Fail to generate sam headers with bowtie1 >= v1.2

[ronin-gw]

I tried to run tophat v2.1.1 with bowtie v1.2.2.0 and got error messages like this.

[2018-01-20 20:30:21] Beginning TopHat run (v2.1.1)
-----------------------------------------------
[2018-01-20 20:30:21] Checking for Bowtie
		  Bowtie version:	 1.2.2.0
[2018-01-20 20:30:22] Checking for Bowtie index files (transcriptome)..
[2018-01-20 20:30:22] Checking for Bowtie index files (genome)..
[2018-01-20 20:30:22] Checking for reference FASTA file
[2018-01-20 20:30:22] Generating SAM header for local/database/bwindex/hg19
[2018-01-20 20:30:24] Reading known junctions from GTF file
[2018-01-20 20:30:45] Preparing reads
	 left reads: min. length=20, max. length=76, 3640357 kept reads (1119 discarded)
	right reads: min. length=20, max. length=76, 3640863 kept reads (613 discarded)
[2018-01-20 20:33:30] Using pre-built transcriptome data..
[2018-01-20 20:33:34] Mapping left_kept_reads to transcriptome gencode.v19.annotation with Bowtie
[2018-01-20 20:36:16] Mapping right_kept_reads to transcriptome gencode.v19.annotation with Bowtie
[2018-01-20 20:38:53] Resuming TopHat pipeline with unmapped reads
[2018-01-20 20:38:53] Mapping left_kept_reads.m2g_um to genome hg19 with Bowtie
	[FAILED]
Error running bowtie:
Error while flushing and closing output
terminate called after throwing an instance of 'int'

The problem seems that tophat fails to generate *_genome.bwt.samheader.sam with bowtie1 because bowtie1 >= v1.2 cannot generate sam headers with the empty input.

Here is some examples of bowtie1 output with /dev/null input.

• bowtie v1.1.2

$ /usr/local/pkg/bowtie/bowtie-1.1.2/bowtie --sam hg19 /dev/null
Warning: Could not find any reads in "/dev/null"
@HD	VN:1.0	SO:unsorted
@SQ	SN:chr1	LN:249250621
@SQ	SN:chr2	LN:243199373
@SQ	SN:chr3	LN:198022430
@SQ	SN:chr4	LN:191154276
@SQ	SN:chr5	LN:180915260
@SQ	SN:chr6	LN:171115067
@SQ	SN:chr7	LN:159138663
@SQ	SN:chr8	LN:146364022
@SQ	SN:chr9	LN:141213431
@SQ	SN:chr10	LN:135534747
@SQ	SN:chr11	LN:135006516
@SQ	SN:chr12	LN:133851895
@SQ	SN:chr13	LN:115169878
@SQ	SN:chr14	LN:107349540
@SQ	SN:chr15	LN:102531392
@SQ	SN:chr16	LN:90354753
@SQ	SN:chr17	LN:81195210
@SQ	SN:chr18	LN:78077248
@SQ	SN:chr19	LN:59128983
@SQ	SN:chr20	LN:63025520
@SQ	SN:chr21	LN:48129895
@SQ	SN:chr22	LN:51304566
@SQ	SN:chrX	LN:155270560
@SQ	SN:chrY	LN:59373566
@SQ	SN:chrM	LN:16569
@SQ	SN:GL000207.1	LN:4262
@SQ	SN:GL000226.1	LN:15008
@SQ	SN:GL000229.1	LN:19913
@SQ	SN:GL000231.1	LN:27386
@SQ	SN:GL000210.1	LN:27682
@SQ	SN:GL000239.1	LN:33824
@SQ	SN:GL000235.1	LN:34474
@SQ	SN:GL000201.1	LN:36148
@SQ	SN:GL000247.1	LN:36422
@SQ	SN:GL000245.1	LN:36651
@SQ	SN:GL000197.1	LN:37175
@SQ	SN:GL000203.1	LN:37498
@SQ	SN:GL000246.1	LN:38154
@SQ	SN:GL000249.1	LN:38502
@SQ	SN:GL000196.1	LN:38914
@SQ	SN:GL000248.1	LN:39786
@SQ	SN:GL000244.1	LN:39929
@SQ	SN:GL000238.1	LN:39939
@SQ	SN:GL000202.1	LN:40103
@SQ	SN:GL000234.1	LN:40531
@SQ	SN:GL000232.1	LN:40652
@SQ	SN:GL000206.1	LN:41001
@SQ	SN:GL000240.1	LN:41933
@SQ	SN:GL000236.1	LN:41934
@SQ	SN:GL000241.1	LN:42152
@SQ	SN:GL000243.1	LN:43341
@SQ	SN:GL000242.1	LN:43523
@SQ	SN:GL000230.1	LN:43691
@SQ	SN:GL000237.1	LN:45867
@SQ	SN:GL000233.1	LN:45941
@SQ	SN:GL000204.1	LN:81310
@SQ	SN:GL000198.1	LN:90085
@SQ	SN:GL000208.1	LN:92689
@SQ	SN:GL000191.1	LN:106433
@SQ	SN:GL000227.1	LN:128374
@SQ	SN:GL000228.1	LN:129120
@SQ	SN:GL000214.1	LN:137718
@SQ	SN:GL000221.1	LN:155397
@SQ	SN:GL000209.1	LN:159169
@SQ	SN:GL000218.1	LN:161147
@SQ	SN:GL000220.1	LN:161802
@SQ	SN:GL000213.1	LN:164239
@SQ	SN:GL000211.1	LN:166566
@SQ	SN:GL000199.1	LN:169874
@SQ	SN:GL000217.1	LN:172149
@SQ	SN:GL000216.1	LN:172294
@SQ	SN:GL000215.1	LN:172545
@SQ	SN:GL000205.1	LN:174588
@SQ	SN:GL000219.1	LN:179198
@SQ	SN:GL000224.1	LN:179693
@SQ	SN:GL000223.1	LN:180455
@SQ	SN:GL000195.1	LN:182896
@SQ	SN:GL000212.1	LN:186858
@SQ	SN:GL000222.1	LN:186861
@SQ	SN:GL000200.1	LN:187035
@SQ	SN:GL000193.1	LN:189789
@SQ	SN:GL000194.1	LN:191469
@SQ	SN:GL000225.1	LN:211173
@SQ	SN:GL000192.1	LN:547496
@PG	ID:Bowtie	VN:1.1.2	CL:"bowtie --wrapper basic-0 --sam hg19 /dev/null"
# reads processed: 0
# reads with at least one reported alignment: 0 (0.00%)
# reads that failed to align: 0 (0.00%)
No alignments

