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ablab / spades

SPAdes Genome Assembler
http://ablab.github.io/spades/
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Error while running SPAdes #1273

Closed sahilrishav2 closed 2 months ago

sahilrishav2 commented 2 months ago

Description of bug

Hi,

I am trying to use SPAdes tool for assembling the fungi genome but an unexpected error is showing:

== Error == system call for: "['/data/jammu-univ/software/SPAdes-3.15.5-Linux/bin/spades-core', '/data/jammu-univ/data/ayushi_data/JNU/Endo_CSE15_sample/Pacbio_data/hybrid_spades_assembly/output_folder/K77/configs/config.info']" finished abnormally, OS return value: 34

Kindly help me regarding this concern.

Thank You

spades.log

spades.log

params.txt

bin/spades.py -1 /data/jammu-univ/data/ayushi_data/JNU/Endo_CSE15_sample/illumina_data/Endo1_S101_R1_001.fastq -2 /data/jammu-univ/data/ayushi_data/JNU/Endo_CSE15_sample/illumina_data/Endo1_S101_R2_001.fastq --pacbio /data/jammu-univ/data/ayushi_data/JNU/Endo_CSE15_sample/Pacbio_data/Endo_combine.fastq -o /data/jammu-univ/data/ayushi_data/JNU/Endo_CSE15_sample/Pacbio_data/hybrid_spades_assembly/output_folder -t 80 -m 500

SPAdes version

SPAdes v3.15.5

Operating System

linux

Python Version

Python 3.11.8

Method of SPAdes installation

binaries

No errors reported in spades.log

asl commented 2 months ago

The log reads:

  0:41:14.159  7030M / 70G   ERROR   General                 (single_read.hpp           :  74)   Invalid read: length of sequence should equal to length of quality line

So your input reads are corrupted (the long ones).