about soapfuse

[BGI2016]

Dear author, when I run the easyfuse tool, soapfuse always terminates. Can I exclude the soapfuse tool and run fetchdata and summarize?

[patricksorn]

Dear @BGI2016 ,

you could supply your own configuration file to the tool excluding soapfuse from the process.
Please take config.ini.docker for that purpose and replace the keys tools and fusiontools like this:

tools = qc,readfilter,fusioncatcher,star,starfusion,infusion,mapsplice,fetchdata,summary
fusiontools = fusioncatcher,starfusion,infusion,mapsplice

Best regards,
Patrick

[BGI2016]

Thank you very much for your reply.If I don't run soapfuse, will it have a big impact on the final result, especially the fetchdata step?

[BGI2016]

Dear @patricksorn ,

I excluded the soapfuse software, but when I execute the fusiontoolparser.py script, I get the following error message:

FileNotFoundError: [Errno 2] No such file or directory: '/output/Sample_SRR1659960_05pc/fusion/soapfuse/final_fusion_genes'

Is it necessary to use the output of soapfuse in fetchdata step?

[patricksorn]

Dear @BGI2016 ,

did you delete your previous results? Unfortunately I think you have to delete your previous results and restart the pipeline using the new configuration file for it to work.

Best regards,
Patrick

[BGI2016]

Dear @patricksorn ,

Thank you very much. I'll restart the pipeline according to your method.

[BGI2016]

Dear @patricksorn,

the following is the running log after I restarted the pipeline. When I ran to fetchdata.py, the pipeline reported an error and terminated.Please help me solve it, thank you.

