Quang Tran

Please find the log file attached. Thanks, [CoaxSAMPLE.log](https://github.com/ndaniel/fusioncatcher/files/7312951/CoaxSAMPLE.log)

The read pairs from fastq files are below. The read R2 got trimmed. Do you allow fusioncatcher work with different lengths from R1 and R2? Total number of lines in...

Hi @ndaniel Please find the fastq files: https://www.dropbox.com/s/zgse1sny96yixug/my_read_R1.fastq.gz?dl=0 https://www.dropbox.com/s/dfn0syuyibrsym9/my_read_R2.fastq.gz?dl=0 Coax

Hi Brent, I got a similar error message - exit status 127. I tried to build "lumpy_filter" from filter.c, however it didn't work. Can you take a look and see...

Thanks, Brent. It worked after fixing the path for lumpy_filter, gsort, and bcftools.

Hi, got the "segment fault (core dumped)" when aligning PacBio reads to hg38: `$ minimap2 -ax map-pb GRCh38_full_analysis_set_plus_decoy_hla.fa HG03065-clr-r54329U_20191115_214119-B01.fq > HG03065-clr-r54329U_20191115_214119-B01.sam ` > [M::mm_idx_gen::52.335*1.35] collected minimizers [M::mm_idx_gen::62.006*1.59] sorted minimizers [M::main::62.006*1.59]...

I got the same error with ONT data from GIAB on hg38: [NOTE] number of threads: 1 [NOTE] (bwt_load) loading the index... [NOTE] (bwt_load) index was loaded in 49.73 seconds...

Hi @haghshenas, I used GCA_000001405.15_GRCh38_no_alt_analysis_set.fna as a reference. And ONT reads from GIAB: ftp://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/data/AshkenazimTrio/HG002_NA24385_son/Ultralong_OxfordNanopore/final/ultra-long-ont.fastq.gz You can start run the fastq, then the error will appear right away. Thanks, Coax

Thanks, Paul. I think the software doesn't get this linux command `"~/"` . I used `"--input ~//file_1.fastq,~//file_2.fastq"`. It can only recognize the first `"~/"`. Coax

Hi @jinzhuangdou, I successfully ran preprocess, but when I run Monopogen `germline`, I added all autosome 1-22 (even with 1 chr22), I got warnings, and it seems the process took...