Zheng-NGS-Lab/SplitFusion

ERROR: config.txt no such file

Opened this issue · 3 comments

asaki1986 commented

Hi,

I am trying to do fusion benchmark using different tools.

I came across error when demo data was applied.

python /home/jjiang/work/fusion/SplitFusion/exec/SplitFusion.py --refGenome /bioinfo/data/Genomes/NCBI/build37/Sequence/WholeGenomeFasta/human_g1k_v37.fasta --annovar /bioinfo/software/packages/annovar-2019-10-24/annovar --samtools /bioinfo/s oftware/bin/samtools --bedtools /bioinfo/software/bin/bedtools --bwa /bioinfo/software/bin/bwa --R /usr/local/bin/R --perl /usr/bin/perl --out ./ --sample_id "Lib001" --fastq_dir ../../SplitFusion/inst/data/example_data/ --r1filename "Lib001".R1.fq --r2filename "Lib001" .R2.fq --thread 10

Error message "/home/jjiang/R/x86_64-pc-linux-gnu-library/3.6/SplitFusion/exec/SplitFusion.1_fastq-bam.sh: line 3: config.txt: No such file or directory
Must specify fastq_dir or bam_dir" came out when command was provided.

Any suggestions will be appreciated.

Thanks,
Junfeng

zhangbaifeng commented
asaki1986 commented

Hi Junfeng, Many thanks for your interest on SplitFusion. Please provide full absolute path for —out and —fastq_dir, eg. —out /home/jjiang/work/fusion/out --fastq_dir /home/jjiang/work/fusion/ SplitFusion/inst/data/example_data/ Best, Baifeng asaki1986 notifications@github.com于2020年7月21日 周二下午7:51写道：
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Hi, I am trying to do fusion benchmark using different tools. I came across error when demo data was applied. python /home/jjiang/work/fusion/SplitFusion/exec/SplitFusion.py --refGenome /bioinfo/data/Genomes/NCBI/build37/Sequence/WholeGenomeFasta/human_g1k_v37.fasta --annovar /bioinfo/software/packages/annovar-2019-10-24/annovar --samtools /bioinfo/s oftware/bin/samtools --bedtools /bioinfo/software/bin/bedtools --bwa /bioinfo/software/bin/bwa --R /usr/local/bin/R --perl /usr/bin/perl --out ./ --sample_id "Lib001" --fastq_dir ../../SplitFusion/inst/data/example_data/ --r1filename "Lib001".R1.fq --r2filename "Lib001" .R2.fq --thread 10 Error message "/home/jjiang/R/x86_64-pc-linux-gnu-library/3.6/SplitFusion/exec/ SplitFusion.1_fastq-bam.sh: line 3: config.txt: No such file or directory Must specify fastq_dir or bam_dir" came out when command was provided. Any suggestions will be appreciated. Thanks, Junfeng — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#2>, or unsubscribe https://github.com/notifications/unsubscribe-auth/ADHMNWUANXFWE3YZKNE7HBDR4V6LPANCNFSM4PDQC32A .

Works! Thanks!

Another question is when I provided a bam file, which had been already proved EML4-ALK positive.
The fusion is listed in NoFilter.txt but removed in the final summary file.

HO0327-GW9T0137B05_L2.raw_data_mapped ALK_intronic---EML4_intronic N.A. 19 25 0 2_29448298__2_42500727 NM_004304 NM_019063 intronic intronic ALK - EML4 - 0 0

It might be removed by the filters, any method to find the filter(cutoff), depth, Quality or others, as those information provided by GATK filters.

Thanks,
Junfeng

zhengzongli commented

Hi Junfeng,

In your example, the fusion breakpoints of both EML4 and ALK are located in introns. Was your data generated using DNA or RNA? Currently, for various reasons, we emphasize on the RNA-level detection. The function for DNA-level detection is under development. For now, you can use the Target mode (e.g. for know gene-gene fusions) to customize your report. You can use the Target mode as an evidence based approach for customized report as you accumulate experiences.

Thanks,
Zongli