[vinay052003]

Hi catbus,
Did you solve the "segmentation fault" problem with tophat_report?
I tried running the updated version by compiling tophat 2.0.4 as well as using the pre-built binaries... but still getting the same error.

[catbus]

2.0.4 solved it for me! I used the pre-built binaries and did not encounter this problem again.

[Enraico]

The 2.0.4 official release solved for me, too. They also fixed the launch bash script for Ubuntu.

[lindenb]

Tophat error when "Reporting output tracks"

(cross posted on biostar: http://www.biostars.org/p/58978/ )

I've compiled tophat-2.0.6 from the sources. It raises a segmentation fault for:

[lindenb@master tophat]$ /commun/data/packages/tophat/bin/tophat_reports --min-a
nchor 8 --splice-mismatches 0 --min-report-intron 50 --max-report-intron 500000 
--min-isoform-fraction 0.15 --output-dir JETER/ --max-multihits 20 --max-seg-mul
tihits 40 --segment-length 25 --segment-mismatches 2 --min-closure-exon 100 --mi
n-closure-intron 50 --max-closure-intron 5000 --min-coverage-intron 50 --max-cov
erage-intron 20000 --min-segment-intron 50 --max-segment-intron 500000 --read-mi
smatches 2 --read-gap-length 2 --read-edit-dist 2 --read-realign-edit-dist 3 --m
ax-insertion-length 3 --max-deletion-length 3 -z gzip --inner-dist-mean 50 --inn
er-dist-std-dev 20 --gtf-annotations Homo_sapiens.GRCh37.69.gtf --gtf-juncs JETE
R/tmp/Homo_sapiens.juncs --no-closure-search --no-coverage-search --no-microexon
-search --sam-header JETER/tmp/chr22_genome.bwt.samheader.sam --report-discordan
t-pair-alignments --report-mixed-alignments --samtools=/commun/data/packages/sam
tools-0.1.18/samtools --bowtie2-max-penalty 6 --bowtie2-min-penalty 2 --bowtie2-
penalty-for-N 1 --bowtie2-read-gap-open 5 --bowtie2-read-gap-cont 3 --bowtie2-re
f-gap-open 5 --bowtie2-ref-gap-cont 3 ./chr22.fa JETER/junctions.bed JETER/inser
tions.bed JETER/deletions.bed JETER/fusions.out JETER/tmp/accepted_hits JETER/tm
p/left_kept_reads.m2g.bam JETER/tmp/left_kept_reads.bam JETER/tmp/right_kept_rea
ds.m2g.bam JETER/tmp/right_kept_reads.bam

tophat_reports v2.0.6 (3670M)
---------------------------------------
[samopen] SAM header is present: 1 sequences.
	Loading 22...
done
	Loading ...done
Loaded 7655 GFF junctions from JETER/tmp/Homo_sapiens.juncs.
Loaded 8026 junctions
Segmentation fault (core dumped)

I'm learning tophat, I've just played with the following makefile:

include tools.mk
REF=./chr22
REF.bowtie=$(foreach S,1.bt2 2.bt2 3.bt2 4.bt2 rev.1.bt2 rev.2.bt2, $(addsuffix .$S,$(REF)) )
GTF=Homo_sapiens.GRCh37.69.gtf
export PATH:=$(PATH):${BOWTIE2.dir}:${samtools.dir}

JETER: s1_r1.fastq s1_r2.fastq ${REF.bowtie} $(REF).fa $(GTF)
	echo ${PATH}
	/commun/data/packages/tophat/bin/tophat2 -G $(GTF) -o $@ $(REF) s1_r1.fastq s1_r2.fastq
s1_r1.fastq:
	gunzip -c /commun/data/projects/20121206.RNASEQ/XX_1_7_1.fastq.gz | head -n 400000 > $@
s1_r2.fastq:
	gunzip -c /commun/data/projects/20121206.RNASEQ/XX_1_7_2.fastq.gz | head -n 400000 > $@
	
$(GTF):
	gunzip -c /commun/data/pubdb/ensembl/release-69/gtf/homo_sapiens/Homo_sapiens.GRCh37.69.gtf.gz| egrep '^22' > $@
	
$(REF).fa: 
	curl -o $(REF).fa.gz "http://hgdownload.cse.ucsc.edu/goldenPath/hg19/chromosomes/chr22.fa.gz"
	gunzip  -c $(REF).fa.gz | sed 's/^>chr/>/' > $@
	rm $(REF).fa.gz


${REF.bowtie}:$(REF).fa
	${BOWTIE2.dir}/bowtie2-build  -f -c $(REF) $(REF)
	${BOWTIE2.dir}/bowtie2-inspect -s $(REF)

how should I fix this problem ?

[lindenb]

error in From my previous mail: I've narrowed the error. The exception is raised from

I've narrowed the error.

The exception is raised from

 (int)length(*ref_str)

in

   src/tophat_reports.cpp

in the line

   if (new_left >= 0 && new_bh.right() <= (int)length(*ref_str))

it seems that ref_str is NULL when length is invoked

Pierre

[catbus]

Dang, history is repeating itself.

Once again, with Tophat 2.0.9 (downloaded from the site, not compiled locally), I am getting a termination with no explanation in the "tophat_reports" step.

