bam2chicago.sh error: empty baitOnRight.bedpe file

[Former user]

Hello,

While running bam2chicago.sh, I get an error: The requested bed file (IHEP37/iHep_37_1189_Final_S2_R1_2_001.hicup_mappedToBaits_baitOnRight.bedpe) could not be opened. Exiting!

which is because the step "Flipping all reads that overlap with the bait on to the right-hand side..." produces an empty baitOnRight file.

Here is a log of all the messages produced by the run:

 sh ../../chicagoTeam-chicago-3512c631887f/chicagoTools/bam2chicago.sh ../../hicup_GrCH38/iHep_37_1189_                       Final_S2_R1_2_001.hicup.bam  ../../../Hep_IPS_May2019/for_Minal/GRCh38/chicago_1frag_lifted_inrmap.baitmap ../../../Hep_IPS_May2019/fo                       r_Minal/GRCh38/DpnII_hg38.rmap IHEP37
Checking rmap and baitmap files...

Rmap and baitmap files checked successfully
Processing sample IHEP37...
Using bam file ../../hicup_GrCH38/iHep_37_1189_Final_S2_R1_2_001.hicup.bam
Using baitmap file ../../../Hep_IPS_May2019/for_Minal/GRCh38/chicago_1frag_lifted_inrmap.baitmap
Using digest map (rmap) file ../../../Hep_IPS_May2019/for_Minal/GRCh38/DpnII_hg38.rmap
Baitmap file contains >4 columns. Checking if ../../../Hep_IPS_May2019/for_Minal/GRCh38/chicago_1frag_lifted_inrmap.baitmap_4col.txt e                       xists...
Found ../../../Hep_IPS_May2019/for_Minal/GRCh38/chicago_1frag_lifted_inrmap.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: The requested bed file (IHEP37/iHep_37_1189_Final_S2_R1_2_001.hicup_mappedToBaits_baitOnRight.bedpe) could not be opened. Exiti                       ng!

Could you please point me to why this might be happening?

Thanks, Shweta

[Anupam Bhattacharya]

I am having the same error message while working on the files. Do you find any solution for the error?

‌

[bif@spandana newFolder_anupam]$ sh ../bam2chicago.sh /storage2/ajay_works/hESC/SRR400251_ref.bam hg19TestDesign/Digest_Human_HindIII_baits_e75_ID.baitmap hg19TestDesign/Digest_Human_HindIII.rmap SRR400251 [nodelete]
Checking rmap and baitmap files...
Rmap and baitmap files checked successfully
Processing sample SRR400251...
Using bam file /storage2/ajay_works/hESC/SRR400251_ref.bam
Using baitmap file hg19TestDesign/Digest_Human_HindIII_baits_e75_ID.baitmap
Using digest map (rmap) file hg19TestDesign/Digest_Human_HindIII.rmap
Baitmap file contains >4 columns. Checking if hg19TestDesign/Digest_Human_HindIII_baits_e75_ID.baitmap_4col.txt exists...
Found hg19TestDesign/Digest_Human_HindIII_baits_e75_ID.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: The requested bed file (SRR400251/SRR400251_ref_mappedToBaits_baitOnRight.bedpe) could not be opened. Exiting!

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