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macmanes-lab / Oyster_River_Protocol

Official Repository of the Oyster River Protocol for Transcriptome Assembly
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Unmatched reads in paired-end files #22

Open rafaeltiveron opened 5 years ago

rafaeltiveron commented 5 years ago

Hello once again,

I trimmed and filtered some bad quality reads and run Oyster River Protocol, getting this:

[ INFO] 2019-02-24 17:44:47 : Loading assembly: /root/Downloads/Amostra01/orthofuse/Amostra01/merged.fasta
[ INFO] 2019-02-24 17:44:49 : Analysing assembly: /root/Downloads/Amostra01/orthofuse/Amostra01/merged.fasta
[ INFO] 2019-02-24 17:44:49 : Results will be saved in /root/Downloads/Amostra01/orthofuse/Amostra01/merged/merged
[ INFO] 2019-02-24 17:44:49 : Calculating contig metrics...
[ INFO] 2019-02-24 17:44:51 : Contig metrics:
[ INFO] 2019-02-24 17:44:51 : -----------------------------------
[ INFO] 2019-02-24 17:44:51 : n seqs                        26816
[ INFO] 2019-02-24 17:44:51 : smallest                        201
[ INFO] 2019-02-24 17:44:51 : largest                        9134
[ INFO] 2019-02-24 17:44:51 : n bases                    11258629
[ INFO] 2019-02-24 17:44:51 : mean len                     419.85
[ INFO] 2019-02-24 17:44:51 : n under 200                       0
[ INFO] 2019-02-24 17:44:51 : n over 1k                      1390
[ INFO] 2019-02-24 17:44:51 : n over 10k                        0
[ INFO] 2019-02-24 17:44:51 : n with orf                     4528
[ INFO] 2019-02-24 17:44:51 : mean orf percent              77.19
[ INFO] 2019-02-24 17:44:51 : n90                             232
[ INFO] 2019-02-24 17:44:51 : n70                             308
[ INFO] 2019-02-24 17:44:51 : n50                             431
[ INFO] 2019-02-24 17:44:51 : n30                             701
[ INFO] 2019-02-24 17:44:51 : n10                            1793
[ INFO] 2019-02-24 17:44:51 : gc                             0.39
[ INFO] 2019-02-24 17:44:51 : bases n                        2243
[ INFO] 2019-02-24 17:44:51 : proportion n                    0.0
[ INFO] 2019-02-24 17:44:51 : Contig metrics done in 2 seconds
[ INFO] 2019-02-24 17:44:51 : Calculating read diagnostics...
[ERROR] 2019-02-24 17:44:55 : Snap found unmatched read IDs in input fastq files
[ERROR]
Left files contained read id
'M01506:25:000000000-AF8M6:1:1101:14555:1661'
and right files contained read id
'M01506:25:000000000-AF8M6:1:1101:14176:1759'.  
at the same position in the file

/root/ORP/oyster.mk:226: recipe for target '/root/Downloads/Amostra01/orthofuse/Amostra01/orthotransrate.done' failed
make: *** [/root/Downloads/Amostra01/orthofuse/Amostra01/orthotransrate.done] Error 1
^C

Is there a way to run Oyster River Protocol with paired-end files and considerating unmatched paired reads (example (input files): forward_reads.fq + reverse_reads.fq + unmatched_reads.fq?

Thank you