Previously, I "solved" this problem by updating to Tophat 2.0.4. I don't know if this is a regression or if it's something weird about this data; it doesn't happen on every dataset.

[2013-08-07 09:29:12] Joining segment hits
[2013-08-07 09:33:53] Reporting output tracks
        [FAILED]
Error running /work/Apps/Bio/tophat/tophat-2.0.9/tophat_reports --min-anchor 8 --splice-mismatches 2 --min-report-intron 50 --max-report-intron 500000 --min-isoform-fraction 0.15 --output-dir Tophat_New_1_FASTA_FILES/Sample_CR3_D00/CR3_D0_ATCACG_L1_PAIR
ED/ --max-multihits 20 --max-seg-multihits 40 --segment-length 25 --segment-mismatches 2 --min-closure-exon 100 --min-closure-intron 50 --max-closure-intron 5000 --min-coverage-intron 50 --max-coverage-intron 20000 --min-segment-intron 50 --max-segment-
intron 500000 --read-mismatches 2 --read-gap-length 2 --read-edit-dist 2 --read-realign-edit-dist 3 --max-insertion-length 3 --max-deletion-length 3 -z gzip -p6 --inner-dist-mean 150 --inner-dist-std-dev 20 --gtf-annotations tophat_index_cr3/index.gff -
-gtf-juncs Tophat_New_1_FASTA_FILES/Sample_CR3_D00/CR3_D0_ATCACG_L1_PAIRED/tmp/index.juncs --no-closure-search --no-coverage-search --sam-header Tophat_New_1_FASTA_FILES/Sample_CR3_D00/CR3_D0_ATCACG_L1_PAIRED/tmp/hg19_genome.bwt.samheader.sam --samtools
=/work/Apps/bin/samtools --bowtie2-max-penalty 6 --bowtie2-min-penalty 2 --bowtie2-penalty-for-N 1 --bowtie2-read-gap-open 5 --bowtie2-read-gap-cont 3 --bowtie2-ref-gap-open 5 --bowtie2-ref-gap-cont 3 /work/Common/Data/Bowtie_Indexes/hg19.fa Tophat_New_
1_FASTA_FILES/Sample_CR3_D00/CR3_D0_ATCACG_L1_PAIRED/junctions.bed Tophat_New_1_FASTA_FILES/Sample_CR3_D00/CR3_D0_ATCACG_L1_PAIRED/insertions.bed Tophat_New_1_FASTA_FILES/Sample_CR3_D00/CR3_D0_ATCACG_L1_PAIRED/deletions.bed Tophat_New_1_FASTA_FILES/Samp
le_CR3_D00/CR3_D0_ATCACG_L1_PAIRED/fusions.out Tophat_New_1_FASTA_FILES/Sample_CR3_D00/CR3_D0_ATCACG_L1_PAIRED/tmp/accepted_hits Tophat_New_1_FASTA_FILES/Sample_CR3_D00/CR3_D0_ATCACG_L1_PAIRED/tmp/left_kept_reads.m2g.bam,Tophat_New_1_FASTA_FILES/Sample_
CR3_D00/CR3_D0_ATCACG_L1_PAIRED/tmp/left_kept_reads.m2g_um.mapped.bam,Tophat_New_1_FASTA_FILES/Sample_CR3_D00/CR3_D0_ATCACG_L1_PAIRED/tmp/left_kept_reads.m2g_um.candidates Tophat_New_1_FASTA_FILES/Sample_CR3_D00/CR3_D0_ATCACG_L1_PAIRED/tmp/left_kept_rea
ds.bam Tophat_New_1_FASTA_FILES/Sample_CR3_D00/CR3_D0_ATCACG_L1_PAIRED/tmp/right_kept_reads.m2g.bam,Tophat_New_1_FASTA_FILES/Sample_CR3_D00/CR3_D0_ATCACG_L1_PAIRED/tmp/right_kept_reads.m2g_um.mapped.bam,Tophat_New_1_FASTA_FILES/Sample_CR3_D00/CR3_D0_ATC
ACG_L1_PAIRED/tmp/right_kept_reads.m2g_um.candidates Tophat_New_1_FASTA_FILES/Sample_CR3_D00/CR3_D0_ATCACG_L1_PAIRED/tmp/right_kept_reads.bam
Loaded 314277 junctions

[catbus]

Solved: removing "--no-discordant" from my tophat parameters caused this to work. (I tried a TON of combinations of parameters, and the "tophat_reports" only gave an error when "--no-discordant" was present.)

Tested on Tophat 2.0.8b and Tophat 2.0.9.

[Claudia34]

Same issue with Tophat 2.0.9and Tophat 2.0.11

Hello,

I'm also experimenting this issue on some datasets using both Tophat 2.0.9 and 2.0.11 and I'm not using the '--no-discordant' option:

tophat -o my_out_dir --bowtie1 --no-coverage --fusion-multireads 1 --fusion-multipairs 1 --max-intron-length 100000 --fusion-min-dist 10000 --fusion-anchor-length 10  --no-convert-bam -p 12 bowtie1_index/my_index my_fastq_file.fastq

The report step fails stochastically for some datasets. Did someone find any patch?

Thank you very much