• bowtie v1.2.2

$ /usr/local/pkg/bowtie/bowtie-1.2.2/bowtie --sam hg19 /dev/null
Error: reads file does not look like a FASTQ file
Command: /usr/local/pkg/bowtie/bowtie-1.2.2/bowtie-align-s --wrapper basic-0 --sam /usr/local/database/bwindex/human_g1k_v37_hrename/hg19 /dev/null

[archu87]

Hi,

I am getting similar error in tophat v2.1.0

[2018-07-23 10:30:10] Beginning TopHat run (v2.1.0)

[2018-07-23 10:30:10] Checking for Bowtie
Bowtie version: 1.1.2.0
[2018-07-23 10:30:11] Checking for Bowtie index files (genome)..
[2018-07-23 10:30:11] Checking for reference FASTA file
Warning: Could not find FASTA file ../bow_tie_build_hg19/hg19.fa
[2018-07-23 10:30:11] Reconstituting reference FASTA file from Bowtie index
Executing: /usr/bin/bowtie-inspect ../bow_tie_build_hg19/hg19 > final_tophat_fusion/tmp/hg19.fa
[2018-07-23 10:32:36] Generating SAM header for ../bow_tie_build_hg19/hg19
[2018-07-23 10:32:56] Preparing reads
left reads: min. length=48, max. length=48, 57435146 kept reads (2628 discarded)
right reads: min. length=48, max. length=48, 57431378 kept reads (6396 discarded)
[2018-07-23 10:49:38] Mapping left_kept_reads to genome hg19 with Bowtie
[2018-07-23 11:44:57] Mapping left_kept_reads_seg1 to genome hg19 with Bowtie (1/2)
[2018-07-23 12:03:16] Mapping left_kept_reads_seg2 to genome hg19 with Bowtie (2/2)
[2018-07-23 12:29:38] Mapping right_kept_reads to genome hg19 with Bowtie
[2018-07-23 13:41:25] Mapping right_kept_reads_seg1 to genome hg19 with Bowtie (1/2)
[2018-07-23 14:14:02] Mapping right_kept_reads_seg2 to genome hg19 with Bowtie (2/2)
[2018-07-23 15:02:24] Searching for junctions via segment mapping
[2018-07-23 15:22:31] Retrieving sequences for splices
[2018-07-23 15:24:50] Indexing splices
[2018-07-23 15:26:29] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie (1/2)
[2018-07-23 15:44:07] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie (2/2)
[2018-07-23 16:03:37] Joining segment hits
[2018-07-23 16:12:25] Mapping right_kept_reads_seg1 to genome segment_juncs with Bowtie (1/2)
[2018-07-23 16:30:37] Mapping right_kept_reads_seg2 to genome segment_juncs with Bowtie (2/2)
[2018-07-23 16:40:57] Joining segment hits
[2018-07-23 16:50:07] Reporting output tracks
[FAILED]
Error running /usr/bin/tophat_reports --min-anchor 8 --splice-mismatches 0 --min-report-intron 50 --max-report-intron 500000 --min-isoform-fraction 0.15 --output-dir final_tophat_fusion/ --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 --bowtie1 --fusion-search --fusion-anchor-length 20 --fusion-min-dist 10000000 --fusion-read-mismatches 2 --fusion-multireads 2 --fusion-multipairs 2 -z