Integrity coverage fails

#52 and #56 may be related to this issue.

I'm building the simplest pipeline on AWS (Linux): spades + docker.
The FastQ files are real bacterial datasets, 5Mb, 100X coverage. When I run the pipeline as follows, it always gives integrity_coverage errors regardless of what parameters I supply, and generates no output. I don't know why it's failing or how to work around it. Note: our normal AWS Spades/Docker pipeline works fine with these datasets.
Email: richardcaseyhpc@protonmail.com

nextflow run spades_pipe.nf --fastq "fastq/sample_R{1,2}.*" -profile docker --genomeSize 5 --minCoverage 0
N E X T F L O W ~ version 19.07.0
Launching spades_pipe.nf [disturbed_mahavira] - revision: 6267a78dba

============================================================
F L O W C R A F T

Built using flowcraft v1.4.1

Input FastQ : 2
Input samples : 1
Reports are found in : ./reports
Results are found in : ./results
Profile : docker

Starting pipeline at Wed Aug 14 19:11:42 UTC 2019

executor > local (8)
[24/294084] process > integrity_coverage_1_1 (sample_R) [100%] 8 of 8, failed: 8 ✔
[- ] process > report_coverage_1_1 -
[- ] process > report_corrupt_1_1 -
[- ] process > trimmomatic_1_2 -
[- ] process > status -
[- ] process > compile_status_buffer -
[- ] process > compile_status -
[- ] process > report -
[- ] process > compile_reports -
Completed at: Wed Aug 14 19:11:51 UTC 2019
Duration : 8.9s
Success : true
Exit status : 0
WARN: The channel create method is deprecated -- it will be removed in a future release
WARN: The channel create method is deprecated -- it will be removed in a future release
WARN: The channel create method is deprecated -- it will be removed in a future release
WARN: The channel create method is deprecated -- it will be removed in a future release
WARN: The channel create method is deprecated -- it will be removed in a future release
WARN: Process configuration syntax $processName has been deprecated -- Replace process.$trimmomatic_1_2 = <value> with a process selector
[eb/6187b2] NOTE: Process integrity_coverage_1_1 (sample_R) terminated with an error exit status (1) -- Execution is retried (1)
[f3/c9c01d] NOTE: Process integrity_coverage_1_1 (sample_R) terminated with an error exit status (1) -- Execution is retried (2)
[e6/8a39ef] NOTE: Process integrity_coverage_1_1 (sample_R) terminated with an error exit status (1) -- Execution is retried (3)
[97/d32042] NOTE: Process integrity_coverage_1_1 (sample_R) terminated with an error exit status (1) -- Execution is retried (4)
[99/ddd7ec] NOTE: Process integrity_coverage_1_1 (sample_R) terminated with an error exit status (1) -- Execution is retried (5)
[d6/f2a129] NOTE: Process integrity_coverage_1_1 (sample_R) terminated with an error exit status (1) -- Execution is retried (6)
[b1/4849d6] NOTE: Process integrity_coverage_1_1 (sample_R) terminated with an error exit status (1) -- Execution is retried (7)
[24/294084] NOTE: Process integrity_coverage_1_1 (sample_R) terminated with an error exit status (1) -- Error is ignored

[kapsakcj]

Also having this issue. And weirdly after running the flowcraft generated nextflow pipeline, my backspace key longer works?

commands used in a flowcraft conda env:

flowcraft build -t "trimmomatic skesa abricate" -o trim_skesa_abricate_flowcraft.nf -n "second-try-flowcraft"
nextflow run trim_skesa_abricate_flowcraft.nf --fastq "reads/*{R1,R2}*.fastq.gz" -profile sge_sing

I see a lot of warnings like this:

WARN: The channel `create` method is deprecated -- it will be removed in a future release

WARN: Process configuration syntax $processName has been deprecated -- Replace `process.$trimmomatic_1_2 = <value>` with a process selector

[85/f9e73a] NOTE: Process `integrity_coverage_1_1 (2015am-0046_CAM4563A161_CGGCTATG-TATAGCCT_L002)` terminated with an error exit status (1) -- Error is ignored

and in the log files like so: work/XX/XXXXXXXXXXXXXXXXXXXX/.command.err I see (edited for brevity):

line 194: uname: command not found
line 146: grep: command not found
line 147: grep: command not found
line 208: date: command not found
Command 'ps' required by nextflow to collect task metrics cannot be found

Perhaps the PATHs are getting set incorrectly?

[cimendes]

Hi @TheSequencingCenter and @kapsakcj! I haven't been able to fully look into your issues. Can you start by telling me what version of nextflow you have? @kapsakcj I'm fairly certain your problem is related to this issue #217 which is high priority but still without any development. For now, my solution would try to downgrade to nextflow version 18.10.1. Sorry about this!

