finished abnormally, OS return value: 21

[lidachuis]

Description of bug

Hi， I found the error, but I don't know how to solve it. Can you give me some advice? In the first run, I thought there was something wrong with the file, and I used fastp to filter it, but the second run still had the same problem.

spades.log

0:00:19.550 1M / 72M ERROR General (kmer_coverage_model.cpp : 187) Invalid kmer coverage histogram, make sure that the coverage is indeed uniform

== Error == system call for: "['/Bioinfo/home/liwei/miniconda3/envs/ttt/bin/spades-core', '/Bioinfo/home/liwei/project/HRN-2022041C01.Fz/flow/tmp/getorganelle/test2/result/check/1/animal_mt.check.fq.spades/K45/configs/config.info']" finished abnormally, OS return value: 21

params.txt

Command line: /Bioinfo/home/liwei/miniconda3/envs/ttt/bin/spades.py -t 30 -s /Bioinfo/home/liwei/project/HRN-2022041C01.Fz/flow/tmp/getorganelle/test2/result/check/1/animal_mt.check.fq.more.fq -k 45 --only-assembler -o /Bioinfo/home/liwei/project/HRN-2022041C01.Fz/flow/tmp/getorganelle/test2/result/check/1/animal_mt.check.fq.spades

System information: SPAdes version: 3.15.5 Python version: 3.10.8 OS: Linux-3.10.0-693.el7.x86_64-x86_64-with-glibc2.17

Output dir: /Bioinfo/home/liwei/project/HRN-2022041C01.Fz/flow/tmp/getorganelle/test2/result/check/1/animal_mt.check.fq.spades Mode: ONLY assembling (without read error correction) Debug mode is turned OFF

Dataset parameters: Standard mode For multi-cell/isolate data we recommend to use '--isolate' option; for single-cell MDA data use '--sc'; for metagenomic data use '--meta'; for RNA-Seq use '--rna'. Reads: Library number: 1, library type: single left reads: not specified right reads: not specified interlaced reads: not specified single reads: ['/Bioinfo/home/liwei/project/HRN-2022041C01.Fz/flow/tmp/getorganelle/test2/result/check/1/animal_mt.check.fq.more.fq'] merged reads: not specified Assembly parameters: k: [45] Repeat resolution is enabled Mismatch careful mode is turned OFF MismatchCorrector will be SKIPPED Coverage cutoff is turned OFF Other parameters: Dir for temp files: /Bioinfo/home/liwei/project/HRN-2022041C01.Fz/flow/tmp/getorganelle/test2/result/check/1/animal_mt.check.fq.spades/tmp Threads: 30

SPAdes version

SPAdes 3.15.5

Operating System

Linux

Python Version

Python 3.10.8

Method of SPAdes installation

conda

No errors reported in spades.log

• [X] Yes

[asl]

Please attach spades.log file as you were requested.

[lidachuis]

ok，these are my log params.txt spades.log

[asl]

So, from the log:

  0:00:02.826     2M / 43M   INFO    General                 (kmer_splitters.hpp        : 131)   Used 70 reads

You're having only 70 reads. This cannot be any meaningful part of any genome with even coverage (since you're assembling in normal multicell mode that expects decent part of a genome with even coverage), hence the error.

[lidachuis]

ok.Thank u