trouble in use

[岳亮]

We have tried all installation options mentioned in github, but it seems the same error when we are going to assemble a circle molecular.

2023-08-23 02:47:30,628 - INFO: /pub/Application/bin/GetOrganelle/GetOrganelleDep/linux/SPAdes/bin/spades.py -t 110  --disable-gzip-output --phred-offset 33 -1 cpyue164/extended_1_paired.fq -2 cpyue164/extended_2_paired.fq --s1 cpyue164/extended_1_unpaired.fq --s2 cpyue164/extended_2_unpaired.fq -k 21,55,85,115 -o cpyue164/extended_spades
2023-08-23 02:47:55,376 - ERROR: Error with running SPAdes: == Error ==  system call for: "['/pub/Application/bin/GetOrganelle/GetOrganelleDep/linux/SPAdes/bin/spades-core', '/home/PATH/extended_spades/K55/configs/config.info']" finished abnormally, OS return value: -6
2023-08-23 02:47:55,400 - ERROR: Assembling failed.

Total cost 633.88 s
Thank you!

We checked the logfile of spades:

=== Stack Trace ===
Verification of expression 'stream_.good()' failed in function 'void io::BinaryFileStream<SeqT>::Init() [with SeqT = io::UniversalPairedRead<io::SingleReadSeq>]'. In file '/spades/assembler/src/common/io/reads/binary_streams.hpp' on line 37. Message 'Stream is not good(), offset_ 24 count_ 0'.
Verification of expression 'stream_.good()' failed in function 'void io::BinaryFileStream<SeqT>::Init() [with SeqT = io::UniversalPairedRead<io::SingleReadSeq>]'. In file '/spades/assembler/src/common/io/reads/binary_streams.hpp' on line 37. Message 'Stream is not good(), offset_ 24 count_ 0'.
spades-core: /spades/assembler/src/common/io/reads/binary_streams.hpp:37: void io::BinaryFileStream<SeqT>::Init() [with SeqT = io::UniversalPairedRead<io::SingleReadSeq>]: Assertion `stream_.good()' failed.


== Error ==  system call for: "['/pub/Application/bin/GetOrganelle/GetOrganelleDep/linux/SPAdes/bin/spades-core', '/home/superadmin/workspace/garuga/2_HQData/cpyue164/extended_spades/K55/configs/config.info']" finished abnormally, OS return value: -6
None

In case you have troubles running SPAdes, you can write to spades....@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.

[jj3111]

Hi, thanks for reaching out here. 

Please always provide the original COMPLETE get_org.log.txt file rather than partial information.

There were multiple similar issues in GitHub, please check them out:

https://github.com/Kinggerm/GetOrganelle/issues/61

https://github.com/Kinggerm/GetOrganelle/issues/251

https://github.com/Kinggerm/GetOrganelle/issues/245

https://github.com/Kinggerm/GetOrganelle/issues/231

Feel free to search for more and let me know your updates.

[Marcin Nowicki]

Hi there,

What worked for me was, installing SPADES 13.3.1 by "conda install -c bioconda spades", and calling it in the get_organelle command using the flag "--which-spades /usr/bin/"

Hope this helps!