Question: denovo pacbio assembly
0
gravatar for 1234anjalianjali1234
9 months ago by
India
1234anjalianjali123430 wrote:

Hi everyone,

I have tried to run the tutorial on supplied on the CANU readthedocs http://canu.readthedocs.io/en/latest/quick-start.html. I downloaded the supplied pacbio file and run the script, but it is giving the error:

ERROR: *Don't panic, but a mostly harmless error occurred and Canu stopped.
Canu release v1.5 failed with:
ERROR:  no reads supplied, and can't find any library information in gkpStore*

my command:

kunal@kunal-CELSIUS-M740Bpower:~/canu$ canu-1.5/Linux-amd64/bin/canu -p ecoli -d ecoli-auto genomeSize=4.8 pacbio.fastq

please help.

assembly • 447 views
ADD COMMENTlink modified 9 months ago by colindaven690 • written 9 months ago by 1234anjalianjali123430

What's the output when you run:

pwd
readlink -f pacbio.fastq
head -n 4 pacbio.fastq
ADD REPLYlink modified 9 months ago • written 9 months ago by Ram15k

kunal@kunal-CELSIUS-M740Bpower:~/canu$ pwd

/home/kunal/canu

kunal@kunal-CELSIUS-M740Bpower:~/canu$ readlink -f pacbio.fastq

/home/kunal/canu/pacbio.fastq

kunal@kunal-CELSIUS-M740Bpower:~/canu$ head -n 4 pacbio.fastq

@m141013_011508_sherri_c100709962550000001823135904221533_s1_p0/54519/26233_32397
TGTAAATTGCGGGGAGTTGAGTAAAAGCGTTTTGTAACGTATGGACAGCGTTATGGCGGCATTTG
GTTCTGGGGTTAAGTATTGTTACCAGTTTGCATACACGGGCAAGTTTTCAGGAAGCGACGAGCTG
ATCGTTAAAGGATGCTAACGGCAATCTGCTGGCGACGGCGACAGCGTTATCCATCATTAAAGATCT
GAAGGTGAAAGGTAGCTCT
+
,/-,*..,..,**)..,,./,.++*./.).,+./-%)/////.+$..--.---/.+.-*"/-*-+-,.(/,+,.-/+/...+..////+-//.//,'./-*)./)/#.,),*'-$.)*+).)././*,)-,/)-.(////-.+//,/./,*.,,')/.,-///).,/,)*//((/../**.+.*./.+.,*/,--//,/,-$..-*)///../..,+..#/(//./////-)(/.../-.//-/''/-*./$./,&-.),',+*,)..#%..-*/./..&-.'..,%&.+.(---.+-/)(./)#,/..--.....--/./+-.//)/($*,)*)-$../&)..)'...((/'///#-(//..*,-..+*,.//,,../,/..%-../.*....//*."-./')'-///.-..)//)/-+.)'-&-.--.//-*/,,*.,./,*+.#,.(*//-..//-//-$#%&/$-//)/.-%./*+,/-//-/,//////*-/.*&.../-/*//+/*..)..//.*/*/*//../.'.-.$*+'-)/-././/-..".,*,()//-+//./",,-.(.-/-.-.*//)..,,(./()...+/.+,%.,.)/,.-,//'////)-///..../*/,./'/--,//,.//(-))
ADD REPLYlink modified 9 months ago • written 9 months ago by 1234anjalianjali123430

With my new command i am getting new error.

command:

canu-1.5/Linux-amd64/bin/canu -correct  -s pacbio.fastq -p ecoli -d ecoli-auto genomeSize=4.8\ pacbio-raw*fastq

output:

ERROR:  File not found or unknown specFile option line '@m141013_011508_sherri_c100709962550000001823135904221533_s1_p0/54519/26233_32397'.
ERROR:  File not found in spec file option '@m141013_011508_sherri_c100709962550000001823135904221533_s1_p0/54519/26233_32397'
ERROR:  File not found or unknown specFile option line CGCCGGGCCTGGGTACGGCTGAAGAAAGATCAGTACGTGGCAAACCAGATATAAAGAAAGCTGCTGACCACGCAAGCACGCTGAACACGGTTAGTTAACTTT
ERROR:  File not found in spec file option 'TGTAAATTGCGGGGAGTTGAGTAAAAGCGTTTTGTAACGTATGGACAGCGTTATGGCGGCATTTGGTTCTGGGGTTAAGTATTGTCAGCCGATTACCAGTTTGC
ERROR:  File not found or unknown specFile option line '+'.
ERROR:  File not found in spec file option '+'
ERROR:  File not found or unknown specFile option line ',/-,*..,..,**)..,,./,.++*./.).,+./-%)/////.+$..--.---/.+.-*"/-*-+-,.(/,+,.-/+/...+..////+-//.//,'./-*)./)/#.,),*'-$.)*+).)././*,)-,/)-.(////-.+//,/./,*.,,')/.,-///).,/,)*//((/../**.+.*./.+.,*/,--//,/,-$..-*)///../..,+..#/(//./////-)(/.../-.//-/''/-*./$./,&-.),',+*,)..#%..-*/./..&-.'..,%&.+.(---.+-/)(./)#,/..--.....--/./+-.//)/($*,)*)-$../&)..)'...((
ERROR:  File not found in spec file option ',/-,*..,..,**)..,,./,.++*./.).,+./-%)/////.+$..--.---/.+.-*"/-*-+-,.(/,+,.-/+/...+..////+-//.//,'./-*)./)/#.,),*'-$.)*+).)././*,)-,/)-.(////-.+//,/./,*.,,')/.,-///).,/,)*//((/../**.+.*./.+.,*/,--//,/,-$..-*)///../..,+..#/(//./////-)(/.../-.//-/''/-*./$./,&-.),',+*,)..#%..-*/./..&-.'..,%&.+.(---.+-/)(./)#,/..--.....--/./+-.//)/($ERROR:  File not found or unknown specFile option line '@m141013_011508_sherri_c100709962550000001823135904221533_s1_p0/54532/2817_4395'.
ERROR:  File not found in spec file option '@m141013_011508_sherri_c100709962550000001823135904221533_s1_p0/54532/2817_4395'
ERROR:  File not found or unknown specFile option line 'CGCTATCACCAGGCTTTTTCCCTTGGCGTGGGCAGCACGAATAAGGCAGGGGTTTTATGACGACGAAAATGGTTTGAGCGTGGCACTCTCCGGCTTCTTGCTGATATGG............

......

ADD REPLYlink modified 9 months ago • written 9 months ago by 1234anjalianjali123430

The spec file (with -s) is not a fastq file. HAve a look at example .spec files in the docs. Cheers

ADD REPLYlink written 9 months ago by colindaven690
0
gravatar for colindaven
9 months ago by
colindaven690
Hannover Medical School
colindaven690 wrote:

Canu did not find any reads. Check whether the file ~/canu/pacbio.fastq is present and contains reads.

Also check using "less pacbio.fastq" if the read file is ok and contains enough reads to do the autocorrection step (should be fairly large, i.e. more than 50 -100 MB I would guess).

Good luck.

ADD COMMENTlink written 9 months ago by colindaven690
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