Error: unable to open file or unable to determine types for file

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Yung-Chih Lai

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Mar 10, 2016, 1:52:55 PM3/10/16
to bedtools-discuss

Hi,

 

I use intersect for two bed files, but it shows that “Error: unable to open file or unable to determine types for file FstGLOB_CEU_u_YRI_u_CHB_score.bed”. Please see the detail below. Could you help me? Many thanks.

 

Best,

 

Gary

 

 

 

gary > uname -a

Darwin dynamic2-095-206.hsc.usc.edu 14.5.0 Darwin Kernel Version 14.5.0: Tue Sep  1 21:23:09 PDT 2015; root:xnu-2782.50.1~1/RELEASE_X86_64 x86_64

gary > bedtools --version

bedtools v2.25.0

gary > ll

total 1855824

-rw-r--r--  1 gary  staff   903M Mar 10 09:47 FstGLOB_CEU_u_YRI_u_CHB_score.bed

-rw-r--r--  1 gary  staff   1.8M Mar  8 06:52 T8EHMC_Flank.bed

-rw-r-----@ 1 gary  staff   911K Mar  8 06:51 T8E_HMC.bed

-rw-r--r--  1 gary  staff   298B Mar 10 09:45 command

gary > bedtools intersect -a FstGLOB_CEU_u_YRI_u_CHB_score.bed -b T8E_HMC.bed > FstGLOB_T8EHMC.bed

Error: unable to open file or unable to determine types for file FstGLOB_CEU_u_YRI_u_CHB_score.bed

gary > head -n 20 FstGLOB_CEU_u_YRI_u_CHB_score.bed

1 10583 10583 rs58108140 0.0799

1 10611 10611 rs189107123 0.0094

1 13302 13302 rs180734498 0.0529

1 13327 13327 rs144762171 0.0043

1 13980 13980 rs151276478 0.0195

1 30923 30923 rs140337953 0.3064

1 51476 51476 rs187298206 0.0072

1 51479 51479 rs116400033 0.2055

1 52058 52058 rs62637813 0.0587

1 52144 52144 rs190291950 -4e-04

1 52238 52238 rs150021059 0.3325

1 54353 54353 rs140052487 0.003

1 54421 54421 rs146477069 0.1419

1 54490 54490 rs141149254 0.1767

1 54676 54676 rs2462492 0.0819

1 54753 54753 rs143174675 0.026

1 55164 55164 rs3091274 0.3548

1 55299 55299 rs10399749 0.0309

1 55313 55313 rs182462964 2e-04

1 55326 55326 rs3107975 0.0237

gary > 

Aaron Quinlan

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Mar 10, 2016, 1:57:09 PM3/10/16
to Yung-Chih Lai, bedtools...@googlegroups.com
Hi Gary,

It looks as though your files are space-delimited. Bedtools expects tab-delimited files.

Best,
Aaron
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Aaron Quinlan

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Mar 10, 2016, 4:54:45 PM3/10/16
to Yung-Chih Lai, bedtools...@googlegroups.com
Can you post the head of  T8E_HMC.bed?

On March 10, 2016 at 2:27:58 PM, Yung-Chih Lai (yungc...@gmail.com) wrote:

Hi Aaron,

Many thanks for your information. I replaced space with tab based on your suggestion, but it showed that "File Tab_FstGLOB_score.bed has inconsistent naming convention for record:1 10582 10584 rs58108140 0.0799". Could you help me again? Please see the detail below.

Thanks a lot,

Gary

gary > uname -a
Darwin dynamic2-095-206.hsc.usc.edu 14.5.0 Darwin Kernel Version 14.5.0: Tue Sep  1 21:23:09 PDT 2015; root:xnu-2782.50.1~1/RELEASE_X86_64 x86_64
gary > bedtools --version
bedtools v2.25.0
gary > ll
total 1855824
-rw-r--r--  1 gary  staff   903M Mar 10 09:47 FstGLOB_CEU_u_YRI_u_CHB_score.bed
-rw-r--r--  1 gary  staff   1.8M Mar  8 06:52 T8EHMC_Flank.bed
-rw-r-----@ 1 gary  staff   911K Mar  8 06:51 T8E_HMC.bed
-rw-r--r--  1 gary  staff   298B Mar 10 11:12 command
gary > tr ' ' '\t' < FstGLOB_CEU_u_YRI_u_CHB_score.bed > Tab_FstGLOB_score.bed 
gary > head Tab_FstGLOB_score.bed
1 10583 10583 rs58108140 0.0799
1 10611 10611 rs189107123 0.0094
1 13302 13302 rs180734498 0.0529
1 13327 13327 rs144762171 0.0043
1 13980 13980 rs151276478 0.0195
1 30923 30923 rs140337953 0.3064
1 51476 51476 rs187298206 0.0072
1 51479 51479 rs116400033 0.2055
1 52058 52058 rs62637813 0.0587
1 52144 52144 rs190291950 -4e-04
gary > bedtools intersect -a Tab_FstGLOB_score.bed -b T8E_HMC.bed > FstGLOB_T8EHMC.bed
***** WARNING: File Tab_FstGLOB_score.bed has inconsistent naming convention for record:
1 10582 10584 rs58108140 0.0799

