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nf-core / rnaseq

RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.
https://nf-co.re/rnaseq
MIT License
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docker: failed to register layer: Error processing tar file(exit status 1) #255

Closed gtg269c closed 5 years ago

gtg269c commented 5 years ago

Command run on AWS EC2 instance to run docker on local instance

nextflow run /home/ubuntu/my-pipelines/nf-core/rnaseq-nfcore/rnaseq --reads '/data/dataset/SRR9667733/*_R{1,2}.fastq.gz.1' --genome GRCh37 -profile docker

It started with out issues 

Jul-15 23:36:33.141 [main] INFO  nextflow.Nextflow - Run Name          : backstabbing_hopper
Reads             : /data/dataset/SRR9667733/*_R{1,2}.fastq.gz.1
Data Type         : Paired-End
Genome            : GRCh37
Strandedness      : None
Trimming          : 5'R1: 0 / 5'R2: 0 / 3'R1: 0 / 3'R2: 0
Aligner           : STAR
STAR Index        : s3://ngi-igenomes/igenomes//Homo_sapiens/Ensembl/GRCh37/Sequence/STARIndex/
GTF Annotation    : s3://ngi-igenomes/igenomes//Homo_sapiens/Ensembl/GRCh37/Annotation/Genes/genes.gtf
BED Annotation    : s3://ngi-igenomes/igenomes//Homo_sapiens/Ensembl/GRCh37/Annotation/Genes/genes.bed
Save prefs        : Ref Genome: No / Trimmed FastQ: No / Alignment intermediates: No
Max Resources     : 128 GB memory, 16 cpus, 10d time per job
Container         : docker - nfcore/rnaseq:1.3
Output dir        : ./results
Launch dir        : /home/ubuntu/my-pipelines/nf-core/rnaseq-nfcore/rnaseq
Working dir       : /home/ubuntu/my-pipelines/nf-core/rnaseq-nfcore/rnaseq/work
Script dir        : /home/ubuntu/my-pipelines/nf-core/rnaseq-nfcore/rnaseq
User              : ubuntu
Config Profile    : docker

However I get the following error. I am not sure if it runs out of space on the EC2 instance or there are other issue with docker. 

Unable to find image 'nfcore/rnaseq:1.3' locally
1.3: Pulling from nfcore/rnaseq
cc1a78bfd46b: Pulling fs layer
420ea9ce27d9: Pulling fs layer
1b219c050547: Pulling fs layer
1c177edca126: Pulling fs layer
49ce9c6e70c7: Pulling fs layer
cc87c418bf51: Pulling fs layer
b080fd1a5c2b: Pulling fs layer
3576700fa2f6: Pulling fs layer
3576700fa2f6: Waiting
1c177edca126: Waiting
b080fd1a5c2b: Waiting
49ce9c6e70c7: Waiting
cc87c418bf51: Waiting
cc1a78bfd46b: Verifying Checksum
cc1a78bfd46b: Download complete
420ea9ce27d9: Download complete
1c177edca126: Verifying Checksum
1c177edca126: Download complete
1b219c050547: Verifying Checksum
1b219c050547: Download complete
49ce9c6e70c7: Verifying Checksum
49ce9c6e70c7: Download complete
b080fd1a5c2b: Verifying Checksum
b080fd1a5c2b: Download complete
cc1a78bfd46b: Pull complete
cc87c418bf51: Verifying Checksum
cc87c418bf51: Download complete
420ea9ce27d9: Pull complete
1b219c050547: Pull complete
1c177edca126: Pull complete
49ce9c6e70c7: Pull complete
cc87c418bf51: Pull complete
b080fd1a5c2b: Pull complete
3576700fa2f6: Download complete
docker: failed to register layer: Error processing tar file(exit status 1): write /opt/conda/envs/nf-core-rnaseq-1.3/lib/libssl.so.1.1: no space left on device.
See 'docker run --help'.
gtg269c commented 5 years ago

I just needed more memory on the root drive. It was resolved.

avilella commented 4 years ago

Hi @gtg269c , I am attempting the same, could you share your aws/container details in your nextflow.config file for me to see what they need to look like? Thx