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baoe / AlignGraph

Algorithm for secondary de novo genome assembly guided by closely related references
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Inconsistent PE files error #4

Open rob123king opened 9 years ago

rob123king commented 9 years ago

I'm able to do a sopadenovo2 assembly with my paired end reads that I got from a sequencing centre but the AlignGraph errors "Inconsistent PE files" is there a way to correct my files so the program does not error?

Thanks Rob

baoe commented 9 years ago

Hi, Rob,

The reason of this error is there exists at least one read in the first PE file which doesn't match a paired-end read in the same line in the second PE file. You may check and make sure each read in the first PE file has a corresponding read in the second PE file, and both reads have the same line number. For example, if the 2nd read is in the 4th line in the first PE file, its paired-end read should also be in the 4th line in the second PE file.

If this doesn't work for your case, you may send me some of the reads so that I can help to figure out the problem.

Best, Bao

From: rob123king [notifications@github.com] Sent: Wednesday, November 05, 2014 7:26 AM To: baoe/AlignGraph Subject: [AlignGraph] Inconsistent PE files error (#4)

I'm able to do a sopadenovo2 assembly with my paired end reads that I got from a sequencing centre but the AlignGraph errors "Inconsistent PE files" is there a way to correct my files so the program does not error?

Thanks Rob

— Reply to this email directly or view it on GitHubhttps://github.com/baoe/AlignGraph/issues/4.

etwatson commented 8 years ago

I am having the same issue. I have confirmed that the PE files are paired correctly. They were created by sampling my reads using reformat.sh from the bbmap suite with the flag verifypaired=t

baoe commented 8 years ago

Hi, Eric,

It should be the read pairing problem. See line 3444 of the AlignGraph.cpp file for details.

Best, Bao

From: Eric Watson [notifications@github.com] Sent: Wednesday, July 27, 2016 12:53 PM To: baoe/AlignGraph Cc: Bao; Comment Subject: Re: [baoe/AlignGraph] Inconsistent PE files error (#4)

I am having the same issue. I have confirmed that the PE files are paired correctly. They were created by sampling my reads using reformat.sh from the bbmap suite with the flag verifypaired=t

— You are receiving this because you commented. Reply to this email directly, view it on GitHubhttps://github.com/baoe/AlignGraph/issues/4#issuecomment-235700358, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AFGl8fiwlIoN-R6cX93KEShnLvEeyDCYks5qZ7cogaJpZM4C3VJv.

cpaight commented 8 years ago

I have the same error. I have confirmed that the reads are in the same order.

baoe commented 8 years ago

Sorry about it. I guess it is because one of your paired read files contain empty lines in the end, and this makes the two files inconsistent. You may simply delete the lines to fix this issue.

Best, Bao

From: cpaight [notifications@github.com] Sent: Thursday, August 04, 2016 1:43 PM To: baoe/AlignGraph Cc: Bao; Comment Subject: Re: [baoe/AlignGraph] Inconsistent PE files error (#4)

I have the same error. I have confirmed that the reads are in the same order.

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baoe commented 8 years ago

Hi, Eric,

Sorry about it. I guess it is because one of your paired read files contain empty lines in the end, and this makes the two files inconsistent. You may simply delete the lines to fix this issue.

Best, Bao

From: Eric Watson [notifications@github.com] Sent: Thursday, August 04, 2016 2:17 PM To: baoe/AlignGraph Cc: Bao; Comment Subject: Re: [baoe/AlignGraph] Inconsistent PE files error (#4)

See line 3444 of the AlignGraph.cpp file for details. Bao, I'm not going to do that. I used another program with the same reads for my assembly.

— You are receiving this because you commented. Reply to this email directly, view it on GitHubhttps://github.com/baoe/AlignGraph/issues/4#issuecomment-237686415, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AFGl8ZRNNNqt_93INvxiTeOV9xpmwDjSks5qclcFgaJpZM4C3VJv.

jacorvar commented 6 years ago

You could use fastq-sort to sort the PE reads and then convert it to a fasta file with fastq_to_fasta.

alephreish commented 4 years ago

At least in my case the problem was due to the fasta files being in interleaved format. To get non-interleaved fasta e.g. with seqkit:

seqkit fq2fa -w0 R1.fq.gz > R1.fa
seqkit fq2fa -w0 R2.fq.gz > R2.fa

This should be mentioned in the README. A direct support for fastq files would be nice.