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ablab / spades

SPAdes Genome Assembler
http://ablab.github.io/spades/
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Read error correction finished #450

Closed FengqingWang0712 closed 4 years ago

FengqingWang0712 commented 4 years ago

Dear all, I'm a beginner. When I assembly some metagenomes, it showed like this and some of the assembly succeed but some failed. Could you please help me find out the problems? Error == something went wrong and file with corrected reads (/bioinf/home/fwang/nuohe_new/test/assembly-output/corrected/2-1073.FDMS190641995-1a.1.clean.fq.00.0_0.cor.fastq) is missing! In case you have troubles running SPAdes, you can write to spades.support@cab.spbu.ru or report an issue on our GitHub repository github.com/ablab/spades Please provide us with params.txt and spades.log files from the output directory.

== Error == system call for: "['/bioinf/home/fwang/miniconda/miniconda3/bin/python', '/bioinf/home/fwang/miniconda/miniconda3/share/spades/spades_pipeline/scripts/compress_all.py', '--input_file', '/bioinf/home/fwang/nuohe_new/test/assembly-output/corrected/corrected.yaml', '--ext_python_modules_home', '/bioinf/home/fwang/miniconda/miniconda3/share/spades', '--max_threads', '16', '--output_dir', '/bioinf/home/fwang/nuohe_new/test/assembly-output/corrected', '--gzip_output']" finished abnormally, OS return value: 1

Thanks very much. params.txt spades.log

asl commented 4 years ago

It's likely an I/O issue. Does the issue reproduce with restart? What if you'd specify --disable-gzip-output?

FengqingWang0712 commented 4 years ago

It's likely an I/O issue. Does the issue reproduce with restart? What if you'd specify --disable-gzip-output? Thanks for your reply. Yes. I tried twice before submitting the issue. It's the same issue. I'll try as you suggested.

FengqingWang0712 commented 4 years ago

It's likely an I/O issue. Does the issue reproduce with restart? What if you'd specify --disable-gzip-output?

Hi. It seems succeed. I got the contigs.fasta file. I think there is something wrong with the .fq.gz files I input. This time, I input the unzip .fq file, it's woking. Thanks very much.