python coltron-1.0.2/coltron/crc.py -e MB12_H3K27ac_peaks_noEncBlack_AllEnhancers.table.txt -b tumor_MB12_H3K27ac_CAGATC_merged.rmdup_sub.bam -g HG19 -n MB12 -o MB12/
Following errors were occurred
/bin/sh: bamliquidator_batch: command not found
bamliquidator_batch -r MB12/MB12_TSS.gff -o MB12/bamliquidator -m -e 200 /b06x-isilon/b06x-a/adshh/raw/ChiP-seq/MB12/MB12_H3K27ac_CAGATC/tumor_MB12_H3K27ac_CA
GATC_merged.rmdup_sub.bam
CREATING SUPER LOCUS COLLECTION
CREATING EXPRESSION DICTIONARY
Traceback (most recent call last):
File "coltron-1.0.2/coltron/crc.py", line 942, in <module>
main()
File "coltron-1.0.2/coltron/crc.py", line 911, in main
expressedNM, expressionDictNM = createExpressionDict(annotationFile, projectFolder, projectName, refseqToNameDict, expCutoff)
File "coltron-1.0.2/coltron/crc.py", line 182, in createExpressionDict
expressionTable = utils.parseTable(expresionFilename, '\t')
File "/b06x-isilon/b06x-a/adshh/scripts/tools/coltron-1.0.2/coltron/utils.py", line 132, in parseTable
fh = open(fn)
File "/b06x-isilon/b06x-a/adshh/scripts/tools/coltron-1.0.2/coltron/utils.py", line 124, in open
return bopen(fileName, mode)
IOError: [Errno 2] No such file or directory: 'MB12/bamliquidator/matrix.txt'
I pre-ran the bamliquidator_batch to generate MB12/bamliquidator/matrix.txt file. Then the tool continued calculation.
At line 852 - there was default path included in the script. I changed this to location in my machine to take the path of chr*.fa files.
GENERATING TF NETWORK
Number of annotated canidate TFs that have motifs: 30
folder MB12/FIMO/ does not exist
BARHL1
EN2
GLI2
INSM1
JUN
JUNB
KLF13
KLF7
LHX1
MAFF
MEF2D
MEIS1
NEUROD1
NFIB
NFIC
NFIX
NHLH1
NHLH2
NR2F1
NR2F2
NR4A2
PAX6
POU3F3
SCRT2
SOX4
UNCX
ZBTB7A
ZIC1
ZIC2
ZIC4
fimo --motif 'Transfac.V$BARHL1_04' --motif 'Transfac.V$BARHL1_05' --motif 'Transfac.V$BARHL1_03' --motif 'Homeodomain.UP00166_1' --motif 'Jolma2013.Barhl1_DBD' --motif 'Jolma2013.Barhl1_DBD_2' --motif 'Jolma2013.Barhl1_DBD_3' --motif 'Uniprobe.UP00166_1' --motif 'Transfac.V$BARHL1_01' --motif 'Transfac.V$EN2_03' --motif 'Homeodomain.UP00163_1' --motif 'Jolma2013.EN2_DBD' --motif 'Jolma2013.EN2_full' --motif 'Jolma2013.En2_DBD' --motif 'Uniprobe.UP00163_1' --motif 'Transfac.V$EN2_01' --motif 'Transfac.V$GLI2_01' --motif 'Transfac.V$GLI2_03' --motif 'Transfac.V$GLI2_04' --motif 'Jolma2013.GLI2_DBD' --motif 'Jolma2013.GLI2_DBD_2' --motif 'Transfac.V$INSM1_01' --motif 'JASPAR2014.MA0155.1' --motif 'Transfac.V$AP1_02' --motif 'Transfac.V$CJUN_Q6' --motif 'JASPAR2014.MA0488.1' --motif 'JASPAR2014.MA0489.1' --motif 'Transfac.V$JUNB_Q6' --motif 'JASPAR2014.MA0490.1' --motif 'Transfac.V$KLF13_01' --motif 'Transfac.V$BTEB3_Q5' --motif 'Jolma2013.KLF13_full' --motif 'Transfac.V$KLF7_04' --motif 'Transfac.V$KLF7_03' --motif 'Uniprobe.UP00093_1' --motif 'Uniprobe.UP00093_2' --motif 'Transfac.V$LIM1_01' --motif 'Homeodomain.UP00262_1' --motif 'Uniprobe.UP00262_1' --motif 'Transfac.V$MAFF_01' --motif 'JASPAR2014.MA0495.1' --motif 'Jolma2013.MAFF_DBD' --motif 'Transfac.V$MEF2D_01' --motif 'Jolma2013.MEF2D_DBD' --motif 'Transfac.V$MEIS1_04' --motif 'Transfac.V$MEIS1_02' --motif 'Transfac.V$MEIS1_01' --motif 'Homeodomain.UP00186_1' --motif 