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parklab / xTea

Comprehensive TE insertion identification with WGS/WES data from multiple sequencing technics
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Issue with generated run_xTEA_pipeline.sh script #71

Closed slavictoast closed 1 year ago

slavictoast commented 1 year ago

Dear all,

I used bwa-mem to align my samples (human WGS) to hg38, transformed sam to bam and bam to sorted bam via samtools. The generated sorted bam files are used as input in the script generation step of xTea following command was used in the bash terminal (I used ... to spare you from the whole paths)

$ xtea -i xTea_sampleIDs.txt -b xTea_sampleID_bam.txt -x null -p .../xTea -o submit_jobs.sh -l '.../xTea/rep_lib_annotation' -r '.../hg38.fa' -g '.../xTea/gencode.v33.annotation.gff3' --xtea '.../xTea/xtea' -f 5907 -y 4 -n 4 -m 15

To use the xTEA_pipeline.sh script for one of the samples I navigated into the generated files containing the script and started it ($ sh '.../SVA/run_xTEA_pipeline.sh' )

Following errors occured: [E::idx_find_and_load] Could not retrieve index file for (path of sorted bam of the sample) -> several times, some other errors and at the end: x_TEA_main.py: error: no such option: --bamsnap

Did I perhaps misunderstood what's needed as the input files and have to additionally transform them? Thank you!

Valentina

slavictoast commented 1 year ago

Update: I was able to erase the first error by indexing the sorted bam files ($ samtools index >sorted bam file<) But the last error remains: Usage: x_TEA_main.py [options]

x_TEA_main.py: error: no such option: --bamsnap

simoncchu commented 1 year ago

You can ignore this error for now. Same as https://github.com/parklab/xTea/issues/19, I'll resolve this one in the next release.

axz91 commented 1 year ago

@simoncchu Hi I have same issue. May I know where is gvcf file located? I could not find it. Thanks