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Remove or minimize docker output from stderr/stdout logs #55

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nhammond opened this issue Apr 29, 2016 · 0 comments
Open

Remove or minimize docker output from stderr/stdout logs #55

nhammond opened this issue Apr 29, 2016 · 0 comments

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@nhammond
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When a user runs a step with, say, fastqc, the stderr/stdout logs should contain only the output from fastqc, nothing about Loom or Docker infrastructure. Can we move Docker-related output into worker log instead of process stderr? Ideally isolate the stdout from the internal process. Almost as good, just run docker pull beforehand so that we don't see all the "Pulling fs layer" output.

Current log looks like this:

Unable to find image 'isaacliao/fastqc:latest' locally
latest: Pulling from isaacliao/fastqc
d15b6a560440: Pulling fs layer
24e1d0c4c316: Pulling fs layer
3a98ef0c64be: Pulling fs layer
9d43faf3bb2d: Pulling fs layer
adca1aa038fa: Pulling fs layer
2445c9b5de8b: Pulling fs layer
a7c1f180ea0d: Pulling fs layer
d660cd126720: Pulling fs layer
185755940809: Pulling fs layer
a7c1f180ea0d: Verifying Checksum
a7c1f180ea0d: Download complete
24e1d0c4c316: Verifying Checksum
24e1d0c4c316: Download complete
2445c9b5de8b: Verifying Checksum
2445c9b5de8b: Download complete
adca1aa038fa: Verifying Checksum
adca1aa038fa: Download complete
185755940809: Verifying Checksum
185755940809: Download complete
3a98ef0c64be: Verifying Checksum
3a98ef0c64be: Download complete
d15b6a560440: Verifying Checksum
d15b6a560440: Download complete
9d43faf3bb2d: Verifying Checksum
9d43faf3bb2d: Download complete
d660cd126720: Verifying Checksum
d660cd126720: Download complete
d15b6a560440: Pull complete
24e1d0c4c316: Pull complete
3a98ef0c64be: Pull complete
9d43faf3bb2d: Pull complete
adca1aa038fa: Pull complete
2445c9b5de8b: Pull complete
a7c1f180ea0d: Pull complete
d660cd126720: Pull complete
185755940809: Pull complete
Digest: sha256:324a4d63c0a4089397fe8bd296e3c0dcf88715dd155bf83768182b3fba636f48
Status: Downloaded newer image for isaacliao/fastqc:latest
Started analysis of sample.fastq
Approx 5% complete for sample.fastq
Approx 10% complete for sample.fastq
Approx 15% complete for sample.fastq
Approx 20% complete for sample.fastq
Approx 25% complete for sample.fastq
Approx 30% complete for sample.fastq
Approx 35% complete for sample.fastq
Approx 40% complete for sample.fastq
Approx 45% complete for sample.fastq
Approx 50% complete for sample.fastq
Approx 55% complete for sample.fastq
Approx 60% complete for sample.fastq
Approx 65% complete for sample.fastq
Approx 70% complete for sample.fastq
Approx 75% complete for sample.fastq
Approx 80% complete for sample.fastq
Approx 85% complete for sample.fastq
Approx 90% complete for sample.fastq
Approx 95% complete for sample.fastq

@nhammond nhammond modified the milestones: release-0.2, release-0.3 May 5, 2016
@nhammond nhammond modified the milestone: release-0.3 Aug 22, 2016
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