nf-core/sarek v2.7.1
Run Name: clever_euler
nf-core/sarek execution completed successfully!
The workflow was completed at 2021-10-23T10:10:19.558+02:00 (duration: 15h 28m 45s)
The command used to launch the workflow was as follows:
nextflow run nf-core/sarek -c ./genotoul_1.config --input /work2/project/sigenae/Philippe/NextFlow/Chicken_Test_2_Full_Samples/input.tsv --genomes_base /work2/project/sigenae/Philippe/NextFlow/Chicken_Test_2_Full_Samples/Data/ --genome Gallus_gallus-5.0 -resume --tools HaplotypeCaller,FreeBayes,mpileup --generate_gvcf
Pipeline Configuration:
| Pipeline Release | master |
|---|---|
| Run Name | clever_euler |
| Max Resources | 120 GB memory, 10 cpus, 4d time per job |
| Container | singularity - nfcore/sarek:2.7.1 |
| Output dir | ./results |
| Launch dir | /work2/project/sigenae/Philippe/NextFlow/Chicken_Test_2_Full_Samples |
| Working dir | /work2/project/sigenae/Philippe/NextFlow/Chicken_Test_2_Full_Samples/work |
| Script dir | /home/sigenae/.nextflow/assets/nf-core/sarek |
| User | sigenae |
| Input | /work2/project/sigenae/Philippe/NextFlow/Chicken_Test_2_Full_Samples/input.tsv |
| Step | mapping |
| Genome | Gallus_gallus-5.0 |
| Nucleotides/s | 1000 |
| Tools | haplotypecaller, freebayes, mpileup |
| MarkDuplicates | Options |
| Java options | "-Xms4000m -Xmx7g" |
| GATK Spark | No |
| Save BAMs mapped | No |
| Skip MarkDuplicates | No |
| GVCF | Yes |
| AWS iGenomes base | s3://ngi-igenomes/igenomes/ |
| Genomes base | /work2/project/sigenae/Philippe/NextFlow/Chicken_Test_2_Full_Samples/Data/ |
| Save Reference | No |
| BWA indexes | /work2/project/sigenae/Philippe/NextFlow/Chicken_Test_2_Full_Samples/Data//Gallus_gallus.Gallus_gallus-5.0.dna.toplevel.fa.{amb,ann,bwt,pac,sa} |
| dict | /work2/project/sigenae/Philippe/NextFlow/Chicken_Test_2_Full_Samples/Data//Gallus_gallus.Gallus_gallus-5.0.dna.toplevel.dict |
| fasta reference | /work2/project/sigenae/Philippe/NextFlow/Chicken_Test_2_Full_Samples/Data//Gallus_gallus.Gallus_gallus-5.0.dna.toplevel.fa |
| known indels | /work2/project/sigenae/Philippe/NextFlow/Chicken_Test_2_Full_Samples/Data//Gallus_gallus_incl_consequences.vcf |
| known indels index | /work2/project/sigenae/Philippe/NextFlow/Chicken_Test_2_Full_Samples/Data//Gallus_gallus_incl_consequences.vcf.idx |
| Publish dir mode | copy |
| Config Profile | standard |
| Config Description | The Genotoul cluster profile |
| Config Contact | support.bioinfo.genotoul@inra.fr |
| Config URL | http://bioinfo.genotoul.fr/ |
| Config Files | /home/sigenae/.nextflow/assets/nf-core/sarek/nextflow.config, /work2/project/sigenae/Philippe/NextFlow/Chicken_Test_2_Full_Samples/./genotoul_1.config |
| Date Started | 2021-10-22T18:41:34.085+02:00 |
| Date Completed | 2021-10-23T10:10:19.558+02:00 |
| Pipeline script file path | /home/sigenae/.nextflow/assets/nf-core/sarek/main.nf |
| Pipeline script hash ID | 7038b78fec38683f7c82b37e6d822ef7 |
| Pipeline repository Git URL | https://github.com/nf-core/sarek |
| Pipeline repository Git Commit | 68b9930a74962f3c42eee71f51e6dd2646269199 |
| Pipeline Git branch/tag | master |
| Nextflow Version | 21.04.1 |
| Nextflow Build | 5556 |
| Nextflow Compile Timestamp | 14-05-2021 15:20 UTC |
nf-core/sarek