Deleted:Tophat2 Error: Splice sequence indexing failed with err =127
0
0
Entering edit mode
11 weeks ago

Hi everyone,

I've been trying to map my RNA-seq results onto an entire genome, and I've encountered a problem with splices.

The script.pbs I submitted to cluster servers is:

#PBS  -N  tophat_cufflinks_1
#PBS -o  tophat_cufflinks_1_out.txt
#PBS -e  tophat_cufflinks_1_error_out.txt
#PBS  -l  nodes=cu01:ppn=24
export PATH=software/tophat2/tophat-2.1.1.Linux_x86_64/:$PATH
export PATH=software/cufflinks/cufflinks-2.2.1.Linux_x86_64/:$PATH
export PATH=software/bowtie2/bowtie2-2.4.4-linux-x86_64/:$PATH

INDEX_DATABASE="/03_mask_repeat_sequences/genome_contig_hifiasm_hic_masked"
INPUT_OUTPUT_DIR="/04_gene_prediction/02_transcriptome_alignment/"
FINAL_GFF_DIR="/04_gene_prediction/02_transcriptome_alignment/Final_results_gff3/"

# 1_1

tophat -p 24 -o "${INPUT_OUTPUT_DIR}CK1_1"  ${INDEX_DATABASE}  "${INPUT_OUTPUT_DIR}reads1/CK1_1_1.fq.gz"  "${INPUT_OUTPUT_DIR}reads2/CK1_1_2.fq.gz"

cufflinks -p 24 -o "${INPUT_OUTPUT_DIR}CK1_1/cufflinks_results"   "${INPUT_OUTPUT_DIR}CK1_1/accepted_hits.bam"

gffread  "${INPUT_OUTPUT_DIR}CK1_1/cufflinks_results/transcript.gtf"  -o-  >  "${FINAL_GFF_DIR}CK1_1_final_results.gff3"

The following is the tophat.log

[2021-11-06 16:24:56] Beginning TopHat run (v2.1.1)
-----------------------------------------------
[2021-11-06 16:24:56] Checking for Bowtie
          Bowtie version:    2.4.4.0
[2021-11-06 16:24:56] Checking for Bowtie index files (genome)..
[2021-11-06 16:24:56] Checking for reference FASTA file
[2021-11-06 16:24:56] Generating SAM header for /home/20092008/data/cuan_xiong_genome/03_mask_repeat_sequences/Repbase2018_mask_data/cuan_xiong_genome_contig_hifiasm_hic_masked
[2021-11-06 16:25:01] Preparing reads
     left reads: min. length=150, max. length=150, 21563922 kept reads (516 discarded)
    right reads: min. length=150, max. length=150, 21545797 kept reads (18641 discarded)
[2021-11-06 16:38:03] Mapping left_kept_reads to genome cuan_xiong_genome_contig_hifiasm_hic_masked with Bowtie2 
[2021-11-06 17:09:35] Mapping left_kept_reads_seg1 to genome cuan_xiong_genome_contig_hifiasm_hic_masked with Bowtie2 (1/6)
[2021-11-06 17:17:04] Mapping left_kept_reads_seg2 to genome cuan_xiong_genome_contig_hifiasm_hic_masked with Bowtie2 (2/6)
[2021-11-06 17:24:38] Mapping left_kept_reads_seg3 to genome cuan_xiong_genome_contig_hifiasm_hic_masked with Bowtie2 (3/6)
[2021-11-06 17:32:24] Mapping left_kept_reads_seg4 to genome cuan_xiong_genome_contig_hifiasm_hic_masked with Bowtie2 (4/6)
[2021-11-06 17:40:05] Mapping left_kept_reads_seg5 to genome cuan_xiong_genome_contig_hifiasm_hic_masked with Bowtie2 (5/6)
[2021-11-06 17:47:31] Mapping left_kept_reads_seg6 to genome cuan_xiong_genome_contig_hifiasm_hic_masked with Bowtie2 (6/6)
[2021-11-06 17:54:54] Mapping right_kept_reads to genome cuan_xiong_genome_contig_hifiasm_hic_masked with Bowtie2 
[2021-11-06 18:25:45] Mapping right_kept_reads_seg1 to genome cuan_xiong_genome_contig_hifiasm_hic_masked with Bowtie2 (1/6)
[2021-11-06 18:33:21] Mapping right_kept_reads_seg2 to genome cuan_xiong_genome_contig_hifiasm_hic_masked with Bowtie2 (2/6)
[2021-11-06 18:41:12] Mapping right_kept_reads_seg3 to genome cuan_xiong_genome_contig_hifiasm_hic_masked with Bowtie2 (3/6)
[2021-11-06 18:49:15] Mapping right_kept_reads_seg4 to genome cuan_xiong_genome_contig_hifiasm_hic_masked with Bowtie2 (4/6)
[2021-11-06 18:56:12] Mapping right_kept_reads_seg5 to genome cuan_xiong_genome_contig_hifiasm_hic_masked with Bowtie2 (5/6)
[2021-11-06 19:03:06] Mapping right_kept_reads_seg6 to genome cuan_xiong_genome_contig_hifiasm_hic_masked with Bowtie2 (6/6)
[2021-11-06 19:09:44] Searching for junctions via segment mapping
[2021-11-06 19:43:38] Retrieving sequences for splices
[2021-11-06 19:46:26] Indexing splices
    [FAILED]
Error: Splice sequence indexing failed with err =127

I'm anxious to know what to deal with this problem, thank you so much!

Tophat2 Splice Error • 136 views
ADD COMMENT
This thread is not open. No new answers may be added
Traffic: 1715 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6