bam2chicago bedtools error

[Former user]

Hi,

Im getting an error when I run the bam2chicago.sh script and Im not sure why. This is my error message but when I check the number of columns in the output file all the rows have 14 columns

Checking rmap and baitmap files... Rmap and baitmap files checked successfully Processing sample Chic_S2... Using bam file Chic_S2_R1_2.hicup.bam Using baitmap file /scratch/rr1859/PR_Chic/chicago/all_dpn_frags_Mer41_CS_forDpn_baits_rmap.baitmap Using digest map (rmap) file /scratch/rr1859/PR_Chic/chicago/hg19_dpn.rmap Baitmap file contains >4 columns. Checking if /scratch/rr1859/PR_Chic/chicago/all_dpn_frags_Mer41_CS_forDpn_baits_rmap.baitmap_4col.txt exists... Found /scratch/rr1859/PR_Chic/chicago/all_dpn_frags_Mer41_CS_forDpn_baits_rmap.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... Error: line number 14 of file Chic_S2/Chic_S2_R1_2.hicup_mappedToBaits_baitOnRight.bedpe has 15 fields, but 14 were expected.

[Mikhail Spivakov]

This error is generated by bedtools, and in our experience usually results from whitespace characters in the input file.

[rr1859]

Hi, I switched to bedtools 2.25.0 and it seems to work fine.