'JASPAR2014.MA0498.1' --motif 'Jolma2013.MEIS1_DBD' --motif 'Uniprobe.UP00186_1' --motif 'Transfac.V$NEUROD_02' --motif 'Transfac.V$NFIB_01' --motif 'Jolma2013.NFIB_full' --motif 'JASPAR2014.MA0161.1' --motif 'Transfac.V$NFIX_02' --motif 'Jolma2013.NFIX_full' --motif 'Transfac.V$NHLH1_02' --motif 'JASPAR2014.MA0048.1' --motif 'Jolma2013.NHLH1_DBD' --motif 'Jolma2013.NHLH1_full' --motif 'Transfac.V$HEN2_Q2' --motif 'Transfac.V$NR2F1_03' --motif 'Transfac.V$NR2F1_04' --motif 'Transfac.V$NR2F1_02' --motif 'JASPAR2014.MA0017.1' --motif 'Jolma2013.NR2F1_DBD' --motif 'Jolma2013.NR2F1_DBD_2' --motif 'Jolma2013.NR2F1_full' --motif 'Transfac.V$NR2F2_04' --motif 'Transfac.V$NR2F2_03' --motif 'Uniprobe.UP00009_1' --motif 'Uniprobe.UP00009_2' --motif 'Transfac.V$NR4A2_02' --motif 'Transfac.V$NURR1_Q3' --motif 'Transfac.V$NR4A2_04' --motif 'Transfac.V$NR4A2_01' --motif 'Transfac.V$NR4A2_03' --motif 'JASPAR2014.MA0160.1' --motif 'Jolma2013.NR4A2_full' --motif 'Jolma2013.NR4A2_full_2' --motif 'Jolma2013.NR4A2_full_3' --motif 'Transfac.V$PAX6_02' --motif 'Transfac.V$PAX6_05' --motif 'Homeodomain.UP00224_1' --motif 'JASPAR2014.MA0069.1' --motif 'Jolma2013.PAX6_DBD' --motif 'Uniprobe.UP00224_1' --motif 'Transfac.V$POU3F3_01' --motif 'Transfac.V$OCTAMER_01' --motif 'Transfac.V$POU3F3_02' --motif 'Transfac.V$POU3F3_03' --motif 'Transfac.V$POU3F3_04' --motif 'Transfac.V$BRN1_Q6' --motif 'Homeodomain.UP00211_1' --motif 'Jolma2013.POU3F3_DBD' --motif 'Jolma2013.POU3F3_DBD_2' --motif 'Jolma2013.POU3F3_DBD_3' --motif 'Uniprobe.UP00211_1' --motif 'Transfac.V$SCRT2_01' --motif 'Jolma2013.SCRT2_DBD' --motif 'Transfac.V$SOX4_03' --motif 'Transfac.V$SOX4_01' --motif 'Transfac.V$SOX4_Q5' --motif 'Transfac.V$SOX5_07' --motif 'Uniprobe.UP00062_1' --motif 'Uniprobe.UP00062_2' --motif 'Transfac.V$UNCX_02' --motif 'Transfac.V$UNCX_04' --motif 'Transfac.V$UNCX_05' --motif 'Transfac.V$UNCX_03' --motif 'Homeodomain.UP00142_1' --motif 'Jolma2013.UNCX_DBD' --motif 'Jolma2013.UNCX_DBD_2' --motif 'Jolma2013.Uncx_DBD' --motif 'Jolma2013.Uncx_DBD_2' --motif 'Uniprobe.UP00142_1' --motif 'Transfac.V$ZBTB7A_01' --motif 'Jolma2013.ZBTB7A_DBD' --motif 'Transfac.V$ZIC1_05' --motif 'Transfac.V$ZIC1_04' --motif 'Transfac.V$ZIC1_06' --motif 'Transfac.V$ZIC1_01' --motif 'Jolma2013.ZIC1_full' --motif 'Uniprobe.UP00102_1' --motif 'Uniprobe.UP00102_2' --motif 'Transfac.V$ZIC2_01' --motif 'Transfac.V$ZIC2_04' --motif 'Transfac.V$ZIC2_05' --motif 'Uniprobe.UP00057_1' --motif 'Uniprobe.UP00057_2' --motif 'Transfac.V$ZIC4_01' --motif 'Jolma2013.ZIC4_DBD' -verbosity 1 -text -oc MB12/FIMO --bgfile MB12/MB12_bg.meme coltron-1.0.2/coltron/data//annotation//VertebratePWMs.txt MB12/MB12_SUBPEAKS.fa > MB12/FIMO/fimo.txt
Warning: text mode turns off computation of q-values
Traceback (most recent call last):
File "coltron-1.0.2/coltron/crc.py", line 942, in <module>
main()
File "coltron-1.0.2/coltron/crc.py", line 931, in main
graph = buildGraph(projectFolder, projectName, motifConvertFile, refseqToNameDict, canidateGenes)
File "coltron-1.0.2/coltron/crc.py", line 617, in buildGraph
target = refseqToNameDict[region[0]] #gene name corresponding to the NMid
KeyError: 'AP1'
This is the same problem I encountered with CRCmapper.py tool here