==========start at : Thu Apr 27 17:11:36 CST 2023 ==========

Going to process the following read files...
Fastq file 0: /data/SRR1659960_05pc_R1.fastq.gz
Fastq file 1: /data/SRR1659960_05pc_R2.fastq.gz
SRR1659960_05pc ['NA']
/output/Sample_SRR1659960_05pc/filtered_reads/out_file-trimmed-pair1_filtered.fastq /output/Sample_SRR1659960_05pc/filtered_reads/out_file-trimmed-pair2_filtered.fastq
Running EasyFuse-qc-SRR1659960_05pc_CMD0
CMD: fastqc --nogroup --extract -t 6 -o /output/Sample_SRR1659960_05pc/qc /data/SRR1659960_05pc_R1.fastq.gz /data/SRR1659960_05pc_R2.fastq.gz
Running EasyFuse-qc-SRR1659960_05pc_CMD1
CMD: /code/miniconda3/bin/python /code/easyfuse/misc/qc_parser.py -i /output/Sample_SRR1659960_05pc/qc/SRR1659960_05pc_R1_fastqc/fastqc_data.txt /output/Sample_SRR1659960_05pc/qc/SRR1659960_05pc_R2_fastqc/fastqc_data.txt -o /output/Sample_SRR1659960_05pc/qc/qc_table.txt
Running EasyFuse-qc-SRR1659960_05pc_CMD2
CMD: /code/miniconda3/bin/python /code/easyfuse/tool_wrapper/skewer_wrapper.py -q /output/Sample_SRR1659960_05pc/qc/qc_table.txt -i /data/SRR1659960_05pc_R1.fastq.gz /data/SRR1659960_05pc_R2.fastq.gz -o /output/Sample_SRR1659960_05pc/qc/skewer -b /code/skewer-0.2.2/skewer -m 0.75
Running EasyFuse-qc-SRR1659960_05pc_CMD3
CMD: /code/miniconda3/bin/python /code/easyfuse/misc/samples.py --db_path=/output/samples.db --sample_id=SRR1659960_05pc --action=append_state --tool=qc
Running EasyFuse-readfilter-SRR1659960_05pc_CMD0
CMD: STAR --genomeDir /ref/star_index/ --outFileNamePrefix /output/Sample_SRR1659960_05pc/filtered_reads/SRR1659960_05pc_ --readFilesCommand zcat --readFilesIn /output/Sample_SRR1659960_05pc/qc/skewer/out_file-trimmed-pair1.fastq.gz /output/Sample_SRR1659960_05pc/qc/skewer/out_file-trimmed-pair2.fastq.gz --outFilterMultimapNmax 100 --outSAMmultNmax 1 --chimSegmentMin 10 --chimJunctionOverhangMin 10 --alignSJDBoverhangMin 10 --alignMatesGapMax 200000 --alignIntronMax 200000 --chimSegmentReadGapMax 3 --alignSJstitchMismatchNmax 5 -1 5 5 --seedSearchStartLmax 20 --winAnchorMultimapNmax 50 --outSAMtype BAM Unsorted --chimOutType Junctions WithinBAM --outSAMunmapped Within KeepPairs --runThreadN 6
Running EasyFuse-readfilter-SRR1659960_05pc_CMD1
CMD: /code/miniconda3/bin/python /code/easyfuse/fusionreadfilter.py --input /output/Sample_SRR1659960_05pc/filtered_reads/SRR1659960_05pc_Aligned.out.bam --output /output/Sample_SRR1659960_05pc/filtered_reads/SRR1659960_05pc_Aligned.out.filtered.bam
Running EasyFuse-readfilter-SRR1659960_05pc_CMD2
CMD: samtools fastq -0 /output/Sample_SRR1659960_05pc/filtered_reads/out_file-trimmed-pair1_filtered_singles.fastq.gz -1 /output/Sample_SRR1659960_05pc/filtered_reads/out_file-trimmed-pair1_filtered.fastq.gz -2 /output/Sample_SRR1659960_05pc/filtered_reads/out_file-trimmed-pair2_filtered.fastq.gz --threads 6 /output/Sample_SRR1659960_05pc/filtered_reads/SRR1659960_05pc_Aligned.out.filtered.bam
Running EasyFuse-readfilter-SRR1659960_05pc_CMD3
CMD: /code/miniconda3/bin/python /code/easyfuse/misc/samples.py --db_path=/output/samples.db --sample_id=SRR1659960_05pc --action=append_state --tool=readfilter
Running EasyFuse-star-SRR1659960_05pc_CMD0
CMD: STAR --genomeDir /ref/star_index/ --outFileNamePrefix /output/Sample_SRR1659960_05pc/expression/star/SRR1659960_05pc_ --runThreadN 6 --runMode alignReads --readFilesIn /output/Sample_SRR1659960_05pc/filtered_reads/out_file-trimmed-pair1_filtered.fastq.gz /output/Sample_SRR1659960_05pc/filtered_reads/out_file-trimmed-pair2_filtered.fastq.gz --readFilesCommand zcat --chimSegmentMin 10 --chimJunctionOverhangMin 10 --alignSJDBoverhangMin 10 --alignMatesGapMax 200000 --alignIntronMax 200000 --chimSegmentReadGapMax 3 --alignSJstitchMismatchNmax 5 -1 5 5 --seedSearchStartLmax 20 --winAnchorMultimapNmax 50 --outSAMtype BAM SortedByCoordinate --chimOutType Junctions SeparateSAMold --chimOutJunctionFormat 1
Running EasyFuse-star-SRR1659960_05pc_CMD1
CMD: /code/miniconda3/bin/python /code/easyfuse/misc/samples.py --db_path=/output/samples.db --sample_id=SRR1659960_05pc --action=append_state --tool=star
