def validate_run(self, log, info, run_code, out):
if "No decoys with label DECOY_ were found" in out:
raise RuntimeError("No DECOY_s found in fasta. Please use other fasta!")
validation.check_stdout(log, out)
validation.check_exitcode(log, run_code)
validation.check_xml(log, info[Keys.PEPXML])
return info
def validate_run(self, log, info, exit_code, stdout):
validation.check_stdout(log,stdout)
validation.check_exitcode(log, exit_code)
validation.check_file(log, info['SPLIB'])
validation.check_file(log, info['TSV'])
validation.check_xml(log, info['TRAML'])
return info
def validate_run(self, log, info, exit_code, stdout):
if 'max_rt_diff = self._stdev_max_rt_per_run * tr_data.getStdev(source, target)' in stdout:
raise RuntimeError("No peptides found which are shared between all runs. Try to increase 'alignment_score'.")
validation.check_stdout(log, stdout)
validation.check_exitcode(log, exit_code)
validation.check_file(log, info['ALIGNMENT_TSV'])
validation.check_file(log, info['ALIGNMENT_YAML'])
out2log = os.path.join(info[Keys.WORKDIR], "feature_alignment.out.txt")
f = open(out2log, "w")
f.write(stdout)
f.close()
info["ALIGNER_STDOUT"] = out2log
# Move out .tr files of pyprophet to be rescue safe
info["TRAFO_FILES"] = []
for fil in info["MPROPHET_TSV"]:
trfile = glob.glob(os.path.dirname(fil) + "/*.tr")
if len(trfile) != 1:
raise RuntimeError("More than one .tr file for " + fil)
basename = os.path.basename(trfile[0])
tgt = os.path.join(info['WORKDIR'], basename)
log.debug("Moved tr file %s into WORKDIR" % basename)
shutil.move(trfile[0], tgt)
info["TRAFO_FILES"].append(tgt)
return info
def validate_run(self, log, info, run_code, out):
for line in out.splitlines():
if "OpenMS peak type estimation indicates that this is not profile data!" in line:
raise RuntimeError("Found centroid data but LFQ must be run on profile mode data!")
validation.check_stdout(log, out)
validation.check_exitcode(log, run_code)
validation.check_xml(log, info['FEATUREXML'])
return info
def validate_run(self, log, info, run_code, out):
if "No decoys with label DECOY_ were found" in out:
raise RuntimeError(
"No DECOY_s found in fasta. Please use other fasta!")
validation.check_stdout(log, out)
validation.check_exitcode(log, run_code)
validation.check_xml(log, info[Keys.PEPXML])
return info
def validate_run(self, log, info, exit_code, stdout):
if "Warning - no spectra searched" in stdout:
raise RuntimeError("No spectra in mzXML!")
if "CometMemAlloc" in stdout:
#print to stdout to reach gUSE rescue functionality. ugly, no?
print "MemoryError"
raise RuntimeError("The job run out of RAM!")
check_stdout(log,stdout)
check_exitcode(log, exit_code)
check_xml(log, info[Keys.PEPXML])
return info
def validate_run(self, log, info, exit_code, stdout):
if "ERROR [root] Parsing </precursorMz> failed. scan number" in stdout:
raise ValueError("the chosen mzXML %s file contains "
"MS2 spectra without precursor information" %
info.get("MZXML"))
validation.check_stdout(log, stdout)
validation.check_exitcode(log, exit_code)
info["MD5_SUMS"] = []
for p in info["Q_FILES"]:
validation.check_file(log, p)
md5sum = open(p + ".md5", "r").read().split(" ")[0].strip()
info["MD5_SUMS"].append(md5sum)
return info
def validate_run(self, log, info, exit_code, stdout):
if "ERROR [root] Parsing </precursorMz> failed. scan number" in stdout:
raise ValueError("the chosen mzXML %s file contains "
"MS2 spectra without precursor information" % info.get("MZXML")
)
validation.check_stdout(log, stdout)
validation.check_exitcode(log, exit_code)
info["MD5_SUMS"] = []
for p in info["Q_FILES"]:
validation.check_file(log, p)
md5sum = open(p + ".md5", "r").read().split(" ")[0].strip()
info["MD5_SUMS"].append(md5sum)
return info
def validate_run(self, log, info, exit_code, stdout):
if "Warning - no spectra searched" in stdout:
raise RuntimeError("No spectra in mzXML!")
