Entering edit mode
5.4 years ago
ALI Hkz
•
0
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)
