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Understand your transcriptome assembly
http://hibberdlab.com/transrate
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Snap found unmatched read IDs in input fastq files #228

Open elainfl opened 5 years ago

elainfl commented 5 years ago

Hello, I am trying to use TransRate

Path/transrate-1.0.3-linux-x86_64/transrate --assembly=assembled.transcripts1.fasta,assembled.transcripts2.fasta,assembled.transcripts3.fasta left=RNAseq1.trimmed.fastq,RNAseq1.unpaired.fastq --right=RNAseq2.trimmed.fastq,RNAseq2.unpaired.sed.fastq

[ INFO] 2019-03-13 17:59:09 : Loading assembly: assembled.transcripts1.fasta [ INFO] 2019-03-13 18:04:31 : Analysing assembly: assembled.transcripts1.fasta [ INFO] 2019-03-13 18:04:31 : Results will be saved in transrate_results/assembled.transcripts1 [ INFO] 2019-03-13 18:04:31 : Calculating contig metrics... [ INFO] 2019-03-13 18:21:02 : Contig metrics: [ INFO] 2019-03-13 18:21:02 : ----------------------------------- [ INFO] 2019-03-13 18:21:02 : n seqs 808362 [ INFO] 2019-03-13 18:21:02 : smallest 100 [ INFO] 2019-03-13 18:21:02 : largest 10337 [ INFO] 2019-03-13 18:21:02 : n bases 212338608 [ INFO] 2019-03-13 18:21:02 : mean len 183.12 [ INFO] 2019-03-13 18:21:02 : n under 200 451171 [ INFO] 2019-03-13 18:21:02 : n over 1k 16170 [ INFO] 2019-03-13 18:21:02 : n over 10k 1 [ INFO] 2019-03-13 18:21:02 : n with orf 20778 [ INFO] 2019-03-13 18:21:02 : mean orf percent 52.74 [ INFO] 2019-03-13 18:21:02 : n90 247 [ INFO] 2019-03-13 18:21:02 : n70 381 [ INFO] 2019-03-13 18:21:02 : n50 689 [ INFO] 2019-03-13 18:21:02 : n30 10337 [ INFO] 2019-03-13 18:21:02 : n10 10337 [ INFO] 2019-03-13 18:21:02 : gc 0.43 [ INFO] 2019-03-13 18:21:02 : bases n 0 [ INFO] 2019-03-13 18:21:02 : proportion n 0.0 [ INFO] 2019-03-13 18:21:02 : Contig metrics done in 991 seconds [ INFO] 2019-03-13 18:21:02 : Calculating read diagnostics... [ERROR] 2019-03-13 18:21:36 : Snap found unmatched read IDs in input fastq files [ERROR] Left files contained read id 'A00155:73:HC5FYDSXX:2:1101:9209:1000' and right files contained read id 'A00155:73:HC5FYDSXX:2:1102:20121:5368'.
at the same position in the file

I read in some issue that it could be happening because of the read number /1 or /2. Despite the modification, it keeps not working so it is not the heading. I don't know how can I understand the error printed and therefore how to solve it.

Can someone help me? thanks a lot

ngroberts commented 4 years ago

I am having the same problem. I thought it might have to do with the way my reads are trimmed but no dice.

KDRichar commented 3 years ago

Was this issue addressed?