Hi, I wrote a ticket yesterday, but you close it and indeed fix the error that was happening, thank you very much for that. Unfortunately, when I run it now, I get and different error:
Checking rmap and baitmap files... Rmap and baitmap files checked successfully Processing sample output_sample... Using bam file ../out_hicup/SRR3535023_1_2.hicup.bam Using baitmap file /Users/pacera/developing/C-HiC/tests/data/test_makeBaitmap/test.baitmap Using digest map (rmap) file /Users/pacera/developing/C-HiC/tests/data/test_makeRmap/restriction_enzyme_test_HindIII_GRCh38.rmap Baitmap file contains >4 columns. Checking if /Users/pacera/developing/C-HiC/tests/data/test_makeBaitmap/test.baitmap_4col.txt exists... Found /Users/pacera/developing/C-HiC/tests/data/test_makeBaitmap/test.baitmap_4col.txt Intersecting with bait fragments (using min overhang of 0.6)... Flipping all reads that overlap with the bait on to the right-hand side... Intersecting with bait fragments again to produce a list of bait-to-bait interactions that can be used separately; note they will also be retained in the main output... Intersecting with restriction fragments (using min overhang of 0.6)... Removing reads that failed the min overhang filter... Adding frag length and signed distance from bait; removing self-ligation fragments (if any; not expected with HiCUP input)... Can't open output_sample/SRR3535023_1_2.hicup_mappedToBaitsBoRAndRFrag_fmore06.bedpe: No such file or directory. rm: output_sample/SRR3535023_1_2.hicup_mappedToBaitsBoRAndRFrag_fmore06.bedpe: No such file or directory
It looks like bam2chicago.sh is not able to generate some file. Please, is that because I am using just two chromosomes and a subset of the total reads? I cannot think on anything else. I have tried to run it using different BAM files using HiCUP, with both hg19 and hg38. Thank you very much for your time.