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Type checker error with bedtools intersect

I want to remove four regions from a bam file. I have two files, the .bam file and the .bed file. I am using the following command:

bedtools2-2.27.0/bedtools intersect -abam input.bam -b filter.bed -v > output_filtered.bam

My filter.bed file is:

NC_000913.3     2747963 2748753
NC_000913.3     3470145 3471329
NC_000913.3     3802039 3804137
NC_000913.3     3807064 3808098

and my BAM file is standard bam:

NB501872:398:HGHWFBGXB:1:11101:26117:1029
1:N:0:CAGATC    -   NC_000913.3 3803471 TTTTTCGAAATCGGAGCCATCACCCAATACATGGAGTTT EEEEAEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEA 0   
NB501872:398:HGHWFBGXB:1:11101:3328:1031
1:N:0:CAGATC    +   NC_000913.3 2748273 GCGCTGGCAACCTTCATGCCCAATGAATACATCACCCAT EEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEAEEEEA 0   
NB501872:398:HGHWFBGXB:1:11101:23381:1032
1:N:0:CAGATC    -   NC_000913.3 4176778 TGCGTGGTATCAAACGTGAAGAAATCGAACGTGGTCAGG EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE 1   
NB501872:398:HGHWFBGXB:1:11101:8594:1034
1:N:0:CAGATC    -   NC_000913.3 2107391 ACTGGATAGTAGGGTTCGTCGCCAACTTTCCACTCTAAT EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE 0   
NB501872:398:HGHWFBGXB:1:11101:16388:1035
1:N:0:CAGATC    +   NC_000913.3 1756723 CTCGAGTTCAACAATGACAACCGTAAACTGCGCATTACC EEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEE 0   
NB501872:398:HGHWFBGXB:1:11101:7169:1035
1:N:0:CAGATC    +   NC_000913.3 1166876 ATTGAGGCTGATCTGATGGTATGGGCAGCCGGGATCAAA EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE 0   
NB501872:398:HGHWFBGXB:1:11101:4800:1036
1:N:0:CAGATC    +   NC_000913.3 2748273 GCGCTGGCAACCTTCATGCCCAATGAATACATCACCCAT EEEEEEEEE/EEEEEEEEEEEEEEEEEEEE<EE<EEEEE 0   
NB501872:398:HGHWFBGXB:1:11101:16607:1036
1:N:0:CAGATC    +   NC_000913.3 1111389 GGATTTGTGGGTTTCCTTTATGCAGCTTCTGCCTTATAT EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE 0   
NB501872:398:HGHWFBGXB:1:11101:16422:1039
1:N:0:CAGATC    -   NC_000913.3 2815223 CCACCTGCGGTAACGGGAACTGTGCGGTTTCGCAGCCGA EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE 0   
NB501872:398:HGHWFBGXB:1:11101:19492:1039
1:N:0:CAGATC    -   NC_000913.3 2415498 TCGCCGCGTTAAATCCGTCACTTTCTGCGCACGCAGCAT <//</A/EEEE/AAEA/EE//EE//EEEEEE/EE/AEE/ 0

When I run the command above, I get the following error:

Error: Type checker found wrong number of fields while tokenizing data line.
Perhaps you have extra TAB at the end of your line? Check with "cat -t"

I've run cat -t on the filter.bed:

NC_000913.3^I2747963^I2748753
NC_000913.3^I3470145^I3471329
NC_000913.3^I3802039^I3804137
NC_000913.3^I3807064^I3808098

I've run cat -t on the input.bam:

NB501872:398:HGHWFBGXB:1:11101:26117:1029 1:N:0:CAGATC^I-^INC_000913.3^I3803471^ITTTTTCGAAATCGGAGCCATCACCCAATACATGGAGTTT^IEEEEAEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEA^I0^I
NB501872:398:HGHWFBGXB:1:11101:3328:1031 1:N:0:CAGATC^I+^INC_000913.3^I2748273^IGCGCTGGCAACCTTCATGCCCAATGAATACATCACCCAT^IEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEAEEEEA^I0^I
NB501872:398:HGHWFBGXB:1:11101:23381:1032 1:N:0:CAGATC^I-^INC_000913.3^I4176778^ITGCGTGGTATCAAACGTGAAGAAATCGAACGTGGTCAGG^IEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE^I1^I
NB501872:398:HGHWFBGXB:1:11101:8594:1034 1:N:0:CAGATC^I-^INC_000913.3^I2107391^IACTGGATAGTAGGGTTCGTCGCCAACTTTCCACTCTAAT^IEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE^I0^I
NB501872:398:HGHWFBGXB:1:11101:16388:1035 1:N:0:CAGATC^I+^INC_000913.3^I1756723^ICTCGAGTTCAACAATGACAACCGTAAACTGCGCATTACC^IEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEE^I0^I
NB501872:398:HGHWFBGXB:1:11101:7169:1035 1:N:0:CAGATC^I+^INC_000913.3^I1166876^IATTGAGGCTGATCTGATGGTATGGGCAGCCGGGATCAAA^IEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE^I0^I
NB501872:398:HGHWFBGXB:1:11101:4800:1036 1:N:0:CAGATC^I+^INC_000913.3^I2748273^IGCGCTGGCAACCTTCATGCCCAATGAATACATCACCCAT^IEEEEEEEEE/EEEEEEEEEEEEEEEEEEEE<EE<EEEEE^I0^I
NB501872:398:HGHWFBGXB:1:11101:16607:1036 1:N:0:CAGATC^I+^INC_000913.3^I1111389^IGGATTTGTGGGTTTCCTTTATGCAGCTTCTGCCTTATAT^IEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE^I0^I
NB501872:398:HGHWFBGXB:1:11101:16422:1039 1:N:0:CAGATC^I-^INC_000913.3^I2815223^ICCACCTGCGGTAACGGGAACTGTGCGGTTTCGCAGCCGA^IEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE^I0^I
NB501872:398:HGHWFBGXB:1:11101:19492:1039 1:N:0:CAGATC^I-^INC_000913.3^I2415498^ITCGCCGCGTTAAATCCGTCACTTTCTGCGCACGCAGCAT^I<//</A/EEEE/AAEA/EE//EE//EEEEEE/EE/AEE/^I0^I

I've tried removing the end of line tabs from the bam file but that didn't work. I tried adding tabs to the end of the lines in the filter.bad file and that didn't work.

I'm at a loss of what to try or how to fix it. Any help and advice would be greatly appreciated.

bedtools rnaseq intersect error type checker
• 684 views • link
written by kmyers2 • kmyers2

That's not a BAM file. If you showed us the command used to make it, we would be able to guess at what format it actually is.

• 0 views • link
written by John Marshall John Marshall

Thanks for the reply. This command was used to generate the file:

bowtie genome.bowtie -M 1 -v 3 -q input.fastq --un input.-unaligned.fastq

I guess I thought this would be a SAM file.

• 0 views • link
written by kmyers2 • kmyers2

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