Question: TopHat Fata Error: Fusion search fails with Bowtie2, how to try Bowtie1 option? Also truncates file during genome alignment
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marissasp • 0 wrote:
I am trying to run TopHat using a GTF annotation to build a transcriptome index, and also search for fusions. The data becomes truncated during the second alignment step, to the reference genome. I also receive a warning to try Bowtie 1 not Bowtie 2 when looking for fusions, but am not sure how to do this within TopHat. The error message is:
Fatal error: Tool execution failed Warning: --fusion-search with Bowtie2 may not work well as it may require much memory space and produce many spurious fusions. Please try --bowtie1 option if this doesn't work. [2016-02-15 12:47:05] Beginning TopHat run (v2.0.14) ----------------------------------------------- [2016-02-15 12:47:05] Checking for Bowtie Bowtie version: 2.2.5.0 [2016-02-15 12:47:05] Checking for Bowtie index files (genome).. [2016-02-15 12:47:05] Checking for reference FASTA file [2016-02-15 12:47:05] Generating SAM header for /galaxy/data/hg19/hg19full/bowtie2_index/hg19full [2016-02-15 12:47:07] Reading known junctions from GTF file [2016-02-15 12:47:53] Preparing reads left reads: min. length=100, max. length=100, 93564119 kept reads (18701 discarded) right reads: min. length=100, max. length=100, 93392573 kept reads (190247 discarded) [2016-02-15 14:01:14] Building transcriptome data files ./tophat_out/tmp/dataset_14372302 [2016-02-15 14:03:11] Building Bowtie index from dataset_14372302.fa [2016-02-15 16:08:31] Mapping left_kept_reads to transcriptome dataset_14372302 with Bowtie2 [2016-02-16 01:15:00] Mapping right_kept_reads to transcriptome dataset_14372302 with Bowtie2 [2016-02-16 10:14:43] Resuming TopHat pipeline with unmapped reads [2016-02-16 10:14:43] Mapping left_kept_reads.m2g_um to genome hg19full with Bowtie2 [main_samview] truncated file. [main_samview] truncated file. [main_samview] truncated file. [2016-02-16 12:24:42] Mapping left_kept_reads.m2g_um_seg1 to genome hg19full with Bowtie2 (1/4) [2016-02-16 12:34:48] Mapping left_kept_reads.m2g_um_seg2 to genome hg19full with Bowtie2 (2/4) [2016-02-16 12:48:29] Mapping left_kept_reads.m2g_um_seg3 to genome hg19full with Bowtie2 (3/4) [2016-02-16 13:02:08] Mapping left_kept_reads.m2g_um_seg4 to genome hg19full with Bowtie2 (4/4) [2016-02-16 13:16:45] Mapping right_kept_reads.m2g_um to genome hg19full with Bowtie2 [main_samview] truncated file. [bam_header_read] EOF marker is absent. The input is probably truncated. [bam_header_read] invalid BAM binary header (this is not a BAM file). [main_samview] fail to read the header from "./tophat_out/tmp/right_kept_reads.m2g_um_unmapped.bam". [2016-02-16 16:25:57] Searching for junctions via segment mapping [FAILED] Error: segment-based junction search failed with err =1 *** glibc detected *** /galaxy-repl/main/deps/tophat/2.0.14/iuc/package_tophat_2_0_14/536f7bb5616d/bin/segment_juncs: double free or corruption (fasttop): 0x0000000002209010 *** Any help is greatly appreciated, thank you very much!!!!
