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epi2me-labs / wf-transcriptomes

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Attempting to run workflow with demo data fails #52

Closed emsisson closed 8 months ago

emsisson commented 8 months ago

Operating System

Other Linux (please specify below)

Other Linux

RHEL 8.7

Workflow Version

wf-transcriptomes/1.0.0 nextflow/23.04.3

Workflow Execution

Command line

EPI2ME Version

No response

CLI command run

nextflow run epi2me-labs/wf-transcriptome \ --fastq differential_expression/differential_expression_fastq \ --de_analysis \ --ref_genome differential_expression/hg38_chr20.fa \ --transcriptome-source reference-guided \ --ref_annotation differential_expression/gencode.v22.annotation.chr20.gtf \ --direct_rna \ --minimap2_index_opts '-k 15' \ --sample_sheet differential_expression/sample_sheet.csv \ --jaffal_refBase differential_expression/chr20/ \ --jaffal_genome hg38_chr20 \ --jaffal_annotation genCode22 \ -profile singularity \ -without-docker \ -with-singularity wf-transcriptomes.sif

Workflow Execution - CLI Execution Profile

singularity

What happened?

Received series of messages CAPSULE: Downloading dependency ... ending with

N E X T F L O W ~ version 23.04.3
Pulling epi2me-labs/wf-transcriptome ... WARN: Cannot read project manifest -- Cause: Remote resource not found: https://api.github.com/repos/epi2me-labs/wf-transcriptome/contents/nextflow.config Remote resource not found: https://api.github.com/repos/epi2me-labs/wf-transcriptome/contents/main.nf

Relevant log output

CAPSULE: Downloading dependency org.multiverse:multiverse-core:jar:0.7.0
CAPSULE: Downloading dependency org.apache.ivy:ivy:jar:2.5.1
CAPSULE: Downloading dependency org.slf4j:jul-to-slf4j:jar:1.7.36
CAPSULE: Downloading dependency org.codehaus.groovy:groovy-templates:jar:3.0.16
CAPSULE: Downloading dependency org.slf4j:jcl-over-slf4j:jar:1.7.36
CAPSULE: Downloading dependency commons-io:commons-io:jar:2.11.0
CAPSULE: Downloading dependency org.codehaus.jsr166-mirror:jsr166y:jar:1.7.0
CAPSULE: Downloading dependency commons-codec:commons-codec:jar:1.15
CAPSULE: Downloading dependency com.google.guava:listenablefuture:jar:9999.0-empty-to-avoid-conflict-with-guava
CAPSULE: Downloading dependency ch.artecat.grengine:grengine:jar:3.0.0
CAPSULE: Downloading dependency com.beust:jcommander:jar:1.35
CAPSULE: Downloading dependency io.nextflow:nf-httpfs:jar:23.04.3
CAPSULE: Downloading dependency jline:jline:jar:2.9
CAPSULE: Downloading dependency io.nextflow:nf-commons:jar:23.04.3
CAPSULE: Downloading dependency ch.qos.logback:logback-core:jar:1.2.11
CAPSULE: Downloading dependency com.github.zafarkhaja:java-semver:jar:0.9.0
CAPSULE: Downloading dependency javax.mail:mail:jar:1.4.7
CAPSULE: Downloading dependency org.codehaus.groovy:groovy-json:jar:3.0.16
CAPSULE: Downloading dependency org.eclipse.jgit:org.eclipse.jgit:jar:6.2.0.202206071550-r
CAPSULE: Downloading dependency com.google.code.findbugs:jsr305:jar:3.0.2
CAPSULE: Downloading dependency org.codehaus.groovy:groovy:jar:3.0.16
CAPSULE: Downloading dependency commons-lang:commons-lang:jar:2.6
CAPSULE: Downloading dependency org.iq80.leveldb:leveldb-api:jar:0.12
CAPSULE: Downloading dependency org.codehaus.gpars:gpars:jar:1.2.1
CAPSULE: Downloading dependency ch.qos.logback:logback-classic:jar:1.2.11
CAPSULE: Downloading dependency org.jsoup:jsoup:jar:1.15.4
CAPSULE: Downloading dependency org.slf4j:log4j-over-slf4j:jar:1.7.36
CAPSULE: Downloading dependency com.google.guava:guava:jar:31.1-jre
CAPSULE: Downloading dependency org.objenesis:objenesis:jar:2.1
CAPSULE: Downloading dependency com.esotericsoftware.kryo:kryo:jar:2.24.0
CAPSULE: Downloading dependency org.slf4j:slf4j-api:jar:1.7.36
CAPSULE: Downloading dependency org.yaml:snakeyaml:jar:2.0
CAPSULE: Downloading dependency com.google.code.gson:gson:jar:2.10.1
CAPSULE: Downloading dependency com.google.errorprone:error_prone_annotations:jar:2.11.0
CAPSULE: Downloading dependency org.codehaus.groovy:groovy-nio:jar:3.0.16
CAPSULE: Downloading dependency dev.failsafe:failsafe:jar:3.1.0
CAPSULE: Downloading dependency com.google.j2objc:j2objc-annotations:jar:1.3
CAPSULE: Downloading dependency io.nextflow:nextflow:jar:23.04.3
CAPSULE: Downloading dependency javax.activation:activation:jar:1.1.1
CAPSULE: Downloading dependency org.codehaus.groovy:groovy-xml:jar:3.0.16
CAPSULE: Downloading dependency org.pf4j:pf4j:jar:3.4.1
CAPSULE: Downloading dependency org.iq80.leveldb:leveldb:jar:0.12
CAPSULE: Downloading dependency com.google.guava:failureaccess:jar:1.0.1
CAPSULE: Downloading dependency com.googlecode.javaewah:JavaEWAH:jar:1.1.13
CAPSULE: Downloading dependency org.checkerframework:checker-qual:jar:3.12.0
CAPSULE: Downloading dependency org.pf4j:pf4j-update:jar:2.3.0
N E X T F L O W  ~  version 23.04.3                                 
Pulling epi2me-labs/wf-transcriptome ...
WARN: Cannot read project manifest -- Cause: Remote resource not found: https://api.github.com/repos/epi2me-labs/wf-transcriptome/contents/nextflow.config
Remote resource not found: https://api.github.com/repos/epi2me-labs/wf-transcriptome/contents/main.nf

