Comments (4)
Could You help to identify the problem?
There are no errors in attached spades.log
file. Will you please attach a correct one from failed run?
from spades.
It is the correct file.
The error is: == Error == system call for: "['/hpc/dla_mm/anasantos/data/miniconda3/envs/unicycler_env/bin/spades-core', '/hpc/dla_mm/anasantos/data/202301_Efaecalis/data/hybrid_genomes/M508826_hybrid/spades_assembly/K111/configs/config.info', '/hpc/dla_mm/anasantos/data/202301_Efaecalis/data/hybrid_genomes/M508826_hybrid/spades_assembly/K111/configs/isolate_mode.info']" finished abnormally, OS return value: 2
from spades.
Looks like you redirected output from several runs into a single output directory – spades.log contains intermixed lines. This is not going to work.
from spades.
I only did:
unicycler -1 namefile_1.fastq.gz -2 namefile_2.fastq.gz -l namefile.fastq -o name_of_directory
from spades.
Related Issues (20)
- Resuming Hybrid Assembly fails HOT 2
- OS return value: -9 HOT 5
- == Error == system call for: spades-core, finished abnormally, OS return value: -9 HOT 1
- Linux build does not run in a directory containing spaces
- Input requirement for hybrid assembly HOT 6
- error while parsing GFA path record HOT 7
- ERROR HOT 5
- Error-6 can not open tmp folder HOT 1
- core dump when runing pathracer HOT 2
- Error code 2. unlink(2) failed HOT 1
- == Error == system call for: finished abnormally, OS return value: 21 (Pair of read files contain unequal amount of reads) HOT 8
- sequence name is empty HOT 3
- Minority mutations used for final assembly (metaspades, hybrid ONT-SR) HOT 2
- spades-core: /spades/assembler/src/common/assembly_graph/core/debruijn_data.hpp:38: void debruijn_graph::CoverageData::inc_coverage(int): Assertion `value >= 0 || coverage_ > unsigned(-value)' failed. HOT 1
- spades 4.0.0 mmap(2) failed. Reason: Cannot allocate memory. Error code: 12 HOT 5
- Files with merged reads were ignored HOT 6
- OS return value: -9
- Cannot find FASTQ files referenced by "Quick start" to test the installation
- Error OS 21
- Error when using conda spades
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from spades.