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Old 12-12-2021, 02:32 AM   #1
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Location: UK

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


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 guillaumeKUnitigsAtLeast32bases_all.fasta.tmp masurca_assembly.o4302352 pe_data.tmp quorum_mer_db.jf work1 guillaumeKUnitigsAtLeast32bases_all.jump.fasta masurca_config.txt pe.cor.fa pe.renamed.fastq super1.err
ESTIMATED_GENOME_SIZE.txt masurca_assembly.e4302352 pe.cor.tmp.log quorum.err
[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
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/

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

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

assembly, error, masurca, superreads

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