if "CometMemAlloc" in stdout:
#print to stdout to reach gUSE rescue functionality. ugly, no?
print "MemoryError"
raise RuntimeError("The job run out of RAM!")
check_stdout(log,stdout)
if exit_code:
log.warn("exit_code is %s", exit_code)
mzxml = info[Keys.MZXML]
log.warn("maybe the input file %s does not exist any more. check this !" % mzxml)
check_exitcode(log, exit_code)
check_xml(log, info[Keys.PEPXML])
return info
def validate_run(self, log, info, exit_code, stdout):
if "Warning - no spectra searched" in stdout:
raise RuntimeError("No spectra in mzXML!")
if "CometMemAlloc" in stdout:
#print to stdout to reach gUSE rescue functionality. ugly, no?
print "MemoryError"
raise RuntimeError("The job run out of RAM!")
check_stdout(log, stdout)
if exit_code:
log.warn("exit_code is %s", exit_code)
mzxml = info[Keys.MZXML]
log.warn(
"maybe the input file %s does not exist any more. check this !"
% mzxml)
check_exitcode(log, exit_code)
check_xml(log, info[Keys.PEPXML])
return info
def validate_run(self, log, info, exit_code, stdout):
validation.check_stdout(log, stdout)
validation.check_exitcode(log, exit_code)
base = os.path.join(info[Keys.WORKDIR], os.path.splitext(os.path.basename(info['FEATURETSV']))[0])
info['MPROPHET_TSV'] = base + "_with_dscore_filtered.csv"
validation.check_file(log, info['MPROPHET_TSV'])
prophet_stats = []
for end in ["_full_stat.csv", "_scorer.bin", "_weights.txt", "_report.pdf", "_dscores_top_target_peaks.txt",
"_dscores_top_decoy_peaks.txt"]:
f = base + end
if os.path.exists(f):
prophet_stats.append(f)
if prophet_stats:
info['MPROPHET_STATS'] = prophet_stats
return info
def validate_run(self, log, info, exit_code, stdout):
validation.check_stdout(log, stdout)
validation.check_exitcode(log, exit_code)
base = os.path.join(
info[Keys.WORKDIR],
os.path.splitext(os.path.basename(info['FEATURETSV']))[0])
info['MPROPHET_TSV'] = base + "_with_dscore_filtered.csv"
validation.check_file(log, info['MPROPHET_TSV'])
prophet_stats = []
for end in [
"_full_stat.csv", "_scorer.bin", "_weights.txt", "_report.pdf",
"_dscores_top_target_peaks.txt", "_dscores_top_decoy_peaks.txt"
]:
f = base + end
if os.path.exists(f):
prophet_stats.append(f)
if prophet_stats:
info['MPROPHET_STATS'] = prophet_stats
return info
def validate_run(self, log, info, exit_code, stdout):
validation.check_stdout(log, stdout)
validation.check_exitcode(log, exit_code)
validation.check_file(log, info['ALIGNMENT_MATRIX'])
return info
def validate_run(self, log, info, exit_code, stdout):
validation.check_stdout(log, stdout)
validation.check_exitcode(log, exit_code)
if info.get('DO_CHROMML_REQUANT', "") != "false":
validation.check_file(log, info['REQUANT_TSV'])
return info
def validate_run(self, log, info, exit_code, stdout):
validation.check_exitcode(log, exit_code)
validation.check_stdout(log, stdout)
validation.check_xml(log, info[Keys.PEPXML])
return info
def validate_run(self, log, info, exit_code, stdout):
validation.check_stdout(log, stdout)
validation.check_exitcode(log, exit_code)
if info.get('DO_CHROMML_REQUANT', "") != "false":
validation.check_file(log, info['REQUANT_TSV'])
return info
def validate_run(self, log, info, exit_code, stdout):
validation.check_exitcode(log, exit_code)
validation.check_stdout(log, stdout)
return info
def validate_run(self, log, info, exit_code, stdout):
validation.check_exitcode(log, exit_code)
validation.check_stdout(log, stdout)
return info
def validate_run(self, log, info, exit_code, stdout):
validation.check_stdout(log,stdout)
validation.check_exitcode(log, exit_code)
validation.check_file(log, info['ALIGNMENT_MATRIX'])
return info
def validate_run(self, log, info, exit_code, stdout):
validation.check_exitcode(log, exit_code)
validation.check_stdout(log,stdout)
validation.check_xml(log, info[Keys.PEPXML])
return info
