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There are multiple input files for each of the following file names: OPTIONAL_FILE #12

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ChristopherRichie opened this issue Sep 29, 2023 · 4 comments
Closed

There are multiple input files for each of the following file names: OPTIONAL_FILE #12

ChristopherRichie opened this issue Sep 29, 2023 · 4 comments

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@ChristopherRichie
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Operating System

Ubuntu 22.04

Other Linux

No response

Workflow Version

v0.5.0

Workflow Execution

Command line

EPI2ME Version

No response

CLI command run

normal='//data/chrisr/older_data_for_backup/CR2839/LVF910_pool/09-29-23_clean_copy/BC06_wf-align/fastq.sorted.aligned.bam'
tumor='//data/chrisr/older_data_for_backup/CR2839/LVF910_pool/09-29-23_clean_copy/BC05_wf-align/fastq.sorted.aligned.bam'
basecaller_config="dna_r9.4.1_e8_sup@v3.3"

nextflow run epi2me-labs/wf-somatic-variation
-c //data/chrisr/nextflow.config.Qi
-profile biowulflocal
--snv false
--sv true
--sample_name 'SV_mysample'
--ref '//data/chrisr/UCSC_Rn6/genome.fa'
--bam_normal $normal
--bam_tumor $tumor
--basecaller_cfg $basecaller_config
--normal_min_coverage 0
--tumor_min_coverage 0
--classify_insert false
--annotation false

Workflow Execution - CLI Execution Profile

custom

What happened?

I am trying to run wf-somatic-variation, using the rat genome, and two samples that have been aligned with wf-align

when I run for SNVs, the wf completes with valid outputs.

when I run with SVs, I get this error:

ERROR ~ Error executing process > 'somatic_sv:report (1)'

Caused by:
Process somatic_sv:report input file name collision -- There are multiple input files for each of the following file names: OPTIONAL_FILE
Tip: you can replicate the issue by changing to the process work dir and entering the command bash .command.run

-- Check '.nextflow.log' file for details

I see "optional_file" in various places around the wf's github, but I do not understand if this is a bug or if I have set up the wrong command.

Relevant log output

// this box does not hold the complete .nextflow.log... so here is the "tail".

