Now, I sued the Tophat2 (V2.1.1) work, my software can run normally, but cant get *.hit.bam. and I've run zhe doftware many time and it's the result.
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The nohup.out :
[2020-02-17 19:49:02] Beginning TopHat run (v2.1.1)
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[2020-02-17 19:49:02] Checking for Bowtie
Bowtie version: 2.3.5.0
[2020-02-17 19:49:02] Checking for Bowtie index files (genome)..
[2020-02-17 19:49:02] Checking for reference FASTA file
[2020-02-17 19:49:02] Generating SAM header for ../../Tomato_SL4.0/S_lycopersicum_chromosomes.4.00
[2020-02-17 19:49:10] Reading known junctions from GTF file
[2020-02-17 19:49:12] Preparing reads
left reads: min. length=150, max. length=150, 25661961 kept reads (66 discarded)
right reads: min. length=150, max. length=150, 25661122 kept reads (905 discarded)
[2020-02-17 20:09:24] Building transcriptome data files SRR6929571/tmp/ITAG4.1_gene_models
[2020-02-17 20:09:33] Building Bowtie index from ITAG4.1_gene_models.fa
[2020-02-17 20:10:20] Mapping left_kept_reads to transcriptome ITAG4.1_gene_models with Bowtie2
[2020-02-17 20:52:52] Mapping right_kept_reads to transcriptome ITAG4.1_gene_models with Bowtie2
[2020-02-17 21:33:57] Resuming TopHat pipeline with unmapped reads
[2020-02-17 21:33:57] Mapping left_kept_reads.m2g_um to genome S_lycopersicum_chromosomes.4.00 with Bowtie2
[2020-02-17 21:45:21] Mapping left_kept_reads.m2g_um_seg1 to genome S_lycopersicum_chromosomes.4.00 wi ...



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