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ablab / spades

SPAdes Genome Assembler
http://ablab.github.io/spades/
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SPAdes test fails on ubuntu 20.4 on wsl2 #649

Closed martintaraz closed 3 years ago

martintaraz commented 3 years ago

I tried to run SPAdes on my Ubuntu installation that is Running on my windows subsystem for linux

spades.py --test crashes with the Error

== Error == system call for: "['/home/martin/spades/SPAdes-3.15.0-Linux/bin/spades-hammer', '/home/martin/spades/spades_test/corrected/configs/config.info']" finished abnormally, OS return value: -11

Do you have an idea what could be the matter here?

Best Regards, Martin

martintaraz commented 3 years ago

Full Logoutput is

Command line: ./SPAdes-3.15.0-Linux/bin/spades.py   --test  

System information:
  SPAdes version: 3.15.0
  Python version: 3.8.5
  OS: Linux-4.19.128-microsoft-standard-x86_64-with-glibc2.29

Output dir: /home/martin/spades/spades_test
Mode: read error correction and assembling
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: paired-end
      orientation: fr
      left reads: ['/home/martin/spades/SPAdes-3.15.0-Linux/share/spades/test_dataset/ecoli_1K_1.fq.gz']
      right reads: ['/home/martin/spades/SPAdes-3.15.0-Linux/share/spades/test_dataset/ecoli_1K_2.fq.gz']
      interlaced reads: not specified
      single reads: not specified
      merged reads: not specified
Read error correction parameters:
  Iterations: 1
  PHRED offset will be auto-detected
  Corrected reads will be compressed
Assembly parameters:
  k: automatic selection based on read length
  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: /home/martin/spades/spades_test/tmp
  Threads: 16
  Memory limit (in Gb): 15

======= SPAdes pipeline started. Log can be found here: /home/martin/spades/spades_test/spades.log

/home/martin/spades/SPAdes-3.15.0-Linux/share/spades/test_dataset/ecoli_1K_1.fq.gz: max reads length: 100
/home/martin/spades/SPAdes-3.15.0-Linux/share/spades/test_dataset/ecoli_1K_2.fq.gz: max reads length: 100

Reads length: 100

===== Before start started. 

===== Read error correction started. 

===== Read error correction started. 

== Running: /home/martin/spades/SPAdes-3.15.0-Linux/bin/spades-hammer /home/martin/spades/spades_test/corrected/configs/config.info

The program was terminated by segmentation fault
=== Stack Trace ===

== Error ==  system call for: "['/home/martin/spades/SPAdes-3.15.0-Linux/bin/spades-hammer', '/home/martin/spades/spades_test/corrected/configs/config.info']" finished abnormally, OS return value: -11

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.

SPAdes log can be found here: /home/martin/spades/spades_test/spades.log

Thank you for using SPAdes!
asl commented 3 years ago

Hello

Consider building SPAdes from sources.