***** WARNING: File Tab_FstGLOB_score.bed has inconsistent naming convention for record:
1 10582 10584 rs58108140 0.0799

gary > ll
total 3706168
-rw-r--r--  1 gary  staff   903M Mar 10 09:47 FstGLOB_CEU_u_YRI_u_CHB_score.bed
-rw-r--r--  1 gary  staff     0B Mar 10 13:22 FstGLOB_T8EHMC.bed
-rw-r--r--  1 gary  staff   1.8M Mar  8 06:52 T8EHMC_Flank.bed
-rw-r-----@ 1 gary  staff   911K Mar  8 06:51 T8E_HMC.bed
-rw-r--r--  1 gary  staff   903M Mar 10 13:19 Tab_FstGLOB_score.bed
-rw-r--r--  1 gary  staff   298B Mar 10 11:12 command
gary > 


Yung-Chih Lai

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Mar 10, 2016, 7:35:08 PM3/10/16
to Aaron Quinlan, bedtools...@googlegroups.com
Hi Aaron,

Many thanks for your information. I replaced space with tab based on your suggestion, but it showed that "File Tab_FstGLOB_score.bed has inconsistent naming convention for record:1 10582 10584 rs58108140 0.0799". Could you help me again? Please see the detail below.

Thanks a lot,

Gary

gary > uname -a
Darwin dynamic2-095-206.hsc.usc.edu 14.5.0 Darwin Kernel Version 14.5.0: Tue Sep  1 21:23:09 PDT 2015; root:xnu-2782.50.1~1/RELEASE_X86_64 x86_64
gary > bedtools --version
bedtools v2.25.0
gary > ll
total 1855824
-rw-r--r--  1 gary  staff   903M Mar 10 09:47 FstGLOB_CEU_u_YRI_u_CHB_score.bed
-rw-r--r--  1 gary  staff   1.8M Mar  8 06:52 T8EHMC_Flank.bed
-rw-r-----@ 1 gary  staff   911K Mar  8 06:51 T8E_HMC.bed
-rw-r--r--  1 gary  staff   298B Mar 10 11:12 command
gary > tr ' ' '\t' < FstGLOB_CEU_u_YRI_u_CHB_score.bed > Tab_FstGLOB_score.bed 
gary > head Tab_FstGLOB_score.bed
1 10583 10583 rs58108140 0.0799
1 10611 10611 rs189107123 0.0094
1 13302 13302 rs180734498 0.0529
1 13327 13327 rs144762171 0.0043
1 13980 13980 rs151276478 0.0195
1 30923 30923 rs140337953 0.3064
1 51476 51476 rs187298206 0.0072
1 51479 51479 rs116400033 0.2055
1 52058 52058 rs62637813 0.0587
1 52144 52144 rs190291950 -4e-04
gary > bedtools intersect -a Tab_FstGLOB_score.bed -b T8E_HMC.bed > FstGLOB_T8EHMC.bed
***** WARNING: File Tab_FstGLOB_score.bed has inconsistent naming convention for record:
1 10582 10584 rs58108140 0.0799

***** WARNING: File Tab_FstGLOB_score.bed has inconsistent naming convention for record:
1 10582 10584 rs58108140 0.0799

gary > ll
total 3706168
-rw-r--r--  1 gary  staff   903M Mar 10 09:47 FstGLOB_CEU_u_YRI_u_CHB_score.bed
-rw-r--r--  1 gary  staff     0B Mar 10 13:22 FstGLOB_T8EHMC.bed
-rw-r--r--  1 gary  staff   1.8M Mar  8 06:52 T8EHMC_Flank.bed
-rw-r-----@ 1 gary  staff   911K Mar  8 06:51 T8E_HMC.bed
-rw-r--r--  1 gary  staff   903M Mar 10 13:19 Tab_FstGLOB_score.bed
-rw-r--r--  1 gary  staff   298B Mar 10 11:12 command
gary > 
On Thu, Mar 10, 2016 at 10:57 AM, Aaron Quinlan <aaronq...@gmail.com> wrote:

Yung-Chih Lai

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Mar 10, 2016, 7:35:08 PM3/10/16
to Aaron Quinlan, bedtools...@googlegroups.com

Hi Aaron,

 

Please see the head of T8E_HMC.bed below. You can check my files using links below. I really appreciate your time and help.

 

Best,

 

Gary

 

http://68.181.92.180/~Gary/temporal/T8E_HMC.bed

http://68.181.92.180/~Gary/temporal/Tab_FstGLOB_score.bed

http://68.181.92.180/~Gary/temporal/FstGLOB_CEU_u_YRI_u_CHB_score.bed

 

gary > head T8E_HMC.bed

chr1   9904   10699  MACS_peak_1   423

chr1   18930  19783  MACS_peak_2   105

chr1   136048 137344 MACS_peak_3   78

chr1   137658 139977 MACS_peak_4   88

chr1   249900 250725 MACS_peak_5   53

chr1   384125 385021 MACS_peak_6   68

chr1   385631 386751 MACS_peak_7   57

chr1   436628 437252 MACS_peak_8   146

chr1   439522 440031 MACS_peak_9   97

chr1   451114 451947 MACS_peak_10  68

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