Sep-29 16:28:50.955 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Sep-29 16:28:50.956 [Task submitter] INFO  nextflow.Session - [2a/3bf05a] Submitted process > output (2)
Sep-29 16:28:50.965 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Sep-29 16:28:50.965 [Task submitter] INFO  nextflow.Session - [39/0c9f4a] Submitted process > output (3)
Sep-29 16:28:50.974 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Sep-29 16:28:50.974 [Task submitter] INFO  nextflow.Session - [ed/72728f] Submitted process > somatic_sv:nanomonsv_parse (2)
Sep-29 16:28:50.984 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Sep-29 16:28:50.985 [Task submitter] INFO  nextflow.Session - [50/28103f] Submitted process > alignment_stats:bamstats (2)
Sep-29 16:28:50.994 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Sep-29 16:28:50.995 [Task submitter] INFO  nextflow.Session - [3e/ed2dcd] Submitted process > getAllChromosomesBed (1)
Sep-29 16:28:51.003 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Sep-29 16:28:51.003 [Task submitter] INFO  nextflow.Session - [01/a6bdfa] Submitted process > somatic_sv:nanomonsv_parse (1)
Sep-29 16:28:51.077 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Sep-29 16:28:51.077 [Task submitter] INFO  nextflow.Session - [38/79e86d] Submitted process > alignment_stats:bamstats (1)
Sep-29 16:28:51.085 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Sep-29 16:28:51.086 [Task submitter] INFO  nextflow.Session - [9a/2aa4a5] Submitted process > output (1)
Sep-29 16:28:51.638 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 15; name: output (3); status: COMPLETED; exit: 0; error: -; workDir: /gpfs/gsfs12/users/chrisr/older_data_for_backup/CR2839/LVF910_pool/09-29-23_clean_copy/work/39/0c9f4a7f2611507f57ad05ea15143f]
Sep-29 16:28:51.673 [Task monitor] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'PublishDir' minSize=10; maxSize=48; workQueue=LinkedBlockingQueue[10000]; allowCoreThreadTimeout=false
Sep-29 16:28:51.683 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 14; name: output (2); status: COMPLETED; exit: 0; error: -; workDir: /gpfs/gsfs12/users/chrisr/older_data_for_backup/CR2839/LVF910_pool/09-29-23_clean_copy/work/2a/3bf05a6d5d48723118d9f82affa2c8]
Sep-29 16:28:51.726 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 8; name: getAllChromosomesBed (1); status: COMPLETED; exit: 0; error: -; workDir: /gpfs/gsfs12/users/chrisr/older_data_for_backup/CR2839/LVF910_pool/09-29-23_clean_copy/work/3e/ed2dcd8e6af6083e8b7052c0ef4dd2]
Sep-29 16:28:51.803 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Sep-29 16:28:51.804 [Task submitter] INFO  nextflow.Session - [5e/29a42b] Submitted process > alignment_stats:mosdepth (2)
Sep-29 16:28:51.812 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Sep-29 16:28:51.812 [Task submitter] INFO  nextflow.Session - [77/36887f] Submitted process > alignment_stats:mosdepth (1)
Sep-29 16:28:52.030 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 13; name: output (1); status: COMPLETED; exit: 0; error: -; workDir: /gpfs/gsfs12/users/chrisr/older_data_for_backup/CR2839/LVF910_pool/09-29-23_clean_copy/work/9a/2aa4a5e5cd893a06317ea59a98ab75]
Sep-29 16:28:52.228 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 11; name: alignment_stats:bamstats (2); status: COMPLETED; exit: 0; error: -; workDir: /gpfs/gsfs12/users/chrisr/older_data_for_backup/CR2839/LVF910_pool/09-29-23_clean_copy/work/50/28103f15c2bed5518ac0a56ba11067]
Sep-29 16:28:52.868 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 10; name: alignment_stats:bamstats (1); status: COMPLETED; exit: 0; error: -; workDir: /gpfs/gsfs12/users/chrisr/older_data_for_backup/CR2839/LVF910_pool/09-29-23_clean_copy/work/38/79e86dfdbde2a0b091ceacb727f73f]
Sep-29 16:28:54.964 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 12; name: somatic_sv:nanomonsv_parse (2); status: COMPLETED; exit: 0; error: -; workDir: /gpfs/gsfs12/users/chrisr/older_data_for_backup/CR2839/LVF910_pool/09-29-23_clean_copy/work/ed/72728fbe2ba9b8e33e949fe73e30db]
Sep-29 16:28:55.278 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 9; name: somatic_sv:nanomonsv_parse (1); status: COMPLETED; exit: 0; error: -; workDir: /gpfs/gsfs12/users/chrisr/older_data_for_backup/CR2839/LVF910_pool/09-29-23_clean_copy/work/01/a6bdfa47045c99c038ecce816308cf]
Sep-29 16:28:55.303 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Sep-29 16:28:55.304 [Task submitter] INFO  nextflow.Session - [4c/083fb1] Submitted process > somatic_sv:nanomonsv_get (1)
Sep-29 16:29:03.766 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 18; name: somatic_sv:nanomonsv_get (1); status: COMPLETED; exit: 0; error: -; workDir: /gpfs/gsfs12/users/chrisr/older_data_for_backup/CR2839/LVF910_pool/09-29-23_clean_copy/work/4c/083fb16bdefd48efb9861c575e5c83]
Sep-29 16:29:03.780 [Actor Thread 13] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /home/chrisr/.nextflow/23.04.3/assets/epi2me-labs/wf-somatic-variation/bin/vcf_nanomon2clairs.py
Sep-29 16:29:03.899 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Sep-29 16:29:03.899 [Task submitter] INFO  nextflow.Session - [bd/27b175] Submitted process > somatic_sv:postprocess_nanomon_vcf (1)
Sep-29 16:29:04.792 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 19; name: somatic_sv:postprocess_nanomon_vcf (1); status: COMPLETED; exit: 0; error: -; workDir: /gpfs/gsfs12/users/chrisr/older_data_for_backup/CR2839/LVF910_pool/09-29-23_clean_copy/work/bd/27b175932b879ec40df4c56ec66140]
Sep-29 16:29:04.804 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Sep-29 16:29:04.805 [Task submitter] INFO  nextflow.Session - [4a/021c9a] Submitted process > somatic_sv:sortVCF (1)
Sep-29 16:29:05.343 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 20; name: somatic_sv:sortVCF (1); status: COMPLETED; exit: 0; error: -; workDir: /gpfs/gsfs12/users/chrisr/older_data_for_backup/CR2839/LVF910_pool/09-29-23_clean_copy/work/4a/021c9a8739b5d13c3a9f448c6bb8c5]
Sep-29 16:29:05.349 [Actor Thread 6] DEBUG nextflow.processor.TaskProcessor - Process somatic_sv:report > collision check staging file names: [OPTIONAL_FILE:2, versions.txt:1, SV_mysample.nanomonsv.result.wf-somatic_sv.vcf.gz.tbi:1, SV_mysample.nanomonsv.result.wf-somatic_sv.vcf.gz:1, params.json:1]
Sep-29 16:29:05.354 [Actor Thread 6] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
  task: name=somatic_sv:report (1); work-dir=null
  error [nextflow.exception.ProcessUnrecoverableException]: Process `somatic_sv:report` input file name collision -- There are multiple input files for each of the following file names: OPTIONAL_FILE
Sep-29 16:29:05.355 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Sep-29 16:29:05.355 [Task submitter] INFO  nextflow.Session - [f7/a16e7c] Submitted process > somatic_sv:output_sv (3)
Sep-29 16:29:05.360 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Sep-29 16:29:05.360 [Task submitter] INFO  nextflow.Session - [6f/f9d93c] Submitted process > somatic_sv:output_sv (2)
Sep-29 16:29:05.363 [Actor Thread 6] ERROR nextflow.processor.TaskProcessor - Error executing process > 'somatic_sv:report (1)'

