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View Code? Open in Web Editor NEWReimplementation of DIANA to leverage lessons learnt and new Panther data server.
License: Apache License 2.0
Reimplementation of DIANA to leverage lessons learnt and new Panther data server.
License: Apache License 2.0
Hello,
I'm trying to run diana-1.0.0 with the tutorial files. However I'm getting the following error:
INFO Attempting to run java -jar '/bin/diana/bin/jar/DianaExtractor-0.3.0.jar' --ms-resolution=20 --mode=uniform --dia-windows=gillet --isotopes=3 --out-dir='~/Desktop/DIANA_BASE/diana-tutorial/gold_std_120225_009.mzML' 'input/gold_std_120225_009.mzML.gz' input/target_345_aquas.traml input/decoy_345_aquas.traml input/irt-kit-final.traml
DEBUG java stdout:
DianaExtractor 0.3.0
swath mzML file: input/gold_std_120225_009.mzML.gz
num isotopes: 3
sub sample ms1: 1
force: true
max diff PPM: 20
max diff Da: 0.0
extraction mode: uniform
traML files:
input/target_345_aquas.traml
input/decoy_345_aquas.traml
input/irt-kit-final.traml
HANDLING FILE input/gold_std_120225_009.mzML.gz
num spectra: 78012
| |
|====================|
DONE WITH input/gold_std_120225_009.mzML.gz
heap size before writing: 1073 / 2330 Mb
writing output file: ~/Desktop/DIANA_BASE/diana-tutorial/gold_std_120225_009.mzML/target_345_aquas.chrom.mzML
DEBUG java stderr:
Exception in thread "main" java.io.FileNotFoundException: ~/Desktop/DIANA_BASE/diana-tutorial/gold_std_120225_009.mzML/target_345_aquas.chrom.mzML (No such file or directory)
at java.io.FileOutputStream.open(Native Method)
at java.io.FileOutputStream.<init>(FileOutputStream.java:221)
at java.io.FileOutputStream.<init>(FileOutputStream.java:171)
at java.io.FileWriter.<init>(FileWriter.java:90)
at se.lth.immun.diana.DianaExtractor$$anonfun$handleSwathFile$1.apply$mcVI$sp(DianaExtractor.scala:299)
at scala.collection.immutable.Range.foreach$mVc$sp(Range.scala:142)
at se.lth.immun.diana.DianaExtractor$.handleSwathFile(DianaExtractor.scala:276)
at se.lth.immun.diana.DianaExtractor$.main(DianaExtractor.scala:224)
at se.lth.immun.diana.DianaExtractor.main(DianaExtractor.scala)
WARNI java failed with exit code 1
#%&8! ANALYSIS FAILED IN SECTION CHROMATOGRAM EXTRACT AND SCORE
===============================================================
Traceback (most recent call last):
File "/bin/diana/bin/diana", line 384, in <module>
sectionLog.toFile(dianaRunID + ".section.csv")
File "/bin/diana/bin/diana", line 148, in toFile
f = open(os.path.join(analysisDir, path), "w")
IOError: [Errno 2] No such file or directory: '~/Desktop/DIANA_BASE/diana-tutorial/2016-06-20-12_29_07-DIANA_RUN.section.csv'
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