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TRON-Bioinformatics / EasyFuse

EasyFuse is a pipeline for accurate fusion gene detection from RNA-seq data.
GNU General Public License v3.0
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error with mapslice while using via docker #47

Open Prathyusha-konda opened 1 year ago

Prathyusha-konda commented 1 year ago

Hi, Thanks for developing the tool - excited to try it.

I got the following error while executing easyfuse mapslice cmd2. I installed the docker image and have been using easyfuse via docker. Could you please let me know how to fix this error? Thank you!!

Running EasyFuse-star-SRR13786145_CMD1 CMD: /code/miniconda3/bin/python /code/easyfuse/misc/samples.py --db_path=/output/samples.db --sample_id=SRR13786145 --action=append_state --tool=star Running EasyFuse-mapsplice-SRR13786145_CMD0 CMD: gunzip -c -f /output/Sample_SRR13786145/filtered_reads/out_file-trimmed-pair1_filtered.fastq.gz > /output/Sample_SRR13786145/filtered_reads/out_file-trimmed-pair1_filtered.fastq Running EasyFuse-mapsplice-SRR13786145_CMD1 CMD: gunzip -c -f /output/Sample_SRR13786145/filtered_reads/out_file-trimmed-pair2_filtered.fastq.gz > /output/Sample_SRR13786145/filtered_reads/out_file-trimmed-pair2_filtered.fastq Running EasyFuse-mapsplice-SRR13786145_CMD2 CMD: mapsplice.py --chromosome-dir /ref/fasta -x /ref/bowtie_index/hg38 -1 /output/Sample_SRR13786145/filtered_reads/out_file-trimmed-pair1_filtered.fastq -2 /output/Sample_SRR13786145/filtered_reads/out_file-trimmed-pair2_filtered.fastq --threads 6 --output /output/Sample_SRR13786145/fusion/mapsplice --qual-scale phred33 --bam --seglen 20 --min-map-len 40 --gene-gtf /ref/Homo_sapiens.GRCh38.86.gtf --fusion Error: Command "['mapsplice.py', '--chromosome-dir', '/ref/fasta', '-x', '/ref/bowtie_index/hg38', '-1', '/output/Sample_SRR13786145/filtered_reads/out_file-trimmed-pair1_filtered.fastq', '-2', '/output/Sample_SRR13786145/filtered_reads/out_file-trimmed-pair2_filtered.fastq', '--threads', '6', '--output', '/output/Sample_SRR13786145/fusion/mapsplice', '--qual-scale', 'phred33', '--bam', '--seglen', '20', '--min-map-len', '40', '--gene-gtf', '/ref/Homo_sapiens.GRCh38.86.gtf', '--fusion']" returned non-zero exit status b'-----[Read Format: FASTQ]\n-----[Read Type: Pair End]\n-----[Total # Reads: 38166284]\n-----[Max Read Length: 150]\n-----[Min Read Length: 36]\n-----[Max Quality Score: 70]\n-----[Min Quality Score: 35]\n-----[Quality Score Scale: Phred+33]\nWarning: Could not open read file "/output/Sample_SRR13786145/fusion/mapsplice/tmp/remap/remap_unmapped.1" for reading; skipping...\nCommand: /code/miniconda3/bin/mapsplice_multi_thread -q --min_len 25 --seg_len 20 --min_intron 50 --max_intron_single 300000 --max_intron_double 300000 -v 1 --max_double_splice_mis 2 --max_single_splice_mis 1 --max_append_mis 3 --max_ins 6 --max_del 6 -k 40 -m 40 -p 6 --chrom_tab /output/Sample_SRR13786145/fusion/mapsplice/tmp/chrom_sizes --ref_seq_path /ref/fasta/ --mapsplice_out /output/Sample_SRR13786145/fusion/mapsplice/tmp/fusion/normal.sam --check_read /output/Sample_SRR13786145/fusion/mapsplice/logs/check_reads_format.log --optimize_repeats --fusion /output/Sample_SRR13786145/fusion/mapsplice/tmp/fusion/fusion_alignments_remap.sam --min_fusion_distance 10000 --qual-scale phred33 --juncdb_index /output/Sample_SRR13786145/fusion/mapsplice/tmp/remap/syn_idx_prefix --min_map_len 0 --output_unmapped /output/Sample_SRR13786145/fusion/mapsplice/tmp/fusion/fusion_unmapped --cluster /output/Sample_SRR13786145/fusion/mapsplice/tmp/cluster/result/cluster.txt -1 /output/Sample_SRR13786145/fusion/mapsplice/tmp/remap/remap_unmapped.1 -2 /output/Sample_SRR13786145/fusion/mapsplice/tmp/remap/remap_unmapped.2 /ref/bowtie_index/hg38 /output/Sample_SRR13786145/fusion/mapsplice/tmp/fusion/debug_info \n\n-----------------------------------------------\n[Sun Jun 4 02:16:05 2023] Beginning Mapsplice run (MapSplice v2.2.1)\n[Sun Jun 4 02:16:05 2023] Bin directory: /code/miniconda3/bin/ \n[Sun Jun 4 02:16:05 2023] Preparing output location /output/Sample_SRR13786145/fusion/mapsplice/\n[Sun Jun 4 02:16:05 2023] Checking files or directory: /output/Sample_SRR13786145/filtered_reads/out_file-trimmed-pair1_filtered.fastq\n[Sun Jun 4 02:16:05 2023] Checking files or directory: /output/Sample_SRR13786145/filtered_reads/out_file-trimmed-pair2_filtered.fastq\n[Sun Jun 4 02:16:05 2023] Checking files or directory: /ref/fasta/\n[Sun Jun 4 02:16:05 2023] Checking Bowtie index files\n[Sun Jun 4 02:16:05 2023] Inspecting Bowtie index files\n[Sun Jun 4 02:16:05 2023] Checking reference sequence length\n[Sun Jun 4 02:16:18 2023] Checking consistency of Bowtie index and reference sequence\n[Sun Jun 4 02:16:18 2023] Checking read format\nAuto detect quality scale failed, user specified [phred33] is used\n[Sun Jun 4 02:19:16 2023] Running MapSplice multi-thread\n[Sun Jun 4 05:16:05 2023] Generating junctions from sam file\n[Sun Jun 4 05:16:41 2023] Filtering junction by min mis and min lpq\n[Sun Jun 4 05:16:42 2023] Filtering junction by ROC argu noncanonical\n[Sun Jun 4 05:16:43 2023] Generating synthetic junction sequences\n[Sun Jun 4 05:17:11 2023] Checking Bowtie index files\n[Sun Jun 4 05:17:11 2023] Building Bowtie index for junction synthetic sequence\n[Sun Jun 4 05:17:18 2023] Running MapSplice multi-thread\n[Sun Jun 4 09:22:55 2023] Running alignment handler\n[Sun Jun 4 09:24:17 2023] Parsing cluster regions\n[Sun Jun 4 09:24:20 2023] Clustering regions\n[Sun Jun 4 09:24:21 2023] Running MapSplice multi-thread fusion\n[Sun Jun 4 14:07:41 2023] Generating fusion junctions from sam file and filter by anchor

ibn-salem commented 3 days ago

Which version of EasyFuse did you use?