Caused by:
  Process `somatic_sv:report` input file name collision -- There are multiple input files for each of the following file names: OPTIONAL_FILE


Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run`
Sep-29 16:29:05.365 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Sep-29 16:29:05.366 [Task submitter] INFO  nextflow.Session - [84/bb4957] Submitted process > somatic_sv:output_sv (1)
Sep-29 16:29:05.367 [Actor Thread 6] DEBUG nextflow.Session - Session aborted -- Cause: Process `somatic_sv:report` input file name collision -- There are multiple input files for each of the following file names: OPTIONAL_FILE
Sep-29 16:29:05.389 [Actor Thread 6] DEBUG nextflow.Session - The following nodes are still active:
[process] alignment_stats:makeQCreport
  status=ACTIVE
  port 0: (queue) OPEN  ; channel: -
  port 1: (value) bound ; channel: versions.txt
  port 2: (value) bound ; channel: params.json
  port 3: (cntrl) -     ; channel: $

[process] output_qc
  status=ACTIVE
  port 0: (queue) OPEN  ; channel: -
  port 1: (cntrl) -     ; channel: $

[process] somatic_sv:report
  status=ACTIVE
  port 0: (value) bound ; channel: -
  port 1: (value) bound ; channel: -
  port 2: (queue) closed; channel: -
  port 3: (value) bound ; channel: eval_json
  port 4: (value) bound ; channel: versions
  port 5: (value) bound ; channel: params.json
  port 6: (cntrl) -     ; channel: $

[process] somatic_sv:output_sv
  status=ACTIVE
  port 0: (queue) OPEN  ; channel: -
  port 1: (cntrl) -     ; channel: $

Sep-29 16:29:05.793 [main] DEBUG nextflow.Session - Session await > all processes finished
Sep-29 16:29:05.793 [main] DEBUG nextflow.Session - Session await > all barriers passed
Sep-29 16:29:05.796 [Actor Thread 21] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
  task: name=somatic_sv:report; work-dir=null
  error [java.lang.InterruptedException]: java.lang.InterruptedException
Sep-29 16:29:05.796 [Actor Thread 16] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
  task: name=alignment_stats:makeQCreport; work-dir=null
  error [java.lang.InterruptedException]: java.lang.InterruptedException
Sep-29 16:29:05.899 [main] WARN  n.processor.TaskPollingMonitor - Killing running tasks (5)
Sep-29 16:29:05.928 [main] DEBUG n.executor.local.LocalTaskHandler - Unable to kill somatic_sv:output_sv (3) -- command: kill -TERM 3447768; exit: 1 
 bash: line 0: kill: (3447768) - No such process

