Eric Watson

I've run into several errors with PoPoolation TE2, and would like to explain them for future users. First, my read headers were not compatible with the scripts, producing this error: Invalid readnames for fastq reads The headers look like this: @UNC10-SN254:517:H8PAKADXX:2:1101:1109:2033 1:N:0:TAGCTT @UNC10-SN254:517:H8PAKADXX:2:1101:1109:2033 2:N:0:TAGCTT ...and converting them to the old-style header fixed the problem: @UNC10-SN254:517:H8PAKADXX:2:1101:1109:2033/1 @UNC10-SN254:517:H8PAKADXX:2:1101:1109:2033/2...

I've run into several errors with PoPoolation TE2, and would like to explain them for future users. First, my read headers were not compatible with the scripts, producing this error: Invalid readnames for fastq reads The headers look like this: @UNC10-SN254:517:H8PAKADXX:2:1101:1109:2033 1:N:0:TAGCTT @UNC10-SN254:517:H8PAKADXX:2:1101:1109:2033 2:N:0:TAGCTT ...and converting them to the old-style header fixed the problem: @UNC10-SN254:517:H8PAKADXX:2:1101:1109:2033/1 @UNC10-SN254:517:H8PAKADXX:2:1101:1109:2033/2...

I've run into several errors with PoPoolation TE2, and would like to explain them for future users. First, my read headers were not compatible with the scripts, producing this error: Invalid readnames for fastq reads The headers look like this: @UNC10-SN254:517:H8PAKADXX:2:1101:1109:2033 1:N:0:TAGCTT @UNC10-SN254:517:H8PAKADXX:2:1101:1109:2033 2:N:0:TAGCTT ...and converting them to the old-style header fixed the problem: @UNC10-SN254:517:H8PAKADXX:2:1101:1109:2033/1 @UNC10-SN254:517:H8PAKADXX:2:1101:1109:2033/2...

I've run into several errors with PoPoolation TE2, and would like to explain them for future users. First, my read headers were not compatible with the scripts, producing this error: Invalid readnames for fastq reads The headers look like this: ~~~ @UNC10-SN254:517:H8PAKADXX:2:1101:1109:2033 1:N:0:TAGCTT @UNC10-SN254:517:H8PAKADXX:2:1101:1109:2033 2:N:0:TAGCTT ...and converting them to the old-style header fixed the problem: ~~~ @UNC10-SN254:517:H8PAKADXX:2:1101:1109:2033/1 @UNC10-SN254:517:H8PAKADXX:2:1101:1109:2033/2...

I've run into several errors with PoPoolation TE2, and would like to explain them for future users. First, my read headers were not compatible with the scripts, producing this error: Invalid readnames for fastq reads The headers look like this: ~~~ @UNC10-SN254:517:H8PAKADXX:2:1101:1109:2033 1:N:0:TAGCTT @UNC10-SN254:517:H8PAKADXX:2:1101:1109:2033 2:N:0:TAGCTT ...and converting them to the old-style header fixed the problem: ~~~ @UNC10-SN254:517:H8PAKADXX:2:1101:1109:2033/1 @UNC10-SN254:517:H8PAKADXX:2:1101:1109:2033/2...

I get the following error when I use ppileup: java -jar /usr/local/repo/popte2-v1.10.04.jar ppileup --bam AB.srt.bam --bam BH.srt.bam --bam BR.srt.bam --bam CAT.srt.bam --bam FHL.srt.bam --bam SC.srt.bam --bam SD.srt.bam --bam SRQ.srt.bam --hier te-hierarchy.txt --output popTE.AB-BH-BR-CAT-FHL-SC-SD-SRQ.ppileup --detailed-log 11/14/17 22:17:14: Finished estimating insert size distribution, TE abundance and sorting of reference chromosomes Exception in thread "main" java.lang.IllegalArgumentException:...

When I try to run se2pe, I get the following error: → java -jar /usr/local/repo/popte2-v1.10.04.jar se2pe --fastq1 /media/data/seq_data_archive/AB_R1.paired.fastq.gz --fastq2 /media/data/seq_data_archive/AB_R2.paired.fastq.gz --bam1 AB_1.sam --bam2 AB_2.sam --sort --output AB.sort.bam 11/14/17 23:28:07: Start pairing up sam-entries 11/14/17 23:28:07: Auto detecting sam or bam file by extension 11/14/17 23:28:07: Reading sam file AB_1.sam 11/14/17 23:28:07: Auto detecting sam or bam file by extension...

When I try to run se2pe, I get the following error: → java -jar /usr/local/repo/popte2-v1.10.04.jar se2pe --fastq1 /media/data/seq_data_archive/AB_R1.paired.fastq.gz --fastq2 /media/data/seq_data_archive/AB_R2.paired.fastq.gz --bam1 AB_1.sam --bam2 AB_2.sam --sort --output AB.sort.bam 11/14/17 23:28:07: Start pairing up sam-entries 11/14/17 23:28:07: Auto detecting sam or bam file by extension 11/14/17 23:28:07: Reading sam file AB_1.sam 11/14/17 23:28:07: Auto detecting sam or bam file by extension...