denovo pacbio assembly

Question

[1234anjalianjali1234]

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.

[Ram]

What's the output when you run:

pwd
readlink -f pacbio.fastq
head -n 4 pacbio.fastq

[1234anjalianjali1234]

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
+
,/-,*..,..,**)..,,./,.++*./.).,+./-%)/////.+$..--.---/.+.-*"/-*-+-,.(/,+,.-/+/...+..////+-//.//,'./-*)./)/#.,),*'-$.)*+).)././*,)-,/)-.(////-.+//,/./,*.,,')/.,-///).,/,)*//((/../**.+.*./.+.,*/,--//,/,-$..-*)///../..,+..#/(//./////-)(/.../-.//-/''/-*./$./,&-.),',+*,)..#%..-*/./..&-.'..,%&.+.(---.+-/)(./)#,/..--.....--/./+-.//)/($*,)*)-$../&)..)'...((/'///#-(//..*,-..+*,.//,,../,/..%-../.*....//*."-./')'-///.-..)//)/-+.)'-&-.--.//-*/,,*.,./,*+.#,.(*//-..//-//-$#%&/$-//)/.-%./*+,/-//-/,//////*-/.*&.../-/*//+/*..)..//.*/*/*//../.'.-.$*+'-)/-././/-..".,*,()//-+//./",,-.(.-/-.-.*//)..,,(./()...+/.+,%.,.)/,.-,//'////)-///..../*/,./'/--,//,.//(-))

[1234anjalianjali1234]

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............

......

[colindaven]

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

Answer 1

[colindaven]

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.