1 long region(s) with batching.
[14:28:55 - ModelLoad] Building model (steps, features, classes): (10000, 10, 5)
[14:28:59 - ModelLoad] Loading weights from /usr/local/anaconda/lib/python3.6/site-packages/medaka/data/r941_flip213_model.hdf5
[14:28:59 - PWorker] Running inference for 0.0M draft bases.
[14:28:59 - Sampler] Initializing sampler for consensus of region tig00004723:0-4256.
Failed to read .bam file 'bas_hmw_bas/2.polish/racon/bas_hmw_bas_racon_4.fa.bam'.[Tue Jun 25 14:28:59 2019]
It's definitely a bam file
(extract_krak) [bsiranos@smsx10srw-srcf-d15-35 processing]$ du -h bas_hmw_bas/2.polish/racon/bas_hmw_bas_racon_4.fa.bam
1.3G bas_hmw_bas/2.polish/racon/bas_hmw_bas_racon_4.fa.bam
(extract_krak) [bsiranos@smsx10srw-srcf-d15-35 processing]$ samtools flagstat bas_hmw_bas/2.polish/racon/bas_hmw_bas_racon_4.fa.bam
406024 + 0 in total (QC-passed reads + QC-failed reads)
173151 + 0 secondary
13155 + 0 supplementary
0 + 0 duplicates
347841 + 0 mapped (85.67% : N/A)
0 + 0 paired in sequencing
0 + 0 read1
0 + 0 read2
0 + 0 properly paired (N/A : N/A)
0 + 0 with itself and mate mapped
0 + 0 singletons (N/A : N/A)
0 + 0 with mate mapped to a different chr
0 + 0 with mate mapped to a different chr (mapQ>=5)
The hell. If this is the fourth iteration, it worked three times previous. Strange. I suggest deleting the bam and rerunning--perhaps the alignment got screwed up somehow?
Can you send me the path to the working directory?
Rerunning the alignment appears to have solved this. Please re-open if this comes up again.
This is still occurring with all of my medaka consensus jobs.
Resolved with building a bam index for that file. THAT WAS DUMB.
Reopening so I can close it when I make the pipeline do this automatically