SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Vendor provided .Bam file size is much larger in size but # of reads are same newbird Bioinformatics 9 10-30-2014 11:06 AM
What reads were assembled by MaSuRCA? seqEQlkw Bioinformatics 0 10-23-2014 07:17 PM
blat: gfBlatLib.c:794: clumpToHspRange: Assertion `range->tEnd <= tSeq->size' failed. inbarpl Bioinformatics 0 11-06-2012 02:33 AM
solexa output files | s_*_seq.txt vs. s_*_sequencece.txt lajoieb Illumina/Solexa 3 04-08-2009 06:52 PM
problems concerning seq.txt and prb.txt hannat Bioinformatics 4 01-27-2009 11:35 PM

Reply
 
Thread Tools
Old 12-12-2021, 02:32 AM   #1
Inexperienced_Researcher
Junior Member
 
Location: UK

Join Date: Dec 2021
Posts: 1
Default MaSuRCa: Super reads failed - kUnitigLengths.txt is of size 0

Hello,

I am trying running an assembly with MaSuRCa but am getting an error at the step: "Computing super reads from PE".

here's the output with the error:

[xxxx@vic xxxx]$ cd Assembly_test/
[xxxx@vic Assembly_test]$ ls
assemble.sh guillaumeKUnitigsAtLeast32bases_all.fasta.tmp masurca_assembly.o4302352 meanAndStdevByPrefix.pe.txt pe_data.tmp quorum_mer_db.jf work1
environment.sh guillaumeKUnitigsAtLeast32bases_all.jump.fasta masurca_config.txt pe.cor.fa pe.renamed.fastq super1.err
ESTIMATED_GENOME_SIZE.txt masurca_assembly.e4302352 masurca_jobscript.sh pe.cor.tmp.log quorum.err test_jobscript.sh
[xxxx@vic Assembly_test]$ cat ESTIMATED_GENOME_SIZE.txt

[xxxx@vic Assembly_test]$ cat masurca_assembly.o4302352
==============================================================
job_number: 4302352
exec_file: job_scripts/4302352
submission_time: Thu Dec 9 09:07:38 2021
owner: xxxx
uid: xxxx
group: xxxx
gid: xxxx
sge_o_home: /home/xxxx
sge_o_log_name: xxxx
sge_o_path: /usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/opt/ganglia/bin:/opt/ganglia/sbin:/opt/rocks/bin:/opt/rocks/sbin:/opt/gridengine/bin/lx-amd64:/opt/gridengine/bin/linux-x64/:/home/xxxx/bin
sge_o_shell: /bin/bash
sge_o_workdir: /cluster/project7/xxxx/Assembly_test
sge_o_host: vic
account: sge
cwd: xxxx
reserve: y
hard resource_list: h_rt=1980000,h_vmem=16G,tmem=16G
mail_options: abes
mail_list: xxxx@vic.local
notify: FALSE
job_name: masurca_assembly
jobshare: 0
shell_list: NONE:/bin/bash
env_list: TERM=NONE
script_file: masurca_jobscript.sh
parallel environment: smp range: 16
project: external
binding: NONE
job_type: NONE
usage 1: cpu=00:00:00, mem=0.00000 GB s, io=0.00000 GB, vmem=N/A, maxvmem=N/A
binding 1: NONE
scheduling info: (Collecting of scheduler job information is turned off)
[Fri 10 Dec 18:31:14 GMT 2021] Processing pe library reads
[Fri 10 Dec 18:58:34 GMT 2021] Average PE read length 250
[Fri 10 Dec 18:58:34 GMT 2021] Using kmer size of 99 for the graph
[Fri 10 Dec 18:58:35 GMT 2021] MIN_Q_CHAR: 33
[Fri 10 Dec 18:58:35 GMT 2021] Creating mer database for Quorum
[Fri 10 Dec 19:25:43 GMT 2021] Error correct PE
[Sat 11 Dec 00:04:24 GMT 2021] Estimating genome size
[Sat 11 Dec 00:04:24 GMT 2021] Estimated genome size:
[Sat 11 Dec 00:04:24 GMT 2021] Creating k-unitigs with k=99
[Sat 11 Dec 00:04:24 GMT 2021] Computing super reads from PE
[Sat 11 Dec 00:04:24 GMT 2021] Super reads failed, check super1.err and files in ./work1/
[xxxx]$

so I had a look at the error file super1.err, here it is:

[xxxx@vic xxxx]$ cat super1.err
mkdir work1
ufasta sizes -H /cluster/project7/Bovidae/Assembly_test/guillaumeKUnitigsAtLeast32bases_all.fasta > work1/kUnitigLengths.txt; wc -l work1/kUnitigLengths.txt | awk '{print $1}' > work1/numKUnitigs.txt; tail -n 1 work1/kUnitigLengths.txt | awk '{print $1+1}' > work1/maxKUnitigNumber.txt
Error with file '/cluster/project7/Bovidae/Assembly_test/guillaumeKUnitigsAtLeast32bases_all.fasta'
Output file "work1/kUnitigLengths.txt" is of size 0, must be at least of size 1. Bye!
mv work1/numKUnitigs.txt work1/createLengthStatisticsFiles.Failed
mv work1/maxKUnitigNumber.txt work1/createLengthStatisticsFiles.Failed
mv work1/kUnitigLengths.txt work1/createLengthStatisticsFiles.Failed

I had a look around but couldn't find a solution,

help would be much appreciated!

thank you
S

Last edited by Inexperienced_Researcher; 12-22-2021 at 06:06 AM. Reason: typos
Inexperienced_Researcher is offline   Reply With Quote
Reply

Tags
assembly, error, masurca, superreads

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 08:10 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2022, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO