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philres / ngmlr

NGMLR is a long-read mapper designed to align PacBio or Oxford Nanopore (standard and ultra-long) to a reference genome with a focus on reads that span structural variations
MIT License
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task terminated while did't report it #62

Open suyanan opened 5 years ago

suyanan commented 5 years ago

multi fastq files need to align, I make this parallel.

  1. One fastq's alignment terminated, but there did't report it, and continue next step. In detail, the command and the log below:

    #command
ngmlr -t 4 -x ont -r hg38.fa -q /export/cleandata/1.ONT/20190429-BNP1018-P4-A1/2-A1-D1_PAD43578/fastq_pass/PAD43578_82e1bd14d04a6f6ad9807b5a28914daec613c654_467.fastq | samtools sort -@ 4 -o ngmlr.bam -
#logs
ngmlr 0.2.7 (build: Jul  2 2018 10:32:15, start: 2019-06-07.18:30:21)
Contact: philipp.rescheneder@univie.ac.at
Writing output (SAM) to stdout
Reading encoded reference from GRCh38_no_alt_analysis_set.fa-enc.2.ngm
Reading 3100 Mbp from disk took 17.72s
Reading reference index from GRCh38_no_alt_analysis_set.fa-ht-13-2.2.ngm
Reading from disk took 45.92s
Opening query file /export/cleandata/1.ONT/20190429-BNP1018-P4-A1/2-A1-D1_PAD43578/fastq_pass/PAD43578_82e1bd14d04a6f6ad9807b5a28914daec613c654_467.fastq
Mapping reads...
Exception bad_alloc occured in thread 0. This usually means you ran out of physical or virtual memory (try ulimit -v)
Terminating

  2. One fastq's alignment did't process completely, but there did't report it, and continue next step.(Also, this maybe the ngmlr's problems.) In detail, the command is like above, and the log below:

    ngmlr 0.2.7 (build: Jul  2 2018 10:32:15, start: 2019-06-09.08:57:42)
Contact: philipp.rescheneder@univie.ac.at
Writing output (SAM) to stdout
Reading encoded reference from GRCh38_no_alt_analysis_set.fa-enc.2.ngm
Reading 3100 Mbp from disk took 14.61s
Reading reference index from GRCh38_no_alt_analysis_set.fa-ht-13-2.2.ngm
Reading from disk took 35.89s
Opening query file /export/cleandata/1.ONT/20190429-BNP1018-P4-A1/2-A1-D1_PAD43578/fastq_pass/PAD43578_82e1bd14d04a6f6ad9807b5a28914daec613c654_260.fastq
Mapping reads...
Processed: 316 (0.98), R/S: 9.87, RL: 21863, Time: 32.30 1.00 62.42, Align: 0.99, 620, 0.99

Actually, the complete alignment log is below:

fastq | samtools sort -@ 4 -o ngmlr.bam -
ngmlr 0.2.7 (build: Jul  2 2018 10:32:15, start: 2019-06-11.17:02:38)
Contact: philipp.rescheneder@univie.ac.at
Writing output (SAM) to stdout
Reading encoded reference from GRCh38_no_alt_analysis_set.fa-enc.2.ngm
Reading 3100 Mbp from disk took 1.34s
Reading reference index from GRCh38_no_alt_analysis_set.fa-ht-13-2.2.ngm
Reading from disk took 3.06s
Opening query file /export/cleandata/1.ONT/20190429-BNP1018-P4-A1/2-A1-D1_PAD43578/fastq_pass/PAD43578_82e1bd14d04a6f6ad9807b5a28914daec613c654_260.fastq
Mapping reads...
Processed: 4000 (0.96), R/S: 2.73, RL: 20069, Time: 3.11 0.11 10.86, Align: 0.99, 570, 0.98
Done (3844 reads mapped (96.10%), 156 reads not mapped, 4428 lines written)(elapsed: 24m, 2 r/s)
[bam_sort_core] merging from 0 files and 4 in-memory blocks...