Question: no input BAM records found in ./tophat_out_SRR5481725/tmp/right_kept_reads.m2g_um.candidates15.bam (possibly due to wrong offset)
0
gravatar for ALI Hkz
9 days ago by
ALI Hkz0
Italy/Siena
ALI Hkz0 wrote:

Hi here is my commands and unfortunately i give this error massage in tophat2!

tophat2 -p 16 --keep-fasta-order -o ./tophat_out_${NAME}\
 --read-mismatches 4\
 --read-gap-length 4\
 --read-edit-dist 4\
 --read-realign-edit-dist 0\
 --min-anchor 4\
 --splice-mismatch 1\
 --GTF gencode.v19.annotation.gtf\
 --transcriptome-index=Transcriptome/gencode.v19.annotation\
 genome/Homo_sapiens\
 trimmed_cut1SRR5481725.fastq trimmed_cut2SRR5481725.fastq

and that's how i get the error massage:

[2018-12-05 11:37:07] Checking for Bowtie index files (transcriptome)..
[2018-12-05 11:37:07] Checking for Bowtie index files (genome)..
[2018-12-05 11:37:07] Checking for reference FASTA file
[2018-12-05 11:37:07] Generating SAM header for genome/Homo_sapiens
[2018-12-05 11:37:10] Reading known junctions from GTF file
[2018-12-05 11:37:28] Preparing reads
         left reads: min. length=12, max. length=250, 27070982 kept reads (7468 discarded)
        right reads: min. length=12, max. length=250, 27072313 kept reads (6137 discarded)
Warning: short reads (<20bp) will make TopHat quite slow and take large amount of memory because they are likely to be mapped in too many places
[2018-12-05 11:57:01] Using pre-built transcriptome data..
[2018-12-05 11:57:20] Mapping left_kept_reads to transcriptome gencode.v19.annotation with Bowtie2
[2018-12-05 14:57:31] Mapping right_kept_reads to transcriptome gencode.v19.annotation with Bowtie2
[2018-12-05 17:31:16] Resuming TopHat pipeline with unmapped reads
[2018-12-05 17:31:16] Mapping left_kept_reads.m2g_um to genome Homo_sapiens with Bowtie2
[2018-12-05 19:17:48] Mapping left_kept_reads.m2g_um_seg1 to genome Homo_sapiens with Bowtie2 (1/10)
[2018-12-05 19:41:45] Mapping left_kept_reads.m2g_um_seg2 to genome Homo_sapiens with Bowtie2 (2/10)
[2018-12-05 20:08:09] Mapping left_kept_reads.m2g_um_seg3 to genome Homo_sapiens with Bowtie2 (3/10)
[2018-12-05 20:30:57] Mapping left_kept_reads.m2g_um_seg4 to genome Homo_sapiens with Bowtie2 (4/10)
[2018-12-05 20:53:39] Mapping left_kept_reads.m2g_um_seg5 to genome Homo_sapiens with Bowtie2 (5/10)
[2018-12-05 21:11:48] Mapping left_kept_reads.m2g_um_seg6 to genome Homo_sapiens with Bowtie2 (6/10)
[2018-12-05 21:28:17] Mapping left_kept_reads.m2g_um_seg7 to genome Homo_sapiens with Bowtie2 (7/10)
[2018-12-05 21:48:55] Mapping left_kept_reads.m2g_um_seg8 to genome Homo_sapiens with Bowtie2 (8/10)
[2018-12-05 22:09:47] Mapping left_kept_reads.m2g_um_seg9 to genome Homo_sapiens with Bowtie2 (9/10)
[2018-12-05 22:27:52] Mapping left_kept_reads.m2g_um_seg10 to genome Homo_sapiens with Bowtie2 (10/10)
[2018-12-05 22:46:23] Mapping right_kept_reads.m2g_um to genome Homo_sapiens with Bowtie2
[2018-12-06 00:37:07] Mapping right_kept_reads.m2g_um_seg1 to genome Homo_sapiens with Bowtie2 (1/10)
[2018-12-06 01:00:12] Mapping right_kept_reads.m2g_um_seg2 to genome Homo_sapiens with Bowtie2 (2/10)
[2018-12-06 01:25:59] Mapping right_kept_reads.m2g_um_seg3 to genome Homo_sapiens with Bowtie2 (3/10)
[2018-12-06 01:48:27] Mapping right_kept_reads.m2g_um_seg4 to genome Homo_sapiens with Bowtie2 (4/10)
[2018-12-06 02:11:40] Mapping right_kept_reads.m2g_um_seg5 to genome Homo_sapiens with Bowtie2 (5/10)
[2018-12-06 02:30:15] Mapping right_kept_reads.m2g_um_seg6 to genome Homo_sapiens with Bowtie2 (6/10)
[2018-12-06 02:48:53] Mapping right_kept_reads.m2g_um_seg7 to genome Homo_sapiens with Bowtie2 (7/10)
[2018-12-06 03:12:21] Mapping right_kept_reads.m2g_um_seg8 to genome Homo_sapiens with Bowtie2 (8/10)
[2018-12-06 03:35:56] Mapping right_kept_reads.m2g_um_seg9 to genome Homo_sapiens with Bowtie2 (9/10)
[2018-12-06 03:54:49] Mapping right_kept_reads.m2g_um_seg10 to genome Homo_sapiens with Bowtie2 (10/10)
[2018-12-06 04:12:52] Searching for junctions via segment mapping
[2018-12-06 04:26:24] Retrieving sequences for splices
[2018-12-06 04:27:42] Indexing splices
Building a SMALL index
[2018-12-06 04:28:05] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/10)
[2018-12-06 04:30:51] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/10)
[2018-12-06 04:33:46] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/10)
[2018-12-06 04:35:51] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/10)
