Super reads failed: Error with file guillaumeKUnitigsAtLeast32bases_all.fasta, kUnitigLengths.txt is of size 0, must be at least of size 1.

[Inexperiencedresearcher]

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: 14043 group: xxxx gid: 14173 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/xxxx/xxxx/Assembly_test sge_o_host: vic account: sge cwd: /cluster/xxxx/xxxx/Assembly_test reserve: y hard resource_list: h_rt=1980000,h_vmem=16G,tmem=16G mail_options: abes mail_list: [email protected] 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@vic Assembly_test]$

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

[xxxx@vic Assembly_test]$ 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

[lly1214]

Hi, did you resolve your problem? I met the same problem. can you help me?

Thanks a lot !