CIMS.pl detected inconsistency... (2)

[kotee...@gmail.com]

Hi. 

I'm now using CIMS.pl, but have some trouble now.

First, I successfully collapsed PCR duplicate.

$ perl /usr/local/CTK/tag2collapse.pl -big -v --random-barcode -EM 30 --seq-error-model alignment -weight --weight-in-name --keep-max-score --keep-tag-name bTG.tag.norRNA.bed bTG.tag.uniq.bed

Then, I got mutations in unique tags.

$ python /usr/local/CTK/joinWrapper.py bTG.mut.txt bTG.tag.uniq.bed 4 4 N bTG.tag.uniq.mutation.txt

Then, I got substitution.

$ perl /usr/local/CTK/getMutationType.pl -t sub bTG.tag.uniq.mutation.txt bTG.tag.uniq.sub.bed

Finally, I used CIMS, but it detected inconsistency...

$ perl /usr/local/CTK/CIMS.pl -n 10 -p -outp bTG.tag.uniq.sub.pos.stat.txt -v bTG.tag.uniq.bed bTG.tag.uniq.sub.bed bTG.tag.uniq.sub.CIMS.txt

The error message is shown below.

Inconsistency detected between the tag file and the mutation file. Make sure the NAME column of the two files use the same IDs

 at /usr/local/CTK/CIMS.pl line 129.

I think the mutation file <bTG.tag.uniq.sub.bed> is originated from the tag file <bTG.tag.uniq.bed>. Why is there an inconsistency? Do you have some idea?

The two inconsistent files are here.

-----

$ head bTG.tag.uniq.bed

chr1    564463    564505    2192730_TTA_181/2#181#TAA    4021.08    +    564463    564505    0    1    42    0

chr1    564463    564503    2192730_TTA_181/1#181#TTA    3992.24    +    564463    564503    0    1    40    0

chr1    564463    564495    3103811_GAT_49/2#49#ATC    1196.26    +    564463    564495    0    1    32    0

chr1    564463    564493    3103811_GAT_49/1#49#GAT    1196.26    +    564463    564493    0    1    30    0

chr1    564463    564526    5241671_ATT_23/1#23#ATT    426.47    +    564463    564526    0    1    63    0

chr1    564463    564528    5241671_ATT_23/2#23#AAT    426.45    +    564463    564528    0    1    65    0

chr1    564463    564531    4004294_GAA_12/2#12#TTC    87.73    +    564463    564531    0    1    68    0

chr1    564463    564531    4004294_GAA_12/1#12#GAA    87.53    +    564463    564531    0    1    68    0

chr1    564463    564509    2834919_TAC_8/2#8#GTA    51.59    +    564463    564509    0    1    46    0

chr1    564463    564507    2834919_TAC_8/1#8#TAC    51.42    +    564463    564507    0    1    44    0

$ head bTG.tag.uniq.sub.bed

chr16    33966061    33966062    1000089_AAT_1/1#1#AAT    17    +

chr19    7677554    7677555    1000095_GCA_1/2#1#TGC    46    +

chr16    89225651    89225652    1000096_TAA_1/1#1#TAA    20    +

chr16    89225651    89225652    1000096_TAA_1/2#1#TTA    19    +

chr12    7032399    7032400    1000098_TAC_1/2#1#GTA    6    +

chr8    145137577    145137578    1000111_ATA_78/1#78#ATA    1    +

chr21    28515643    28515644    1000116_AAC_1/1#1#AAC    1    -

chr11    118771416    118771417    1000124_ATA_6/2#6#TAT    1    -

chr1    16029265    16029266    1000142_TAA_3/2#3#TTA    69    +

chr1    566311    566312    1000175_AAC_1/2#1#GTT    49    +

-----

I am always grateful for your help !!

Thank you!!

Best,

 Koteen

[fenghui...@gmail.com]

Hi Koteen,

The CIMS.pl program will re-evaluate if the number of substitution in the "bTG.tag.uniq.sub.bed" and the number of unique tags covering the substitution are equal or not, if not, the error message  "Inconsistency detected between the tag file and the mutation file. Make sure the NAME column of the two files use the same IDs" will show up. 

In this case, I would suggest go back and check if the id name in your uniq tag file is unique or not. if it's not, CIMS.pl will usually get more numbers than the substitution number and this will raise this error. 

Best,

Huijuan

[kotee...@gmail.com]

Hi Huijuan,

Thank you !!

[Cris Mar]

Hello Huijuan,

I have the same exact problem and checked everything suggested in this response, the files, name IDs look fine (unique).

I also followed the suggestions from here: https://zhanglab.c2b2.columbia.edu/index.php/CTK_FAQ "for CIMS.pl complains of inconsistency of files ends unexpectedly" but still getting the error.

CMD = CIMS.pl -big -n 10 -p -outp Protein1.pool.tag.uniq.del.pos.stat.txt -v Protein1.pool.tag.uniq.rgb.bed Protein1.pool.tag.uniq.del.bed Protein1.pool.tag.uniq.del.CIMS.txt
clean mutations ...
5274 mutations of size 1 found

generating CIMS position file /Volumes/CrisPassportMac/cache/CIMS.pl_1593400876_0.95884091088465/mutation.pos.txt...

sort -k 4,4 /Volumes/CrisPassportMac/cache/CIMS.pl_1593400876_0.95884091088465/mutation.clean.bed > /Volumes/CrisPassportMac/cache/CIMS.pl_1593400876_0.95884091088465/mutation.bed

cut -f 4 /Volumes/CrisPassportMac/cache/CIMS.pl_1593400876_0.95884091088465/mutation.bed | awk -F "[" '{print $1}' > /Volumes/CrisPassportMac/cache/CIMS.pl_1593400876_0.95884091088465/mutation.id

python /usr/local/CTK/joinWrapper.py Protein1.pool.tag.uniq.rgb.bed /Volumes/CrisPassportMac/cache/CIMS.pl_1593400876_0.95884091088465/mutation.id 4 1 N /Volumes/CrisPassportMac/cache/CIMS.pl_1593400876_0.95884091088465/tmp
  File "/usr/local/CTK/joinWrapper.py", line 57
    except Exception, exc:
                    ^
SyntaxError: invalid syntax
CMD=python /usr/local/CTK/joinWrapper.py Protein1.pool.tag.uniq.rgb.bed /Volumes/CrisPassportMac/cache/CIMS.pl_1593400876_0.95884091088465/mutation.id 4 1 N /Volumes/CrisPassportMac/cache/CIMS.pl_1593400876_0.95884091088465/tmp failed: 256
wc: /Volumes/CrisPassportMac/cache/CIMS.pl_1593400876_0.95884091088465/tmp: open: No such file or directory
Argument "" isn't numeric in numeric ne (!=) at /usr/local/CTK/CIMS.pl line 129.

Inconsistency detected between the tag file and the mutation file. Make sure the NAME column of the two files use the same IDs
 at /usr/local/CTK/CIMS.pl line 129.

Thanks for any insight!

Cris

[Cris]

Hi,

I figured it out. Everything was done correctly according to the suggestions.

The problem was that I was changing between conda environments (to use python 2.7 for joinwrapper.py) but hadn't installed bio:perl in that environment to run CIMS and CITS.pl files.

Just in case someone runs into the same problem.

Cris

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