Rnaseq: cannot find fastq.gz?

[arnoldliaoILMN]

I got this error:

Oct-25 14:45:24.737 [Actor Thread 2] ERROR nextflow.Nextflow - Cannot find any reads matching: /data/aliao/rnaseq/BrainmRNA20131201/*fastq.gz

but I do have fastq.gz in my dir:

aliao@playground:/data/aliao/rnaseq/BrainmRNA20131201$ ls -lah /data/aliao/rnaseq/BrainmRNA20131201/
total 7.5G
drwxrwxr-x  5 aliao aliao 4.0K Oct 25 14:45 .
drwxrwxr-x 10 aliao aliao 4.0K Oct 25 14:41 ..
-r--r--r--  1 aliao aliao 964M Oct 25 10:50 BrainmRNA_S5_L001_R1_001.fastq.gz
-r--r--r--  1 aliao aliao 976M Oct 25 10:52 BrainmRNA_S5_L001_R2_001.fastq.gz
-r--r--r--  1 aliao aliao 928M Oct 25 10:54 BrainmRNA_S5_L002_R1_001.fastq.gz
-r--r--r--  1 aliao aliao 941M Oct 25 10:55 BrainmRNA_S5_L002_R2_001.fastq.gz
-r--r--r--  1 aliao aliao 961M Oct 25 10:57 BrainmRNA_S5_L003_R1_001.fastq.gz
-r--r--r--  1 aliao aliao 972M Oct 25 10:59 BrainmRNA_S5_L003_R2_001.fastq.gz
-r--r--r--  1 aliao aliao 946M Oct 25 11:00 BrainmRNA_S5_L004_R1_001.fastq.gz
-r--r--r--  1 aliao aliao 955M Oct 25 11:02 BrainmRNA_S5_L004_R2_001.fastq.gz
drwxrwxr-x  3 aliao aliao 4.0K Oct 25 14:45 .nextflow
-rw-rw-r--  1 aliao aliao 4.5K Oct 25 14:45 .nextflow.log
-rw-rw-r--  1 aliao aliao 4.5K Oct 25 14:39 .nextflow.log.1
-rw-rw-r--  1 aliao aliao 4.4K Oct 25 14:39 .nextflow.log.2
-rw-rw-r--  1 aliao aliao 4.4K Oct 25 14:37 .nextflow.log.3
-rw-rw-r--  1 aliao aliao 3.4K Oct 25 14:36 .nextflow.log.4
-rw-rw-r--  1 aliao aliao 3.4K Oct 25 14:34 .nextflow.log.5
-rw-rw-r--  1 aliao aliao 3.4K Oct 25 10:53 .nextflow.log.6
-rw-rw-r--  1 aliao aliao 2.4K Oct 25 10:53 .nextflow.log.7
-rw-rw-r--  1 aliao aliao 2.1K Oct 25 10:51 .nextflow.log.8
drwxrwxr-x  3 aliao aliao 4.0K Oct 25 10:51 results
lrwxrwxrwx  1 aliao aliao   33 Oct 25 14:44 sample1.fastq.gz -> BrainmRNA_S5_L001_R1_001.fastq.gz
lrwxrwxrwx  1 aliao aliao   33 Oct 25 14:45 sample2.fastq.gz -> BrainmRNA_S5_L001_R2_001.fastq.gz
drwxrwxr-x  2 aliao aliao 4.0K Oct 25 10:51 work

[arnoldliaoILMN]

this was my command:

nextflow run /my-pipelines/rnaseq-master --genome GRCh37 --reads "/data/aliao/rnaseq/BrainmRNA20131201/*fastq.gz"

[likelet]

you can try --reads '*{1,2}.fastq.gz' to parse sample1.fastq.gz, sample2.fastq.gz under your folder

[apeltzer]

Please follow @likelet s advice and re-open if this doesn' help :-)

[ewels]

Maybe we should add a mention of the squiggly brackets to the error message

[jullor]

Hej,

Sorry if this is a stupid question but I got a similar error as above and cannot figure out how to fix it.

The error is

ERROR ~ Cannot find any reads matching: ~/Documents/DrosoFiles/seqFiles/*.fastq.gz
NB: Path needs to be enclosed in quotes!
NB: Path requires at least one * wildcard!
If this is single-end data, please specify --singleEnd on the command line.

even though the files are present in the provided directory

ll ~/Documents/DrosoFiles/seqFiles/*.fastq.gz
-r-xr-xr-x. 1 julie.lorent users 1,3G 10 jan 10.32 /home/julie.lorent/Documents/DrosoFiles/seqFiles/control_high_1.fastq.gz*
-r-xr-xr-x. 1 julie.lorent users 1,3G 10 jan 10.33 /home/julie.lorent/Documents/DrosoFiles/seqFiles/rps19_input_1.fastq.gz*

I used
nextflow run nf-core/rnaseq -with-singularity -profile singularity,standard --singleEnd --genome BDGP6 --reads "~/Documents/DrosoFiles/seqFiles/*.fastq.gz" &

[ewels]

Not a stupid question @jullor - using --singleEnd as you have _should_ mean that the pattern works..

[ewels]

Small side-note: you don't need -with-singularity if you have -profile singularity..

What version of the pipeline are you running? Could you paste the whole log header please?

[jullor]

N E X T F L O W  ~  version 0.29.0
Launching `nf-core/rnaseq` [awesome_hoover] - revision: e8376373da [master]
ERROR ~ Cannot find any reads matching: ~/Documents/DrosoFiles/seqFiles/*.fastq.gz
NB: Path needs to be enclosed in quotes!
NB: Path requires at least one * wildcard!
If this is single-end data, please specify --singleEnd on the command line.
 -- Check '.nextflow.log' file for details

Is it what you need or should I paste the content of the .nextflow.log file as well?

Removing -with-singularity indeed did not change anything. Also I have no idea why but replacing ~ with /home/julie.lorent/ (which should be the same thing) gives another error:

nextflow run nf-core/rnaseq -profile singularity,standard --singleEnd --genome BDGP6 --reads "/home/julie.lorent/Documents/DrosoFiles/seqFiles/*.fastq.gz" &

N E X T F L O W  ~  version 0.29.0
Launching `nf-core/rnaseq` [peaceful_blackwell] - revision: e8376373da [master]
ERROR ~ Unexpected error [StackOverflowError]
 -- Check '.nextflow.log' file for details

[ewels]

Aha, yes that's good - Nextflow version 0.29.0 is super old in nextflow terms (24 April 2018) so that's probably the reason. Try nextflow self-update and try again...

[jullor]

Great, thank you very much! It's running now..

[ewels]

Fantastic! Thanks for letting us know.. Now that you're ahead of nextflow version 0.32.0 or so, nextflow will warn you if the same thing happens in the future (a new feature was added at our request around then to define a minimum required version).

Phil