Question: PacBio CCS read denovo assembly failed
0
gravatar for phongphak.06
2.6 years ago by
phongphak.0610
phongphak.0610 wrote:

Hello!
I'm beginning to the field of bioinformatics (I'm 1st year student in bioinformatics and systems biology program) and I got uncorrected PacBio sequences from Xylaria sp. consist of 64 files are bax.h5, CCS reads, filtered_subreads and filtered_subreads_longest which I assembled by using celera assembler and I found error in overlap based trimming step (runCA -p xylaria-trim -d xylaria-trim -s xylaria-trim.spec xylaria-untrimmed.frg; I created Spec file followed by sample in this link http://wgs-assembler.sourceforge.net/wiki/index.php/Escherichia_coli_K12_MG1655,_using_uncorrected_PacBio_reads,_with_CA8.2). So, the errors shown as follows


ERROR: Failed with signal HUP (1)
================================================================================

runCA failed.

----------------------------------------
Stack trace:

 at wgs-8.3rc1/Linux-amd64/bin/runCA line 1649
        main::caFailure('gatekeeper failed', '/storage/home/phongphak.kho/xylaria-trim/xylaria-trim.gkpStor...') called at wgs-8.3rc1/Linux-amd64/bin/runCA line 1978
        main::preoverlap('/storage/home/phongphak.kho/pacbio/xylaria-untrimmed.frg') called at wgs-8.3rc1/Linux-amd64/bin/runCA line 6551

----------------------------------------
Last few lines of the relevant log file (/storage/home/phongphak.kho/xylaria-trim/xylaria-trim.gkpStore.err):


Starting file '/storage/home/phongphak.kho/pacbio/xylaria-untrimmed.frg'.

Processing SINGLE-ENDED SANGER QV encoding reads from:
      '/storage/home/phongphak.kho/pacbio/Pacbio.RunÚyH¥n·æ±-þ0}-©ÚºÎò¹¬ç¬.ccs.fastq.zip'
FASTQ quality name line too long in read 'ºíûqY¼*ئ&                      m¾w˲.:~¨©½u^ÇT
vÖ5Ý0÷$ò¬ªíoÓ<L
               ¥WþÁ°ú^©uZÚÉ«æ>
                              g      T7¶í0uù½Ì
                               2Ü7rÛ²


PS. forFRG file, I used CCS reads, filtered_subreads and filtered_subreads_longest to created

ADD COMMENTlink modified 2.6 years ago by orange30 • written 2.6 years ago by phongphak.0610
0
gravatar for orange
2.6 years ago by
orange30
Korea, Republic Of
orange30 wrote:

may be the formate of ccs file. try to use .gz instead of .zip or don't compress the ccs fastq file.

ADD COMMENTlink written 2.6 years ago by orange30
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