The Tophta2 ERR, [ERRno 2]

Question

[ynau_kanghuadu]

Now, I sued the Tophat2 (V2.1.1) work, my software can run normally, but cant get *.hit.bam. and I've run the software many time and it's the result.

The nohup.out:

[2020-02-17 19:49:02] Beginning TopHat run (v2.1.1)
-----------------------------------------------
[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 with Bowtie2 (1/6)
[2020-02-17 21:47:41] Mapping left_kept_reads.m2g_um_seg2 to genome S_lycopersicum_chromosomes.4.00 with Bowtie2 (2/6)
[2020-02-17 21:50:02] Mapping left_kept_reads.m2g_um_seg3 to genome S_lycopersicum_chromosomes.4.00 with Bowtie2 (3/6)
[2020-02-17 21:52:21] Mapping left_kept_reads.m2g_um_seg4 to genome S_lycopersicum_chromosomes.4.00 with Bowtie2 (4/6)
[2020-02-17 21:54:39] Mapping left_kept_reads.m2g_um_seg5 to genome S_lycopersicum_chromosomes.4.00 with Bowtie2 (5/6)
[2020-02-17 21:57:00] Mapping left_kept_reads.m2g_um_seg6 to genome S_lycopersicum_chromosomes.4.00 with Bowtie2 (6/6)
[2020-02-17 21:59:15] Mapping right_kept_reads.m2g_um to genome S_lycopersicum_chromosomes.4.00 with Bowtie2 
[2020-02-17 22:12:49] Mapping right_kept_reads.m2g_um_seg1 to genome S_lycopersicum_chromosomes.4.00 with Bowtie2 (1/6)
[2020-02-17 22:16:04] Mapping right_kept_reads.m2g_um_seg2 to genome S_lycopersicum_chromosomes.4.00 with Bowtie2 (2/6)
[2020-02-17 22:19:18] Mapping right_kept_reads.m2g_um_seg3 to genome S_lycopersicum_chromosomes.4.00 with Bowtie2 (3/6)
[2020-02-17 22:22:14] Mapping right_kept_reads.m2g_um_seg4 to genome S_lycopersicum_chromosomes.4.00 with Bowtie2 (4/6)
[2020-02-17 22:25:07] Mapping right_kept_reads.m2g_um_seg5 to genome S_lycopersicum_chromosomes.4.00 with Bowtie2 (5/6)
[2020-02-17 22:28:04] Mapping right_kept_reads.m2g_um_seg6 to genome S_lycopersicum_chromosomes.4.00 with Bowtie2 (6/6)
[2020-02-17 22:30:55] Searching for junctions via segment mapping
[2020-02-17 22:38:51] Retrieving sequences for splices
[2020-02-17 22:39:12] Indexing splices
Building a SMALL index
[2020-02-17 22:39:27] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2020-02-17 22:40:24] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2020-02-17 22:41:13] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2020-02-17 22:42:02] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2020-02-17 22:42:51] Mapping left_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2020-02-17 22:43:40] Mapping left_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2020-02-17 22:44:27] Joining segment hits
[2020-02-17 22:46:22] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2020-02-17 22:48:13] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2020-02-17 22:49:31] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2020-02-17 22:50:40] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2020-02-17 22:51:44] Mapping right_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2020-02-17 22:52:46] Mapping right_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2020-02-17 22:53:45] Joining segment hits
[2020-02-17 22:55:59] Reporting output tracks
        [FAILED]
Error: [Errno 2] No such file or directory: 'SRR6929571/tmp/accepted_hits2_sorted.bam'
Found 160151 junctions from happy spliced reads

An the run.log: (Last few lines)

/root/Software/biosoft/tophat-2.1.1.Linux_x86_64/samtools_0.1.18 sort SRR6929571/tmp/accepted_hits0.bam SRR6929571/tmp/accepted_hits0_sorted
/root/Software/biosoft/tophat-2.1.1.Linux_x86_64/samtools_0.1.18 sort SRR6929571/tmp/accepted_hits1.bam SRR6929571/tmp/accepted_hits1_sorted
/root/Software/biosoft/tophat-2.1.1.Linux_x86_64/samtools_0.1.18 sort SRR6929571/tmp/accepted_hits2.bam SRR6929571/tmp/accepted_hits2_sorted
/root/Software/biosoft/tophat-2.1.1.Linux_x86_64/samtools_0.1.18 sort SRR6929571/tmp/accepted_hits3.bam SRR6929571/tmp/accepted_hits3_sorted
/root/Software/biosoft/tophat-2.1.1.Linux_x86_64/samtools_0.1.18 merge -f -h SRR6929571/tmp/S_lycopersicum_chromosomes.4.00_genome.bwt.samheader.sam SRR6929571/accepted_hits.bam SRR6929571/tmp/accepted_hits0_sorted.bam SRR6929571/tmp/accepted_hits1_sorted.bam SRR6929571/tmp/accepted_hits2_sorted.bam SRR6929571/tmp/accepted_hits3_sorted.bam

So, if you see this err, please help me!

Thank you.

[ynau_kanghuadu]

This is my frist time using the forum, So the above table description format is messy. Here , my tophat.log err is : ``` Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)

Mapping left_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)

Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)

Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (6/6) ```

The above runs are fine

This err is :

Reporting output tracks [FAILED]

Error: [Errno 2] No such file or directory: 'SRR6929571/tmp/accepted_hits2_sorted.bam

Found 160151 junctions from happy spliced reads

[Asaf]

This post requires some formatting. Please don't use the answer to add more data, you can add a comment or edit your post. As for your question, the names of the files you gave bowtie2 to write the output to contain weird directories that don't exist, please check your command.

[AsoInfo]

Please have a look at the following question:

Tophat Error : Oserror: [Errno 2] No Such File Or Directory

Try using the option --keep-tmp.