[2018-12-06 04:37:37] Mapping left_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/10)
[2018-12-06 04:39:14] Mapping left_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/10)
[2018-12-06 04:40:38] Mapping left_kept_reads.m2g_um_seg7 to genome segment_juncs with Bowtie2 (7/10)
[2018-12-06 04:42:13] Mapping left_kept_reads.m2g_um_seg8 to genome segment_juncs with Bowtie2 (8/10)
[2018-12-06 03:35:56] Mapping right_kept_reads.m2g_um_seg9 to genome Homo_sapiens with Bowtie2 (9/10)
[2018-12-06 03:54:49] Mapping right_kept_reads.m2g_um_seg10 to genome Homo_sapiens with Bowtie2 (10/10)
[2018-12-06 04:12:52] Searching for junctions via segment mapping
[2018-12-06 04:26:24] Retrieving sequences for splices
[2018-12-06 04:27:42] Indexing splices
Building a SMALL index
[2018-12-06 04:28:05] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/10)
[2018-12-06 04:30:51] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/10)
[2018-12-06 04:33:46] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/10)
[2018-12-06 04:35:51] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/10)
[2018-12-06 04:37:37] Mapping left_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/10)
[2018-12-06 04:39:14] Mapping left_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/10)
[2018-12-06 04:40:38] Mapping left_kept_reads.m2g_um_seg7 to genome segment_juncs with Bowtie2 (7/10)
[2018-12-06 04:42:13] Mapping left_kept_reads.m2g_um_seg8 to genome segment_juncs with Bowtie2 (8/10)
[2018-12-06 04:43:56] Mapping left_kept_reads.m2g_um_seg9 to genome segment_juncs with Bowtie2 (9/10)
[2018-12-06 04:45:36] Mapping left_kept_reads.m2g_um_seg10 to genome segment_juncs with Bowtie2 (10/10)
[2018-12-06 04:47:11] Joining segment hits
[2018-12-06 04:57:09] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/10)
[2018-12-06 05:00:08] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/10)
[2018-12-06 05:03:05] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/10)
[2018-12-06 05:05:12] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/10)
[2018-12-06 05:07:05] Mapping right_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/10)
[2018-12-06 05:08:48] Mapping right_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/10)
[2018-12-06 05:10:25] Mapping right_kept_reads.m2g_um_seg7 to genome segment_juncs with Bowtie2 (7/10)
[2018-12-06 05:12:15] Mapping right_kept_reads.m2g_um_seg8 to genome segment_juncs with Bowtie2 (8/10)
[2018-12-06 05:14:11] Mapping right_kept_reads.m2g_um_seg9 to genome segment_juncs with Bowtie2 (9/10)
[2018-12-06 05:15:53] Mapping right_kept_reads.m2g_um_seg10 to genome segment_juncs with Bowtie2 (10/10)
[2018-12-06 05:17:26] Joining segment hits
[2018-12-06 05:27:18] Reporting output tracks
        [FAILED]
Error running /usr/bin/tophat_reports --min-anchor 8 --splice-mismatches 1 --min-report-intron 50 --max-report-intron 500000 --min-isoform-fraction 0.15 --output-dir ./tophat_out_SRR5481725/ --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 4 --read-gap-length 4 --read-edit-dist 4 --read-realign-edit-dist 0 --max-insertion-length 3 --max-deletion-length 3 -z gzip -p16 --inner-dist-mean 50 --inner-dist-std-dev 20 --gtf-annotations Transcriptome/gencode.v19.annotation.gff --gtf-juncs ./tophat_out_SRR5481725/tmp/gencode.juncs --no-closure-search --no-coverage-search --no-microexon-search --sam-header ./tophat_out_SRR5481725/tmp/Homo_sapiens_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 genome/Homo_sapiens.fa ./tophat_out_SRR5481725/junctions.bed ./tophat_out_SRR5481725/insertions.bed ./tophat_out_SRR5481725/deletions.bed ./tophat_out_SRR5481725/fusions.out ./tophat_out_SRR5481725/tmp/accepted_hits ./tophat_out_SRR5481725/tmp/left_kept_reads.m2g.bam,./tophat_out_SRR5481725/tmp/left_kept_reads.m2g_um.mapped.bam,./tophat_out_SRR5481725/tmp/left_kept_reads.m2g_um.candidates ./tophat_out_SRR5481725/tmp/left_kept_reads.bam ./tophat_out_SRR5481725/tmp/right_kept_reads.m2g.bam,./tophat_out_SRR5481725/tmp/right_kept_reads.m2g_um.mapped.bam,./tophat_out_SRR5481725/tmp/right_kept_reads.m2g_um.candidates ./tophat_out_SRR5481725/tmp/right_kept_reads.bam
Warning: no input BAM records found in ./tophat_out_SRR5481725/tmp/right_kept_reads.m2g_um.candidates15.bam (possibly due to wrong offset)
rna-seq software error • 79 views
ADD COMMENTlink modified 9 days ago by Pierre Lindenbaum115k • written 9 days ago by ALI Hkz0
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 690 users visited in the last hour