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alekseyzimin / masurca

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Run-time error, cannot open file #245

Open jkreinz opened 3 years ago

jkreinz commented 3 years ago

I'm trying to compare runs of two assemblies, a short read only and a short read + pacbio. I've run the simple one-liner commands specified in the tutorial (i.e. not using the config file) and both the short read only and hybrid assembly run into the same issue. The runs appeared frozen for ~5 days and then finally both showed the following "cannot open file" run-time error. Nonetheless, the PE log messages say the job completes but the primary.genome.scf.fasta file is missing.

the PE only assembly(/ohta1/apps/MaSuRCA-4.0.4/bin/masurca -t 30 -i Salmon Sim.Stabilising.p1.1.6400000_R1.fastq.gz,SalmonSim.Stabilising.p1.1.6400000_R2.fastq.gz) error:

Run-time error

Cannot open file

..now exiting to system...
/ohta1/apps/MaSuRCA-4.0.4/bin/deduplicate_contigs.sh: line 32:
Could not find input file in command line

the hybrid assembly (/ohta1/apps/MaSuRCA-4.0.4/bin/masurca -t 30 -i shortreads/SalmonSim.Stabilising.p1.1.6400000_R1.fastq.gz,shortreads/SalmonSim.Stabilising.p1.1.6400000_R2.fastq.gz -r longreads/SalmonSim.Stabilising.p1.3.30k.PacBio.fastq.gz) error:

Run-time error

Cannot open file

..now exiting to system...
/ohta1/apps/MaSuRCA-4.0.4/bin/mega_reads_assemble_cluster2.sh: line 180:
Could not find input file in command line

Input file name:/9232868/2: syntax error in expression (error token is "not find input file in command line

Input file name:/9232868/2")
/ohta1/apps/MaSuRCA-4.0.4/bin/mega_reads_assemble_cluster2.sh: line 181: [: -lt: unary operator expected
/ohta1/apps/MaSuRCA-4.0.4/bin/mega_reads_assemble_cluster2.sh: line 182: [: -gt: unary operator expected
alekseyzimin commented 3 years ago

Can you specify the full path to your reads files instead of the relative path?