ValueError: file does not contain alignment data

[ccmeth]

Dear MAPS team,

Recently, I tried to use MAPS for tackling PLAC-seq data, however, an error appeared at the beginning of this process (the data I used is GM12878 provided there). Could you please tell me how to address this problem?

Wed Feb 23 16:17:32 2022 starting mapping and filtering operation Wed Feb 23 16:17:32 2022 calling bwa for /home/bd/test_maps/SRR3467175_R1.fastq Wed Feb 23 16:17:32 2022 calling bwa for /home/bd/test_maps/SRR3467175_R2.fastq Traceback (most recent call last): File "/home/bd/MAPS-master/bin/feather/feather_pipe", line 125, in main() File "/home/bd/MAPS-master/bin/feather/feather_pipe", line 53, in main filter_output_filename = filter_main(fastq1, fastq2, bwa_index, mapq, outdir, prefix, threads, optical, to_file = False) File "/home/bd/MAPS-master/bin/feather/feather_filter_chr.py", line 50, in filter_main bwa = pysam.AlignmentFile(bwa_filename) File "pysam/libcalignmentfile.pyx", line 742, in pysam.libcalignmentfile.AlignmentFile.cinit File "pysam/libcalignmentfile.pyx", line 947, in pysam.libcalignmentfile.AlignmentFile._open ValueError: file does not contain alignment data

Hao

[garci1294]

@ccmeth were you able to find the solution for this issue?

Thanks, Jesus

[j-andrews7]

For anyone who runs into this, it seems to stem from the FASTA file not being in the same location as an actual BWA index. You must have the other BWA index files in the same location.

Error message could be improved, @ijuric