an error

[Sunnysum]

I have installed ocaml and used the command make,but it occured an error:
Cannot set stack reserve: File "coff.ml", line 946, characters 4-10: Assertion failed

[sdjebali]

This is weird as there is no coff.ml file in my code have you tried to used the precompiled binary available here? https://github.com/sdjebali/Comptr/blob/master/comptr

…

On Fri, Aug 23, 2019 at 3:46 PM Sunnysum ***@***.***> wrote: I have installed ocaml and used the command make,but it occured an error: Cannot set stack reserve: File "coff.ml", line 946, characters 4-10: Assertion failed — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#1?email_source=notifications&email_token=AATLUAPMKD2ZQJYOOBYIKBTQF7S2DA5CNFSM4IO7ZXU2YY3PNVWWK3TUL52HS4DFUVEXG43VMWVGG33NNVSW45C7NFSM4HHBPQPA>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AATLUALV3NHMVX7AMZRREP3QF7S2DANCNFSM4IO7ZXUQ> .

-- *********************************************************** Sarah Djebali - PhD INRA GenPhySE, ch. de Borderouge 31326 Castanet-Tolosan, France Tel. +33 5 61 28 51 22 sarah.djebali-quelen at inra dot fr

[Sunnysum]

I haven't used ocaml before , I run ocaml on windows and I just try :

$ comptr
-bash: comptr: command not found

$ ocaml comptr
File ".\comptr", line 1, characters 0-1:
1 | ELF>▒&A@@▒
@@# @@@@@▒@@@@▒▒ ▒▒kh▒kh▒▒▒▒ hhlhhlh▒@@ddp▒td0▒0▒F0▒F▒E▒EQ▒td
^
Error: Illegal character (\127)

[sdjebali]

Unfortunately comptr will not work under windows, it is made for unix systems.. Sorry about that

…

On Sat, Aug 24, 2019 at 3:32 AM Sunnysum ***@***.***> wrote: I haven't used ocaml before , I run ocaml on windows and I just try : $ comptr -bash: comptr: command not found $ ocaml comptr File ".\comptr", line 1, characters 0-1: 1 | ELF>▒&A@@▒ @@# @@@@@▒@@@@▒▒ ▒▒kh▒kh▒▒▒▒ hhlhhlh▒@@ddp <https://github.com/ddp> ▒td0▒0▒F0▒F▒E▒EQ▒td ^ Error: Illegal character (\127) — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#1?email_source=notifications&email_token=AATLUAPWUAX5A3VA72XFZOTQGCFRNA5CNFSM4IO7ZXU2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD5BVDQA#issuecomment-524505536>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AATLUANX2SLE5G4YVYBFY7LQGCFRNANCNFSM4IO7ZXUQ> .

-- *********************************************************** Sarah Djebali - PhD INRA GenPhySE, ch. de Borderouge 31326 Castanet-Tolosan, France Tel. +33 5 61 28 51 22 sarah.djebali-quelen at inra dot fr

[sdjebali]

in file1 the separator should be a tab not a pipe

…

On Mon, Aug 26, 2019 at 11:50 AM syyya ***@***.***> wrote: I run it on unix , but it occured another error: Command line has been read Input file1 is /home/Comptr-master/data/file2.gtf Input file2 is /home/Comptr-master/data/file1.gtf I have treated (sorted and put in temp file) the input files according to what the user wants Hashtbl of transcripts has 83844 keys/transcripts Incorrectly formatted gtf file with not even 3 fields separated by tabs! and data in my file1 : chr1 | StringTie | transcript | 17611 | 24868 | 1000 | - | . | gene_id "STRG.3"; transcript_id "STRG.3.1"; cov "7.262026"; FPKM "1.297164"; TPM "1.997384"; -- | -- | -- | -- | -- | -- | -- | -- | -- data in my file2 : chr1 transcript 120241 181157 0 - . transcript_id "compmerge.4078.Brain.chr1"; What is wrong with my data format? thanks! — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#1?email_source=notifications&email_token=AATLUAP6RCRFI3QTZOB4EP3QGORPVA5CNFSM4IO7ZXU2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD5D4QNY#issuecomment-524798007>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AATLUAMZSX6O7ZENQNMQUE3QGORPVANCNFSM4IO7ZXUQ> .

-- *********************************************************** Sarah Djebali - PhD INRA GenPhySE, ch. de Borderouge 31326 Castanet-Tolosan, France Tel. +33 5 61 28 51 22 sarah.djebali-quelen at inra dot fr

[Sunnysum]

I run “./comptr file1.gtf file1.gtf” ,it worked,so I think there are some problems with file 2,but I can’t find it.

data in my file1 :
chr1 StringTie transcript 17369 17436 1000 - . gene_id "STRG.1"; transcript_id "STRG.1.1"; reference_id "ENST00000619216.1"; ref_gene_id "ENSG00000278267.1"; ref_gene_name "MIR6859-2"; cov "1.278520"; FPKM "0.228373"; TPM "0.351651";

data in my file2 :
chr1 transcript 120241 181157 0 - . transcript_id "compmerge.4078.Brain.chr1";

Error when I run :
./comptr file1.gtf file2.gtf

Command line has been read

Input file1 is /home/liusiyu/Comptr-master/data/brain2.gtf

Input file2 is /home/liusiyu/Comptr-master/data/brain1.gtf

I have treated (sorted and put in temp file) the input files according to what the user wants

Hashtbl of transcripts has 83844 keys/transcripts

Incorrectly formatted gtf file with not even 3 fields separated by tabs!

thanks!