Application activity log entry

No response

emsisson commented 8 months ago

Pasting URL https://api.github.com/repos/epi2me-labs/wf-transcriptome/contents/main.nf into web browser on desktop computer fails, also.

cjw85 commented 8 months ago

This likely results from GitHub API rate limits. Are you in a network environment where there might be many people simultaneously trying to access resources through the GitHub API?

emsisson commented 8 months ago

I do work for a large academic medical center (roughly 24,000 FTEs), and I certainly do not know everything that everybody else is doing, so it is possible. Do you recommend that I try again outside normal working hours?

emsisson commented 8 months ago

I tried again this morning about 7:20 AM local time, and I saw the same result.

Then I entered URL https://api.github.com/repos/epi2me-labs/wf-transcriptome/contents/main.nf into the web browser on my iPad. While my computer connects via VPN to my employer's network, the iPad connects to the Internet through my residential ISP and not through the VPN. That failed, also; see attached screenshot.

screenshot

Are you certain that the file is present and that some redirect mechanism is not intercepting requests for it?

mehc555 commented 8 months ago

Having the same issue

Edit: There's a typo in the example, missing a s at the end of 'transcriptome'

nextflow run epi2me-labs/wf-transcriptome

nrhorner commented 8 months ago

Edit: There's a typo in the example, missing a s at the end of 'transcriptome'

nextflow run epi2me-labs/wf-transcriptome

Oh, well spotted. Thanks

nrhorner commented 8 months ago

The demo command has been updated and is now visible on the prerelease branch. Closing ticket.

emsisson commented 8 months ago

The fix works for me, also. Thank you.