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BGI-Qingdao / TGS-GapCloser

A gap-closing software tool that uses long reads to enhance genome assembly.
GNU General Public License v3.0
183 stars 13 forks source link

Racon polishing correct? #12

Closed schellt closed 4 years ago

schellt commented 4 years ago

Dear Lidong, I executed TGS-GapCloser as follows: TGS-GapCloser.sh --scaff scaffolds.fasta --reads pacbio.fa --output gapclose --racon /path/to/racon-1.4.3/build/bin/racon --tgstype pb --thread 64

According to the exit status the execution was successful but when I check the STDERR, there are following errors:

/path/to/TGS-GapCloser-release_v1.0.1/TGS-GapCloser.sh: line 490: 48470 Illegal instruction     (core dumped) $RACON -t $THREAD $TGS_READS $OUT_PREFIX.$curr_tag.paf $OUT_PREFIX.ont.$curr_tag.fasta > $OUT_PREFIX.ont.$curr_tag.racon.fasta 2> $OUT_PREFIX.$curr_tag.racon.log
/path/to/TGS-GapCloser-release_v1.0.1/TGS-GapCloser.sh: line 490: 15978 Illegal instruction     (core dumped) $RACON -t $THREAD $TGS_READS $OUT_PREFIX.$curr_tag.paf $OUT_PREFIX.ont.$curr_tag.fasta > $OUT_PREFIX.ont.$curr_tag.racon.fasta 2> $OUT_PREFIX.$curr_tag.racon.log
/path/to/TGS-GapCloser-release_v1.0.1/TGS-GapCloser.sh: line 490: 48472 Illegal instruction     (core dumped) $RACON -t $THREAD $TGS_READS $OUT_PREFIX.$curr_tag.paf $OUT_PREFIX.ont.$curr_tag.fasta > $OUT_PREFIX.ont.$curr_tag.racon.fasta 2> $OUT_PREFIX.$curr_tag.racon.log

Do you think that these errors harmful? The file gapclose.racon.log looks fine to me:

[racon::Polisher::initialize] loaded target sequences 1.372103 s
[racon::Polisher::initialize] loaded sequences 1382.637417 s
[racon::Polisher::initialize] loaded overlaps 1474.567420 s
[racon::Polisher::initialize] aligning overlaps [====================] 592.444451 s
[racon::Polisher::initialize] transformed data into windows 18.428096 s
[racon::Polisher::initialize] loaded target sequences 1.362661 s
[racon::Polisher::initialize] loaded sequences 1342.986217 s
[racon::Polisher::initialize] loaded overlaps 1453.761094 s
[racon::Polisher::initialize] aligning overlaps [====================] 571.474114 s
[racon::Polisher::initialize] transformed data into windows 19.142867 s
[racon::Polisher::initialize] loaded target sequences 1.428398 s
[racon::Polisher::initialize] loaded sequences 1361.938485 s
[racon::Polisher::initialize] loaded overlaps 1298.255777 s
[racon::Polisher::initialize] aligning overlaps [====================] 532.658983 s
[racon::Polisher::initialize] transformed data into windows 15.609135 s

I just recognized that despite --tgstype pb is specified, the names of intermediate files contain ont. I guess this is just unawareness of the script.

Thank you very much in advance. Best regards, Tilman

cchd0001 commented 4 years ago

Hi Tilman,

It was caused by racon. Please check whether your installed racon suits your operating enverionment. You could still get the gap-closing result without error correction by racon. However, it could affect the accuracy of the long-read selection.

The intermediate files are always named by ont. It could be misleading . We will update it soon .

Best wishes Lidong Guo

schellt commented 4 years ago

Dear Lidong, it was really a configuration problem with one of our nodes. Sorry to bother you. Best, Tilman