Running EasyFuse-mapsplice-SRR1659960_05pc_CMD0
CMD: gunzip -c -f /output/Sample_SRR1659960_05pc/filtered_reads/out_file-trimmed-pair1_filtered.fastq.gz > /output/Sample_SRR1659960_05pc/filtered_reads/out_file-trimmed-pair1_filtered.fastq
Running EasyFuse-mapsplice-SRR1659960_05pc_CMD1
CMD: gunzip -c -f /output/Sample_SRR1659960_05pc/filtered_reads/out_file-trimmed-pair2_filtered.fastq.gz > /output/Sample_SRR1659960_05pc/filtered_reads/out_file-trimmed-pair2_filtered.fastq
Running EasyFuse-mapsplice-SRR1659960_05pc_CMD2
CMD: mapsplice.py --chromosome-dir /ref/fasta -x /ref/bowtie_index/hg38 -1 /output/Sample_SRR1659960_05pc/filtered_reads/out_file-trimmed-pair1_filtered.fastq -2 /output/Sample_SRR1659960_05pc/filtered_reads/out_file-trimmed-pair2_filtered.fastq --threads 6 --output /output/Sample_SRR1659960_05pc/fusion/mapsplice --qual-scale phred33 --bam --seglen 20 --min-map-len 40 --gene-gtf /ref/Homo_sapiens.GRCh38.86.gtf --fusion
Running EasyFuse-mapsplice-SRR1659960_05pc_CMD3
CMD: /code/miniconda3/bin/python /code/easyfuse/misc/samples.py --db_path=/output/samples.db --sample_id=SRR1659960_05pc --action=append_state --tool=mapsplice
Running EasyFuse-fusioncatcher-SRR1659960_05pc_CMD0
CMD: /code/fusioncatcher/1.0/bin/fusioncatcher --input /output/Sample_SRR1659960_05pc/filtered_reads/out_file-trimmed-pair1_filtered.fastq.gz,/output/Sample_SRR1659960_05pc/filtered_reads/out_file-trimmed-pair2_filtered.fastq.gz --data /ref/fusioncatcher_index/ --output /output/Sample_SRR1659960_05pc/fusion/fusioncatcher -p 6
Running EasyFuse-fusioncatcher-SRR1659960_05pc_CMD1
CMD: /code/miniconda3/bin/python /code/easyfuse/misc/samples.py --db_path=/output/samples.db --sample_id=SRR1659960_05pc --action=append_state --tool=fusioncatcher
Running EasyFuse-starfusion-SRR1659960_05pc_CMD0
CMD: STAR-Fusion --chimeric_junction /output/Sample_SRR1659960_05pc/expression/star/SRR1659960_05pc_Chimeric.out.junction --genome_lib_dir /ref/starfusion_index/ --CPU 6 --output_dir /output/Sample_SRR1659960_05pc/fusion/starfusion
Running EasyFuse-starfusion-SRR1659960_05pc_CMD1
CMD: /code/miniconda3/bin/python /code/easyfuse/misc/samples.py --db_path=/output/samples.db --sample_id=SRR1659960_05pc --action=append_state --tool=starfusion
Running EasyFuse-infusion-SRR1659960_05pc_CMD0
CMD: /code/miniconda3/envs/py27/bin/python /code/InFusion-0.8/infusion -1 /output/Sample_SRR1659960_05pc/filtered_reads/out_file-trimmed-pair1_filtered.fastq.gz -2 /output/Sample_SRR1659960_05pc/filtered_reads/out_file-trimmed-pair2_filtered.fastq.gz --skip-finished --min-unique-alignment-rate 0 --min-unique-split-reads 0 --allow-non-coding --out-dir /output/Sample_SRR1659960_05pc/fusion/infusion /ref/infusion.cfg
Running EasyFuse-infusion-SRR1659960_05pc_CMD1
CMD: /code/miniconda3/bin/python /code/easyfuse/misc/samples.py --db_path=/output/samples.db --sample_id=SRR1659960_05pc --action=append_state --tool=infusion
Running EasyFuse-fetchdata-SRR1659960_05pc_CMD0
CMD: /code/miniconda3/bin/python /code/easyfuse/fetchdata.py -i /output/Sample_SRR1659960_05pc -o /output/Sample_SRR1659960_05pc/fetchdata -s SRR1659960_05pc -c /data/config.ini --fq1 /output/Sample_SRR1659960_05pc/filtered_reads/out_file-trimmed-pair1_filtered.fastq.gz --fq2 /output/Sample_SRR1659960_05pc/filtered_reads/out_file-trimmed-pair2_filtered.fastq.gz --fusion_support 1
Error: Command "['/code/miniconda3/bin/python', '/code/easyfuse/fetchdata.py', '-i', '/output/Sample_SRR1659960_05pc', '-o', '/output/Sample_SRR1659960_05pc/fetchdata', '-s', 'SRR1659960_05pc', '-c', '/data/config.ini', '--fq1', '/output/Sample_SRR1659960_05pc/filtered_reads/out_file-trimmed-pair1_filtered.fastq.gz', '--fq2', '/output/Sample_SRR1659960_05pc/filtered_reads/out_file-trimmed-pair2_filtered.fastq.gz', '--fusion_support', '1']" returned non-zero exit status
b''
==========end at : Thu Apr 27 17:23:52 CST 2023 ==========

[BGI2016]

Dear @patricksorn ,

I am currently using version 1.3.7, can version 1.3.6 run completely without prompting the above error?