Best,

Inês

[kapsakcj]

It was with the latest version of nextflow 19.07. I'll try downgrading and see if that fixes it. Thanks for the quick response!

[kapsakcj]

Downgrading to nf 18.10.1 made the nf pipeline run properly using the -profile standard option. Seems like the -profile sge_sing won't work for me, but that's likely due to my compute environment

[stefcardinale]

Hello, I am also stuck with this issue after running any pipeline including spades, trimmomatic etc. The problem seems lying with the integrity_coverage.py template file, a process that is automatically added in front of all these workflows. I can't understand what is wrong, as I've basically just followed precisely the instructions provided. Note: I am running these in a conda environment.

This is the output of running: _nextflow run trimmomatic.nf --fastq "/data/x_R{1,2}x"

executor > local (8)
[22/d4554d] process > integrity_coverage_1_1 (X_genome1) [100%] 8 of 8, failed: 8 ✔
[- ] process > report_coverage_1_1 -
[- ] process > report_corrupt_1_1 -
[- ] process > fastqc_1_2 -
[- ] process > fastqc_report_1_2 -
[- ] process > trim_report_1_2 -
[- ] process > compile_fastqc_status_1_2 -
[- ] process > trimmomatic_1_2 -
[- ] process > status -
[- ] process > compile_status_buffer -
[- ] process > compile_status -
[- ] process > report -
[- ] process > compile_reports -
Completed at: Thu Oct 17 11:39:08 CEST 2019
Duration : 50.6s
Success : true
Exit status : 0
[55/dfd963] NOTE: Missing output file(s) *_encoding expected by process integrity_coverage_1_1 (X_genome1) -- Execution is retried (3)
[7a/e59573] NOTE: Missing output file(s) *_encoding expected by process integrity_coverage_1_1 (X_genome1) -- Execution is retried (4)
[9f/5ce485] NOTE: Missing output file(s) *_encoding expected by process integrity_coverage_1_1 (X_genome1) -- Execution is retried (5)
[b5/0f5b00] NOTE: Missing output file(s) *_encoding expected by process integrity_coverage_1_1 (X_genome1) -- Execution is retried (6)
[91/b68c08] NOTE: Missing output file(s) *_encoding expected by process integrity_coverage_1_1 (X_genome1) -- Execution is retried (7)
[22/d4554d] NOTE: Missing output file(s) *_encoding expected by process integrity_coverage_1_1 (X_genome1) -- Error is ignored

Anyone has any suggestion on what might be going on? is it a problem with the utf-8 encoding?
Thanks!

[cimendes]

Hello! Can you please check one of the working directories for the integrity_coverage_1_1 process, for example work/55/dfd963* and paste here the contents of the .command.log file?

[stefcardinale]

Hello, thanks for writing. This file is empty. Also, I want to clarify that I have the same issue after building the workflow with FlowCraft as well as with assemblerflow, and also after downgrading NextFlow to version 18.10.1 as suggested above.
I am following instructions provided online for these tools (which should work out-of-the-box supposedly).

[cimendes]

Can you share the .nextflow.log file?

[stefcardinale]

nexflow.log

[cimendes]

Hello, on your log file it says you're running nextflow version 19.07.0, but you also tried with version 18.10.1? Can you send me the log of that run? By default, a flowcraft pipeline will use singularity container, do you have this installed? You can change it to docker by adding -profile docker to your nextflow command.

As a side note the bug causing flowcraft pipelines to break on nextflow latest verion has been addressed here but I haven't had the oportunity to test it yet. (cc @kapsakcj)

[stefcardinale]

Hello, uh so after some more tests I can report that with v. 18.10.1 the process completed successfully with '-profile docker' but failed with '-profile standard'. With version 19.07.0 it failed with both profile options, however the error is different:

-with -profile standard:
[83/474dab] NOTE: Missing output file(s) *_encoding expected by process integrity_coverage_1_1 (Salm_genome2) -- Execution is retried (3)

-with '-profile docker':
[4d/24d4a6] NOTE: Process integrity_coverage_1_1 (Salm_genome2) terminated with an error exit status (1) -- Execution is retried (1)

Note:

• I have both docker and singularity installed system-wide.

• I installed nextflow using curl

[jacarrico]

@stefcardinale are you running it in a cluster or a single server ? From your pot I suspect it is a single server. I am asking to see how this issue can be related to the issue of @kapsakcj on using -profile sge_sing. All these issues seem derived from Nextflow versions and not FlowCraft but we will look into them.