PacBio CCS read denovo assambly failed

[PKhongthon]

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...ds,_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:reoverlap('/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

[rhall]

Looks like an issue with the fastq file, any insight into why all the special characters are in the file name? Also I don't think CA will work from a 'zip' format fastq file.
Recreate the frg file, checking that the fastq is in normal unix text format.

Out of interest why are you including the CCS reads in the assembly? The filtered_subreads.fasta file is all you need for denovo assembly:

http://wgs-assembler.sourceforge.net/wiki/index.php/PBcR#Correcting_and_Assembling_PacBio_RS_sequences