No input files were found

[tang27abu]

Hi Erin,

I get the no input files detected error when I run the cecrete workflow today. It said it cannot find the fastq file at /storage/hpc/group/cov-sur/datasets/MO-M08605-230210/fastq/reads but I have put all fastq.gz file at that location as before.

(base) [zl7w2@lewis4-r730-dtn1-node879 datasets]$ cov-sur-pipeline.sh  ../meta_all/MO_info_2-14-23.xlsx  MO-M08605-230210
/storage/hpc/group/cov-sur/datasets/MO-M08605-230210/fastq already exists, skipping download.
NOTE: Nextflow is not tested with Java 1.8.0_352 -- It's recommended the use of version 11 up to 18

Checking UPHL-BioNGS/Cecret ...
UPHL-BioNGS/Cecret contains uncommitted changes -- cannot pull from repository
NOTE: Nextflow is not tested with Java 1.8.0_352 -- It's recommended the use of version 11 up to 18

N E X T F L O W  ~  version 22.04.5
Launching `https://github.com/UPHL-BioNGS/Cecret` [stupefied_noyce] DSL2 - revision: d191242b07 [master]
Currently using the Cecret workflow for use with amplicon Illumina library prep on MiSeq with a corresponding reference genome.

Author: Erin Young
email: eriny@utah.gov
Version: v.3.5.20230201

The maximum number of CPUS used in this workflow is 8
Using the subworkflow for SARS-CoV-2
The files and directory for results is cecret
A table summarizing results will be created: cecret/cecret_results.csv

[-        ] process > fasta_prep       -
[-        ] process > cecret:seqyclean -
No reference genome was selected. Set with 'params.reference_genome'
A bedfile for primers is required. Set with 'params.primer_bed'.
No fastq or fastq.gz files were found at /storage/hpc/group/cov-sur/datasets/MO-M08605-230210/fastq/reads or /storage/hpc/group/cov-sur/datasets/MO-M08605-230210/fastq/single_reads
No such variable: ch_dataset

 -- Check script '/home/zl7w2/assets/UPHL-BioNGS/Cecret/main.nf' at line: 363 or see '.nextflow.log' file for more details
FATAL : No input files were found!
No paired-end fastq files were found at /storage/hpc/group/cov-sur/datasets/MO-M08605-230210/fastq/reads. Set 'params.reads' to directory with paired-end reads
No single-end fastq files were found at /storage/hpc/group/cov-sur/datasets/MO-M08605-230210/fastq/single_reads. Set 'params.single_reads' to directory with single-end reads
No fasta files were found at /storage/hpc/group/cov-sur/datasets/MO-M08605-230210/fastq/fastas. Set 'params.fastas' to directory with fastas.
No multifasta files were found at /storage/hpc/group/cov-sur/datasets/MO-M08605-230210/fastq/multifastas. Set 'params.multifastas' to directory with multifastas.
No sample sheet was fount at . Set 'params.sample_sheet' to sample sheet file.

