EXCEPTION: error opening file: tmp/s2228.fq ()

[Shellfishgene]

I tried to run ORNA on a large dataset (each fastq file ~45 GB, paired end), but it fails with the above error. The DSK step seems to work fine, and then ORNA runs for a while and produces various fq files in the tmp directory, s2228.fq is the one with the largest number. It is present and contains normal fastq data as far as I can see. I tried a test with just very small fastq files, ORNA runs fine with these. I tried this on two different machines with the same error, so I don't think it's a file system issue. I guess it happens at the start of the second iteration.

> /opt/ORNA/ORNA -pair1 all.R1.fastq.gz -pair2 all.R2.fastq.gz -sorting 1 -nb-cores 12 -output normalized -type fastq -kmer 25

Given Parameters
----------------
Base:   1.7
kmer size:      25
Mode: ORNA-Q
Number of cores:        12
----------------
[DSK: nb solid kmers found : 507317221   ]  100  %   elapsed:  97 min 17 sec   remaining:   0 min 0  sec   cpu: 247.4 %   mem: [1737, 4411, 4415] MB
[Building BooPHF]  100  %   elapsed:   2 min 8  sec   remaining:   0 min 0  sec
[MPHF: populate                          ]  100  %   elapsed:   3 min 19 sec   remaining:   0 min 0  sec   cpu: 100.0 %   mem: [1285, 1285, 4415] MB
[Bloom: read solid kmers                 ]  100  %   elapsed:   0 min 44 sec   remaining:   0 min 0  sec   cpu: 577.4 %   mem: [2145, 2145, 4415] MB
[Debloom: build extension                ]  100  %   elapsed:   1 min 46 sec   remaining:   0 min 0  sec   cpu: 896.9 %   mem: [2493, 2493, 4415] MB
[Debloom: finalization                   ]  100  %   elapsed:   0 min 56 sec   remaining:   0 min 0  sec   cpu: 154.9 %   mem: [2372, 2372, 4415] MB
[Debloom: cascading                      ]  100  %   elapsed:   0 min 32 sec   remaining:   0 min 0  sec   cpu: 878.4 %   mem: [2373, 2373, 4415] MB
[Graph: nb branching found : 46454780    ]  100  %   elapsed:   1 min 46 sec   remaining:   0 min 0  sec   cpu: 2112.5 %   mem: [3904, 3904, 4415] MB
Populating node abundances
Running ORNA-Q in paired end mode
1841
EXCEPTION: error opening file: tmp/s2228.fq ()