gzip -p4 --inner-dist-mean 50 --inner-dist-std-dev 20 --no-closure-search --no-coverage-search --no-microexon-search --library-type fr-unstranded --sam-header final_tophat_fusion/tmp/hg19_genome.bwt.samheader.sam --report-discordant-pair-alignments --report-mixed-alignments --samtools=/usr/bin/samtools_0.1.18 --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 final_tophat_fusion/tmp/hg19.fa final_tophat_fusion/junctions.bed final_tophat_fusion/insertions.bed final_tophat_fusion/deletions.bed final_tophat_fusion/fusions.out final_tophat_fusion/tmp/accepted_hits final_tophat_fusion/tmp/left_kept_reads.mapped.bam,final_tophat_fusion/tmp/left_kept_reads.candidates final_tophat_fusion/tmp/left_kept_reads.bam final_tophat_fusion/tmp/right_kept_reads.mapped.bam,final_tophat_fusion/tmp/right_kept_reads.candidates final_tophat_fusion/tmp/right_kept_reads.bam
what(): basic_string::substr: __pos (which is 40) > this->size() (which is 0)

Any help or suggestion is much appreciated.

[supriyank23]

tophat2 -o /home/supriya/CIRCexplorer2/circ2/tophat_fusion \ -p 15 \ --fusion-search
--keep-fasta-order
--bowtie1
--no-coverage-search
/home/supriya/CIRCexplorer2/circ2/bowtie1_index
/home/supriya/CIRCexplorer2/circ2/CIRCexplorer2_align_output/tophat/unmapped.fastq

[2024-08-20 10:36:39] Beginning TopHat run (v2.1.1)

[2024-08-20 10:36:39] Checking for Bowtie
Bowtie version: 1.3.1.0
[2024-08-20 10:36:39] Checking for Bowtie index files (genome)..
[2024-08-20 10:36:39] Checking for reference FASTA file
[2024-08-20 10:36:39] Generating SAM header for /home/supriya/CIRCexplorer2/circ2/bowtie1_index
[2024-08-20 10:36:41] Preparing reads
left reads: min. length=35, max. length=76, 1975414 kept reads (170848 discarded)
[2024-08-20 10:36:50] Mapping left_kept_reads to genome bowtie1_index with Bowtie
[FAILED]
Error running:
/home/supriya/tophat-2.1.1.Linux_x86_64/bam2fastx --all /home/supriya/CIRCexplorer2/circ2/tophat_fusion/tmp/left_kept_reads.bam|/usr/bin/bowtie -v 2 -k 20 -m 20 -S -p 15 --sam-nohead --max /dev/null /home/supriya/CIRCexplorer2/circ2/bowtie1_index -|/home/supriya/tophat-2.1.1.Linux_x86_64/fix_map_ordering --read-mismatches 2 --read-gap-length 2 --read-edit-dist 2 --read-realign-edit-dist 3 --index-outfile /home/supriya/CIRCexplorer2/circ2/tophat_fusion/tmp/left_kept_reads.mapped.bam.index --bowtie1 --sam-header /home/supriya/CIRCexplorer2/circ2/tophat_fusion/tmp/bowtie1_index_genome.bwt.samheader.sam - /home/supriya/CIRCexplorer2/circ2/tophat_fusion/tmp/left_kept_reads.mapped.bam /home/supriya/CIRCexplorer2/circ2/tophat_fusion/tmp/left_kept_reads_unmapped.bam

how to solve this problem