(base) [zl7w2@lewis4-r730-dtn1-node879 datasets]$ cd /storage/hpc/group/cov-sur/datasets/MO-M08605-230210/fastq/reads
(base) [zl7w2@lewis4-r730-dtn1-node879 reads]$ ls -ls
total 3650239
12888 -rw-rw-r--. 1 zl7w2 cov-sur-group 13111442 Feb 14 15:07 356816-MO-M08605-230210_S50_L001_R1_001.fastq.gz
13780 -rw-rw-r--. 1 zl7w2 cov-sur-group 14023475 Feb 14 15:07 356816-MO-M08605-230210_S50_L001_R2_001.fastq.gz
33462 -rw-rw-r--. 1 zl7w2 cov-sur-group 34190484 Feb 14 15:08 597295-MO-M08605-230210_S27_L001_R1_001.fastq.gz
35057 -rw-rw-r--. 1 zl7w2 cov-sur-group 35828958 Feb 14 15:08 597295-MO-M08605-230210_S27_L001_R2_001.fastq.gz
24849 -rw-rw-r--. 1 zl7w2 cov-sur-group 25371499 Feb 14 15:07 597341-MO-M08605-230210_S28_L001_R1_001.fastq.gz
25872 -rw-rw-r--. 1 zl7w2 cov-sur-group 26416332 Feb 14 15:07 597341-MO-M08605-230210_S28_L001_R2_001.fastq.gz
23351 -rw-rw-r--. 1 zl7w2 cov-sur-group 23855243 Feb 14 15:08 597343-MO-M08605-230210_S29_L001_R1_001.fastq.gz
25167 -rw-rw-r--. 1 zl7w2 cov-sur-group 25708540 Feb 14 15:08 597343-MO-M08605-230210_S29_L001_R2_001.fastq.gz
35477 -rw-rw-r--. 1 zl7w2 cov-sur-group 36248520 Feb 14 15:07 597357-MO-M08605-230210_S30_L001_R1_001.fastq.gz
37955 -rw-rw-r--. 1 zl7w2 cov-sur-group 38669224 Feb 14 15:07 597357-MO-M08605-230210_S30_L001_R2_001.fastq.gz
17001 -rw-rw-r--. 1 zl7w2 cov-sur-group 17321859 Feb 14 15:08 598112-MO-M08605-230210_S31_L001_R1_001.fastq.gz
17928 -rw-rw-r--. 1 zl7w2 cov-sur-group 18273532 Feb 14 15:08 598112-MO-M08605-230210_S31_L001_R2_001.fastq.gz
39437 -rw-rw-r--. 1 zl7w2 cov-sur-group 40314354 Feb 14 15:09 598126-MO-M08605-230210_S32_L001_R1_001.fastq.gz
44302 -rw-rw-r--. 1 zl7w2 cov-sur-group 45297568 Feb 14 15:09 598126-MO-M08605-230210_S32_L001_R2_001.fastq.gz
38873 -rw-rw-r--. 1 zl7w2 cov-sur-group 39734805 Feb 14 15:07 598196-MO-M08605-230210_S33_L001_R1_001.fastq.gz
40483 -rw-rw-r--. 1 zl7w2 cov-sur-group 41389321 Feb 14 15:07 598196-MO-M08605-230210_S33_L001_R2_001.fastq.gz
36625 -rw-rw-r--. 1 zl7w2 cov-sur-group 37423322 Feb 14 15:07 598965-MO-M08605-230210_S34_L001_R1_001.fastq.gz
38757 -rw-rw-r--. 1 zl7w2 cov-sur-group 39612973 Feb 14 15:07 598965-MO-M08605-230210_S34_L001_R2_001.fastq.gz
26719 -rw-rw-r--. 1 zl7w2 cov-sur-group 27282254 Feb 14 15:08 598966-MO-M08605-230210_S35_L001_R1_001.fastq.gz
28533 -rw-rw-r--. 1 zl7w2 cov-sur-group 29147909 Feb 14 15:09 598966-MO-M08605-230210_S35_L001_R2_001.fastq.gz

[erinyoung]

Thanks for your issue!

Your reads are there, and they should get picked up.

This is the error that concerns me:

No such variable: ch_dataset

So I'm very grateful that you shared the entire error message. I should have a fix within the hour.

[erinyoung]

I have a new release that should fix your issue.

Can you update your workflow and try again? Let me know if this fixes your issue or if you still encounter your problem.

[tang27abu]

Hi Erin, Last week, that error occurred when I run the workflow through staphb-toolkit using staphb-tk cecret command. However, when I run the workflow using nextflow run UPHL-BioNGS/Cecret, it worked. Now, I try the staphb-toolkit one, it still doesn't work and the error is same.

[k-florek]

@tang27abu

Running the cecret workflow with the StaPH-B Toolkit shouldn't be any different than using nextflow run UPHL-BioNGS/Cecret -r master If a new version of cecret is available you could try to specify the new version when using the StaPH-B Toolkit -wv flag i.e. -wv 3.5.20230216.

If you are still having issues let me know by opening an issue here: https://github.com/StaPH-B/staphb_toolkit/issues

Thanks!!