[sdjebali]

filed no 2 (source) is missing in your input file2 it should be chr1 <mypgm> transcript 120241 181157 0 - . transcript_id "compmerge.4078.Brain.chr1"; and not chr1 transcript 120241 181157 0 - . transcript_id "compmerge.4078.Brain.chr1";

…

On Mon, Aug 26, 2019 at 1:08 PM syyya ***@***.***> wrote: I run “./comptr file1.gtf file1.gtf” ,it worked,so I think there are some problems with file 2,but I can’t find it. data in my file1 : chr1 StringTie transcript 17369 17436 1000 - . gene_id "STRG.1"; transcript_id "STRG.1.1"; reference_id "ENST00000619216.1"; ref_gene_id "ENSG00000278267.1"; ref_gene_name "MIR6859-2"; cov "1.278520"; FPKM "0.228373"; TPM "0.351651"; data in my file2 : chr1 transcript 120241 181157 0 - . transcript_id "compmerge.4078.Brain.chr1"; Error when I run : ./comptr file1.gtf file2.gtf Command line has been read Input file1 is /home/liusiyu/Comptr-master/data/brain2.gtf Input file2 is /home/liusiyu/Comptr-master/data/brain1.gtf I have treated (sorted and put in temp file) the input files according to what the user wants Hashtbl of transcripts has 83844 keys/transcripts Incorrectly formatted gtf file with not even 3 fields separated by tabs! thanks! — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#1?email_source=notifications&email_token=AATLUAP7GEXJ7CKEU7QI2STQGO2S3A5CNFSM4IO7ZXU2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD5EBUKA#issuecomment-524818984>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AATLUAPZZTTCUYJCZTS3PILQGO2S3ANCNFSM4IO7ZXUQ> .

-- *********************************************************** Sarah Djebali - PhD INRA GenPhySE, ch. de Borderouge 31326 Castanet-Tolosan, France Tel. +33 5 61 28 51 22 sarah.djebali-quelen at inra dot fr

[Sunnysum]

Hello,
I added the gene_id in the last column,then it worked.
could you explain the specific meaning of these outputs? What does each type mean?
My output:
['compmerge.0.Brain.chr1;']
['', 'Intergenic_or_antisense', '.']

['compmerge.5.Brain.chr1;']
['', 'Exact', 'STRG.40.1;,']

['compmerge.3.Brain.chr1;']
['', 'Overlap', 'STRG.40.1;,']
...
there are six types :Intergenic_or_antisense、extension、exact、overlap、inclusion、monoexonic.
Thank you!

[sdjebali]

Hi, in the help of the tool (typing comptr with no option for examople) there is an explanation of the different outputs Here is what it says The output classes are the following and are chosen in the following order in case of multiple possible assignments: - Unstranded: the assessed transcript is unstranded, - Monoexonic: the assessed transcript is mono-exonic, - Intergenic_or_antisense: the assessed transcript is stranded and spliced but does not strandedly overlap any reference transcript, - Exact: there is a reference transcript with all its introns equal to the assessed transcript and reciprocally, - Inclusion: there is a reference transcript with a subset of introns corresponding to all introns of the assessed transcript, - Extension: there is a reference transcript with all its introns equal to the assessed transcript but the assessed transcript has additional introns, - Overlap: there is a reference transcript overlapped by the assessed transcript Best, Sarah

…

On Fri, Sep 6, 2019 at 3:44 AM syyya ***@***.***> wrote: Hello, I added the gene_id in the last column,then it worked. could you explain the specific meaning of these outputs? What does each type mean? My output: ['compmerge.0.Brain.chr1;'] ['', 'Intergenic_or_antisense', '.'] ['compmerge.5.Brain.chr1;'] ['', 'Exact', 'STRG.40.1;,'] ['compmerge.3.Brain.chr1;'] ['', 'Overlap', 'STRG.40.1;,'] ... there are six types :Intergenic_or_antisense、extension、exact、overlap、inclusion、monoexonic. Thank you! — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#1?email_source=notifications&email_token=AATLUAJ5IIIDUCATMPB3MO3QIGYYFA5CNFSM4IO7ZXU2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD6BOQ7Y#issuecomment-528672895>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AATLUAPZMHTUKIAPOYEKSFTQIGYYFANCNFSM4IO7ZXUQ> .

-- *********************************************************** Sarah Djebali - PhD INRA GenPhySE, ch. de Borderouge 31326 Castanet-Tolosan, France Tel. +33 5 61 28 51 22 sarah.djebali-quelen at inra dot fr