Error while calling TEs from pooled samples
Closed this issue · 4 comments
I was trying to apply RetroSeq call to a dataset consisting of two discover-out files and their corresponding BAM-files. The programs starts to run, but then the following errors appears and I get an empty VCF file.
I'd very much appreciate any workaround or fix to circumvent this problem.
Thanks,
Fritjof
retroseq.pl -call -bam samples.fofn -filter rmsk.bed.tab -ref ref.fa -input out_files.fofn -output rs_call
RetroSeq: A tool for discovery and genotyping of transposable elements from short read alignments
Version: 1.41
Author: Thomas Keane (thomas.keane@sanger.ac.uk)
Found 2 BAM files
Found sample: SAMPLE17_SAMPLE18
Calling sample SAMPLE17_SAMPLE18
Beginning paired-end calling...
Use of uninitialized value $currentType in concatenation (.) or string at /./home/flammers/programs/RetroSeq-1.41/bin/retroseq.pl line 768, <$tfh> line 1.
Use of uninitialized value $currentType in concatenation (.) or string at /./home/flammers/programs/RetroSeq-1.41/bin/retroseq.pl line 769, <$tfh> line 1.
Use of uninitialized value $currentType in string eq at /./home/flammers/programs/RetroSeq-1.41/bin/retroseq.pl line 765, <$tfh> line 2.
Use of uninitialized value $currentType in concatenation (.) or string at /./home/flammers/programs/RetroSeq-1.41/bin/retroseq.pl line 768, <$tfh> line 2.
Use of uninitialized value $currentType in concatenation (.) or string at /./home/flammers/programs/RetroSeq-1.41/bin/retroseq.pl line 769, <$tfh> line 2.
PE Call:
PE Call:
Creating VCF file of calls....
Hi Fritjof - could you post the first couple of lines from the out_files.fofn file? And if this is a fofn, could you post the first couple of lines from each of the fofns?
Thomas
Hi,
It's a fofn and each files looks like this:
out_files.fofn:
sample17_full.out
sample18_full.out
==> sample17_full.out <==
scaffold79 1618 1708 LTR FCC3FBRACXX:4:2205:20625:62168#ACCAGACT - - 90
scaffold79 5136 5226 LTR FCC3FBRACXX:4:1101:12484:88749#ACCAGACT + + 90
scaffold79 8308 8398 LTR FCC3FBRACXX:4:1302:3013:12429#ACCAGACT + + 90
scaffold79 36914 37004 LTR FCC3FBRACXX:4:2302:10297:100920#ACCAGACT - + 90
scaffold79 36918 37008 LTR FCC3FBRACXX:4:2213:10145:89557#ACCAGACT - + 90
scaffold79 37073 37163 LTR FCC3FBRACXX:4:1211:3229:30589#ACCAGACT + + 90
scaffold79 58155 58245 LTR FCC3FBRACXX:4:2311:17897:2633#ACCAGACT + + 90
scaffold79 58156 58246 LTR FCC3FBRACXX:4:2203:6575:14023#ACCAGACT + + 90
scaffold79 68043 68133 LTR FCC3FBRACXX:4:2309:2462:29601#ACCAGACT - + 90
scaffold79 74252 74342 LTR FCC3FBRACXX:4:1214:8663:36197#ACCAGACT - + 90
==> sample18_full.out <==
scaffold79 8611 8701 LTR FCC3FBRACXX:3:1314:19505:17838#CTATAACT - - 90
scaffold79 37076 37166 LTR FCC3FBRACXX:3:2308:19292:64771#CTATAACT + + 90
scaffold79 52824 52914 LTR FCC3FBRACXX:3:1206:4991:28683#CTATAACT + + 90
scaffold79 74233 74323 LTR FCC3FBRACXX:3:2212:5392:41065#CTATAACT - + 90
scaffold79 88831 88921 LTR FCC3FBRACXX:3:1314:9199:91200#CTATAACT + - 90
scaffold79 97459 97549 LTR FCC3FBRACXX:3:2205:3623:50966#CCTATAAC + + 90
scaffold79 102332 102422 LTR FCC3FBRACXX:3:1308:13328:36541#CTATAACT + + 90
scaffold79 102358 102448 LTR FCC3FBRACXX:3:1114:21020:56188#CTATAACT + + 90
scaffold79 136963 137053 LTR FCC3FBRACXX:3:2102:2100:43276#CTATAACT + - 90
scaffold79 136984 137074 LTR FCC3FBRACXX:3:1307:16783:73826#CTATAACT + - 90
Those files look fine. I can't see any obvious reason why this should be happening. I've just made a commit on the master to print out the offending line causing the error. Could you download the master zip and run the calling phase? It should die with an error and print the line causing the problem.
Hi Thomas, thanks! Now it is the following. Apparently the fofn is not recognized correctly and is parsed as if it was the outfile itself. I switched to using the file prefix and then it worked.
Version: 1.41
Author: Thomas Keane (thomas.keane@sanger.ac.uk)
Found 2 BAM files
Found sample: SAMPLE17_SAMPLE18
Calling sample SAMPLE17_SAMPLE18
Beginning paired-end calling...
Failed to detect the TE type to be called from line: sample17_full.out
Tue Jul 8 10:41:54 CEST 2014