error

[robeach78]

I am getting this error:

DGKNH0G1F8J7:data rferrari$ ./ExoProfiler.sh k1.bed ESR1.tf sorted_combined_T30_ChIP_exo_PR_14282_CGATGT.bam
ERROR:suds.client:
<SOAP-ENV:Envelope xmlns:ns0="http://schemas.xmlsoap.org/soap/envelope/" xmlns:ns1="urn:RSATWS" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/">
SOAP-ENV:Header/
ns0:Body
ns1:compare_matrices

both
<matrix_1>AC MA0112.3
XX
ID ESR1
XX
DE MA0112.3 ESR1; from JASPAR
P0 A C G T
1 232 65 101 88
2 402 6 206 0
3 0 0 623 34
4 2 0 638 0
5 0 0 3 549
6 1 452 0 2
7 471 0 30 0
8 108 338 53 23
9 127 223 340 65
10 235 88 284 13
11 0 23 1 510
12 2 0 632 0
13 491 1 1 0
14 0 460 2 0
15 15 455 0 0
16 0 143 7 502
17 35 68 209 204
XX
CC program: jaspar
CC matrix.nb: 1
CC consensus.strict: aaGGTCAcggTGACCTg
CC consensus.strict.rc: CAGGTCACCGTGACCTT
CC consensus.IUPAC: arGGTCAcsrTGACCTk
CC consensus.IUPAC.rc: MAGGTCAYSGTGACCYT
CC consensus.regexp: a[ag]GGTCAc[cg][ag]TGACCT[gt]
CC consensus.regexp.rc: [AC]AGGTCA[CT][CG]GTGACC[CT]T
XX
//
</matrix_1>
<matrix_2>AC MA0112.3_perm1
XX
ID MA0112.3_perm1
XX
DE GTAsTaCCGrrTkACGc
P0 A C G T
1 2 0 632 0
2 0 143 7 502
3 471 0 30 0
4 127 223 340 65
5 0 0 3 549
6 232 65 101 88
7 15 455 0 0
8 0 460 2 0
9 2 0 638 0
10 235 88 284 13
11 402 6 206 0
12 0 23 1 510
13 35 68 209 204
14 491 1 1 0
15 1 452 0 2
16 0 0 623 34
17 108 338 53 23
XX
CC residue_type:
CC program: transfac
CC matrix.nb: 1
CC accession: MA0112.3_perm1
CC AC: MA0112.3_perm1
CC id: MA0112.3
CC name: MA0112.3_perm1
CC version:
CC name: MA0112.3_perm1
CC description:
CC transfac_consensus:
CC matrix.nb: 1
CC consensus.strict: GTAgTaCCGgaTgACGc
CC consensus.strict.rc: GCGTCATCCGGTACTAC
CC consensus.IUPAC: GTAsTaCCGrrTkACGc
CC consensus.IUPAC.rc: GCGTMAYYCGGTASTAC
CC consensus.regexp: GTA[cg]TaCCG[ag][ag]T[gt]ACGc
CC consensus.regexp.rc: GCGT[AC]A[CT][CT]CGGTA[CG]TAC
XX
//
</matrix_2>
transfac
transfac
DR
matrix_number,Ncor
Ncor 0.4

</ns1:compare_matrices>
</ns0:Body>
</SOAP-ENV:Envelope>
Traceback (most recent call last):
File "../00_matrixScanWS/matrixScanWS.py", line 372, in
result = call_compare_matrices_2sets(rsat_service, matrix, one_perm_matrix, Ncor_threshold)
File "../00_matrixScanWS/matrixScanWS.py", line 219, in call_compare_matrices_2sets
return perform_compare_matrices(service, arguments_comp)
File "../00_matrixScanWS/matrixScanWS.py", line 185, in perform_compare_matrices
result = service.compare_matrices(args)
File "/Library/Python/2.7/site-packages/suds-0.4-py2.7.egg/suds/client.py", line 542, in call
return client.invoke(args, kwargs)
File "/Library/Python/2.7/site-packages/suds-0.4-py2.7.egg/suds/client.py", line 602, in invoke
result = self.send(soapenv)
File "/Library/Python/2.7/site-packages/suds-0.4-py2.7.egg/suds/client.py", line 649, in send
result = self.failed(binding, e)
File "/Library/Python/2.7/site-packages/suds-0.4-py2.7.egg/suds/client.py", line 702, in failed
r, p = binding.get_fault(reply)
File "/Library/Python/2.7/site-packages/suds-0.4-py2.7.egg/suds/bindings/binding.py", line 265, in get_fault
raise WebFault(p, faultroot)
suds.WebFault: Server raised fault: 'Execution error: Smartmatch is experimental at /workspace/rsat/perl-scripts/lib/RSA2.cgi.lib line 3170.
Smartmatch is experimental at /workspace/rsat/perl-scripts/lib/RSA2.cgi.lib line 3170.
command: /workspace/rsat/perl-scripts/compare-matrices -file1 '/workspace/rsat/public_html/tmp/www-data/2018/03/01/compare-matrices_infile1_2018-03-01.132210_jLpjm8' -file2 '/workspace/rsat/public_html/tmp/www-data/2018/03/01/compare-matrices_infile2_2018-03-01.132210_qzNOHY' -format1 'transfac' -format2 'transfac' -strand 'DR' -return 'matrix_number,Ncor' -lth 'Ncor' '0.4' -o '/workspace/rsat/public_html/tmp/compare-matrices.2018-03-01.132210/.tab''
INFO: Read 836 of 1240 input regions.
INFO: Begin to parse reads from BAM file for n=836 regions.
INFO: Finished parsing of BAM file.
../01_5primeCounter/5PrimeCounter.py:367: VisibleDeprecationWarning: using a non-integer number instead of an integer will result in an error in the future
ext_consensus = before * '.' + consenus + after * '.'
INFO: Read 836 of 1240 input regions.
INFO: Begin to parse reads from BAM file for n=836 regions.
INFO: Finished parsing of BAM file.
../01_5primeCounter/5PrimeCounter.py:367: VisibleDeprecationWarning: using a non-integer number instead of an integer will result in an error in the future
ext_consensus = before * '.' + consenus + after * '.'
Traceback (most recent call last):
File "../01_5primeCounter/5PrimeCounter.py", line 458, in
sites = parse_matrix_scan(file_to_analyze)
File "../01_5primeCounter/5PrimeCounter.py", line 93, in parse_matrix_scan
for line in open(inFile):
IOError: [Errno 2] No such file or directory: './output_matrix_k1.bed_scan_0-001_perm1.txt'
INFO: Read 836 of 1240 input regions.
INFO: Begin to parse reads from BAM file for n=836 regions.
INFO: Finished parsing of BAM file.
INFO: Begin to fetch sequences....
INFO: Finished sequences.
[1] "output_k1.bed_5PrimeCounter_wperm" "perm"
[1] FALSE
[1] TRUE
null device
1
Error in data.frame(all_perm_files_up, all_perm_files_down, as.is = TRUE) :
arguments imply differing number of rows: 0, 1
Calls: apply -> data.frame
Execution halted
[1] "output_k1.bed_5PrimeCounter"
[1] FALSE
[1] FALSE
null device
1
[1] "output_k1.bed_5PrimeCounter_wgenome" "genome_seq"
[1] TRUE
[1] FALSE
null device
1
null device
1
DGKNH0G1F8J7:data rferrari$