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Failing in mecq stage #33

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DerangePsycho opened this issue Sep 24, 2019 · 0 comments
Open

Failing in mecq stage #33

DerangePsycho opened this issue Sep 24, 2019 · 0 comments

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@DerangePsycho
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quake V0.3
kat 1.69
jellyfish 2.3.0

I am currently working on rampart. I already installed all the dependencies. After that, i tried a test run on ecoli sample data and it already failed with mecq stage
Here is the command:

(base) hydra@Biohazard:~/Desktop/5_30_19-Try_rampart/190613$ rampart -v ecoli_full_job.xml

This is were the error starts:
`
2019-09-24 00:50:53 DEBUG ProcessRunner:153 - Return code was '0' for [ln -s -f /home/hydra/Desktop/5_30_19-Try_rampart/190613/rampart_out/1_mecq/quake/ecoli/DRR015910_2.cor_single.fastq /home/hydra/Desktop/5_30_19-Try_rampart/190613/rampart_out/1_mecq/output/quake/DRR015910_2.cor_single.fastq]. Redirecting stderr.
2019-09-24 00:50:53 DEBUG DefaultProcessService:162 - Finished executing command [ln -s -f /home/hydra/Desktop/5_30_19-Try_rampart/190613/rampart_out/1_mecq/quake/ecoli/DRR015910_2.cor_single.fastq /home/hydra/Desktop/5_30_19-Try_rampart/190613/rampart_out/1_mecq/output/quake/DRR015910_2.cor_single.fastq]. Output:

2019-09-24 00:50:53 ERROR Mecq:181 - MECQ job "quake" for sample "rampart_out" did not produce the expected output file: /home/hydra/Desktop/5_30_19-Try_rampart/190613/rampart_out/1_mecq/quake/ecoli/DRR015910_1.cor.fastq
2019-09-24 00:50:53 ERROR AbstractConanTask:255 - Process 'MECQ' failed to execute, exit code: 2
2019-09-24 00:50:53 ERROR AbstractConanTask:257 - Execution exception follows
uk.ac.ebi.fgpt.conan.service.exception.ProcessExecutionException: java.io.IOException: Stage MECQ failed to produce valid output.
at uk.ac.tgac.rampart.stage.RampartProcess.execute(RampartProcess.java:187)
at uk.ac.ebi.fgpt.conan.core.process.AbstractConanProcess.execute(AbstractConanProcess.java:298)
at uk.ac.ebi.fgpt.conan.core.task.AbstractConanTask.execute(AbstractConanTask.java:233)
at uk.ac.ebi.fgpt.conan.core.task.AbstractConanTask.execute(AbstractConanTask.java:32)
at uk.ac.ebi.fgpt.conan.util.AbstractConanCLI.execute(AbstractConanCLI.java:453)
at uk.ac.tgac.rampart.RampartCLI.execute(RampartCLI.java:421)
at uk.ac.tgac.rampart.RampartCLI.main(RampartCLI.java:453)
Caused by: java.io.IOException: Stage MECQ failed to produce valid output.
at uk.ac.tgac.rampart.stage.RampartProcess.execute(RampartProcess.java:158)
... 6 more
2019-09-24 00:50:53 DEBUG AbstractConanTask:258 - Is this event to abort: false Output: [Ljava.lang.String;@48f278eb
2019-09-24 00:50:53 ERROR AbstractConanTask:550 - Task 'RAMPART' failed its current process, exit code: 2
2019-09-24 00:50:53 ERROR AbstractConanTask:556 - Output follows...
No output captured

2019-09-24 00:50:53 INFO AbstractConanTask:288 - Task 'RAMPART' execution ended. Runtime: 0:00:00.043
uk.ac.ebi.fgpt.conan.service.exception.ProcessExecutionException: java.io.IOException: Stage MECQ failed to produce valid output.
uk.ac.ebi.fgpt.conan.core.task.AbstractConanTask.execute(AbstractConanTask.java:267)
uk.ac.ebi.fgpt.conan.core.task.AbstractConanTask.execute(AbstractConanTask.java:32)
uk.ac.ebi.fgpt.conan.util.AbstractConanCLI.execute(AbstractConanCLI.java:453)
uk.ac.tgac.rampart.RampartCLI.execute(RampartCLI.java:421)
uk.ac.tgac.rampart.RampartCLI.main(RampartCLI.java:453)

`

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