Deleted:Tophat2 Error: Splice sequence indexing failed with err =127

Question

[mixiaoluo88]

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!