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EichlerLab / smrtsv2

Structural variant caller
MIT License
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blasr error message during alignment stage #10

Closed rozaimirazali closed 5 years ago

rozaimirazali commented 5 years ago

This is how the align/bam/log/ directory looks like:

-rw-rw-r-- 1 rmohamadrazali SDR_gref_ymokrab 309 Feb 18 18:07 2.log -rw-rw-r-- 1 rmohamadrazali SDR_gref_ymokrab 309 Feb 18 21:31 4.log -rw-rw-r-- 1 rmohamadrazali SDR_gref_ymokrab 309 Feb 19 01:40 8.log -rw-rw-r-- 1 rmohamadrazali SDR_gref_ymokrab 309 Feb 19 06:00 6.log -rw-rw-r-- 1 rmohamadrazali SDR_gref_ymokrab 309 Feb 19 09:46 5.log -rw-rw-r-- 1 rmohamadrazali SDR_gref_ymokrab 309 Feb 19 13:48 1.log -rw-rw-r-- 1 rmohamadrazali SDR_gref_ymokrab 309 Feb 19 18:15 7.log -rw-rw-r-- 1 rmohamadrazali SDR_gref_ymokrab 308 Feb 19 19:51 9.log -rw-rw-r-- 1 rmohamadrazali SDR_gref_ymokrab 309 Feb 19 23:14 3.log -rw-rw-r-- 1 rmohamadrazali SDR_gref_ymokrab 308 Feb 20 00:24 0.log -rw-rw-r-- 1 rmohamadrazali SDR_gref_ymokrab 132 Feb 20 00:24 28.log

All the *.log files showed no errors except for 28.log, which shows the following error message:

Aligning batch 28... [INFO] 2019-02-20T00:24:27 [blasr] started. Error, you must provide at least one reads file and a genome file.

I don't understand why it is unable to use the provided reads and genome files. For example, in 0.log i did not get the above error message but this one instead:

Aligning batch 0... [INFO] 2019-02-19T23:14:54 [blasr] started. [INFO] 2019-02-20T00:04:23 [blasr] ended. Sorting... [bam_sort_core] merging from 4 files and 1 in-memory blocks... Indexing... Compressing unaligned reads... Cleaning temp "/gpfs/projects/SDR_gref_ymokrab/sv/analysis/tmp/aln_align_batch_0"...

My command was: smrtsv.py --tempdir ../tmp --verbose --log log.txt run --batches 32 --threads 32 GRCh37.fa multi_runs.fofn

rozaimirazali commented 5 years ago

I found the reason for this error. There are 10 subreads bam files but the --batches is set at 32. It's a typo. 32 was meant for the number of threads and not batches.

paudano commented 5 years ago

The number of batches can be far less or far more than the number of input files. It should not cause this error. If it did, then I should fix something in SMRT-SV.

rozaimirazali commented 5 years ago

I am re-running it with --batches equal to the number of bams. will let you know of the outcome