Sep-29 16:29:05.950 [main] DEBUG nextflow.trace.WorkflowStatsObserver - Workflow completed > WorkflowStats[succeededCount=18; failedCount=0; ignoredCount=0; cachedCount=0; pendingCount=4; submittedCount=3; runningCount=-3; retriesCount=0; abortedCount=5; succeedDuration=2m 56s; failedDuration=0ms; cachedDuration=0ms;loadCpus=-3; loadMemory=0; peakRunning=8; peakCpus=15; peakMemory=0; ]
Sep-29 16:29:05.951 [main] DEBUG nextflow.trace.TraceFileObserver - Workflow completed -- saving trace file
Sep-29 16:29:05.954 [main] DEBUG nextflow.trace.ReportObserver - Workflow completed -- rendering execution report
Sep-29 16:29:06.021 [main] DEBUG nextflow.trace.ReportObserver - Execution report summary data:
  [{"cpuUsage":{"mean":76.8,"min":74.8,"q1":75.8,"q2":76.8,"q3":77.8,"max":78.8,"minLabel":"somatic_sv:getParams","maxLabel":"getParams","q1Label":"somatic_sv:getParams","q2Label":"somatic_sv:getParams","q3Label":"somatic_sv:getParams"},"process":"getParams","mem":null,"memUsage":null,"timeUsage":null,"vmem":null,"reads":{"mean":80039,"min":80039,"q1":80039,"q2":80039,"q3":80039,"max":80039,"minLabel":"getParams","maxLabel":"somatic_sv:getParams","q1Label":"getParams","q2Label":"getParams","q3Label":"getParams"},"cpu":{"mean":76.8,"min":74.8,"q1":75.8,"q2":76.8,"q3":77.8,"max":78.8,"minLabel":"somatic_sv:getParams","maxLabel":"getParams","q1Label":"somatic_sv:getParams","q2Label":"somatic_sv:getParams","q3Label":"somatic_sv:getParams"},"time":{"mean":7.5,"min":7,"q1":7.25,"q2":7.5,"q3":7.75,"max":8,"minLabel":"getParams","maxLabel":"somatic_sv:getParams","q1Label":"getParams","q2Label":"getParams","q3Label":"getParams"},"writes":{"mean":4690,"min":4690,"q1":4690,"q2":4690,"q3":4690,"max":4690,"minLabel":"getParams","maxLabel":"somatic_sv:getParams","q1Label":"getParams","q2Label":"getParams","q3Label":"getParams"}},{"cpuUsage":{"mean":123.85,"min":104.3,"q1":114.08,"q2":123.85,"q3":133.63,"max":143.4,"minLabel":"getVersions","maxLabel":"somatic_sv:getVersions","q1Label":"getVersions","q2Label":"getVersions","q3Label":"getVersions"},"process":"getVersions","mem":{"mean":280365056,"min":121630720,"q1":200997888,"q2":280365056,"q3":359732224,"max":439099392,"minLabel":"somatic_sv:getVersions","maxLabel":"getVersions","q1Label":"somatic_sv:getVersions","q2Label":"somatic_sv:getVersions","q3Label":"somatic_sv:getVersions"},"memUsage":null,"timeUsage":null,"vmem":{"mean":2396456960,"min":2228875264,"q1":2312666112,"q2":2396456960,"q3":2480247808,"max":2564038656,"minLabel":"somatic_sv:getVersions","maxLabel":"getVersions","q1Label":"somatic_sv:getVersions","q2Label":"somatic_sv:getVersions","q3Label":"somatic_sv:getVersions"},"reads":{"mean":27481908.5,"min":8255980,"q1":17868944.25,"q2":27481908.5,"q3":37094872.75,"max":46707837,"minLabel":"somatic_sv:getVersions","maxLabel":"getVersions","q1Label":"somatic_sv:getVersions","q2Label":"somatic_sv:getVersions","q3Label":"somatic_sv:getVersions"},"cpu":{"mean":123.85,"min":104.3,"q1":114.08,"q2":123.85,"q3":133.63,"max":143.4,"minLabel":"getVersions","maxLabel":"somatic_sv:getVersions","q1Label":"getVersions","q2Label":"getVersions","q3Label":"getVersions"},"time":{"mean":11473,"min":2666,"q1":7069.5,"q2":11473,"q3":15876.5,"max":20280,"minLabel":"somatic_sv:getVersions","maxLabel":"getVersions","q1Label":"somatic_sv:getVersions","q2Label":"somatic_sv:getVersions","q3Label":"somatic_sv:getVersions"},"writes":{"mean":5452,"min":5238,"q1":5345,"q2":5452,"q3":5559,"max":5666,"minLabel":"somatic_sv:getVersions","maxLabel":"getVersions","q1Label":"somatic_sv:getVersions","q2Label":"somatic_sv:getVersions","q3Label":"somatic_sv:getVersions"}},{"cpuUsage":{"mean":105.3,"min":105.2,"q1":105.25,"q2":105.3,"q3":105.35,"max":105.4,"minLabel":"bam_ingress_tumor:check_for_alignment (1)","maxLabel":"bam_ingress_normal:check_for_alignment (1)","q1Label":"bam_ingress_tumor:check_for_alignment (1)","q2Label":"bam_ingress_tumor:check_for_alignment (1)","q3Label":"bam_ingress_tumor:check_for_alignment (1)"},"process":"check_for_alignment","mem":{"mean":443650048,"min":443568128,"q1":443609088,"q2":443650048,"q3":443691008,"max":443731968,"minLabel":"bam_ingress_tumor:check_for_alignment (1)","maxLabel":"bam_ingress_normal:check_for_alignment (1)","q1Label":"bam_ingress_tumor:check_for_alignment (1)","q2Label":"bam_ingress_tumor:check_for_alignment (1)","q3Label":"bam_ingress_tumor:check_for_alignment (1)"},"memUsage":null,"timeUsage":null,"vmem":{"mean":2571544576,"min":2571538432,"q1":2571541504,"q2":2571544576,"q3":2571547648,"max":2571550720,"minLabel":"bam_ingress_normal:check_for_alignment (1)","maxLabel":"bam_ingress_tumor:check_for_alignment (1)","q1Label":"bam_ingress_normal:check_for_alignment (1)","q2Label":"bam_ingress_normal:check_for_alignment (1)","q3Label":"bam_ingress_normal:check_for_alignment (1)"},"reads":{"mean":46296162,"min":46201194,"q1":46248678,"q2":46296162,"q3":46343646,"max":46391130,"minLabel":"bam_ingress_normal:check_for_alignment (1)","maxLabel":"bam_ingress_tumor:check_for_alignment (1)","q1Label":"bam_ingress_normal:check_for_alignment (1)","q2Label":"bam_ingress_normal:check_for_alignment (1)","q3Label":"bam_ingress_normal:check_for_alignment (1)"},"cpu":{"mean":105.3,"min":105.2,"q1":105.25,"q2":105.3,"q3":105.35,"max":105.4,"minLabel":"bam_ingress_tumor:check_for_alignment (1)","maxLabel":"bam_ingress_normal:check_for_alignment (1)","q1Label":"bam_ingress_tumor:check_for_alignment (1)","q2Label":"bam_ingress_tumor:check_for_alignment (1)","q3Label":"bam_ingress_tumor:check_for_alignment (1)"},"time":{"mean":19920,"min":19880,"q1":19900,"q2":19920,"q3":19940,"max":19960,"minLabel":"bam_ingress_normal:check_for_alignment (1)","maxLabel":"bam_ingress_tumor:check_for_alignment 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Sep-29 16:29:06.699 [main] DEBUG nextflow.trace.TimelineObserver - Workflow completed -- rendering execution timeline
Sep-29 16:29:06.784 [main] DEBUG nextflow.cache.CacheDB - Closing CacheDB done
Sep-29 16:29:06.832 [main] DEBUG nextflow.script.ScriptRunner - > Execution complete -- Goodbye

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@julibeg
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julibeg commented Oct 4, 2023

Hi @ChristopherRichie!

I was able to reproduce the error and the bug will be fixed in the next release. A workaround for the meantime would be to run with --annotation true as this will avoid the name collision.

@ChristopherRichie
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thanks, i will give it a try!

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julibeg commented Oct 18, 2023

This has been fixed in the most recent release (v0.5.1). Please reopen this issue if the problem persists (when running with with --annotation false).

@julibeg julibeg closed this as completed Oct 18, 2023
@ChristopherRichie
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ChristopherRichie commented Oct 18, 2023 via email

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