Closed gq1 closed 4 months ago
nf-core lint
overall result: Passed :white_check_mark: :warning:Posted for pipeline commit 0458cd4
+| ✅ 130 tests passed |+
#| ❔ 19 tests were ignored |#
!| ❗ 3 tests had warnings |!
Still more storage needed:
INFO: Creating SIF file...
FATAL: While making image from oci registry: error fetching image to cache: while building SIF from layers: while creating SIF: while creating container: write /home/runner/.apptainer/cache/oci-tmp/tmp_936536538: copy_file_range: no space left on device
After increasing the memory to 15G, there is a bug in this module:
Process `SANGERTOL_GENOMEASSEMBLY:GENOMEASSEMBLY:HIC_MAPPING:BAMTOBED_SORT (baUndUnlc1)` terminated with an error exit status (2)
Command executed:
samtools view -@4 -u -F0x400 baUndUnlc1_mkdup.bam | bamToBed | sort -k4 --parallel=4 -S 7.5G -T . > baUndUnlc1_merged_sorted.bed
@ksenia-krasheninnikova Can you round the half memory? It seems the sort command only take the whole number as buffer memorey.
@ksenia-krasheninnikova I finished my test now.
ubuntu2204-4c
has 4 CPUs and 16G memory, the same like the free version. You probably can give all of them to nextflow and I hope it will run fast. But my last run took 15mins, comparing your previous run only 12 mins. But still it is good to merge this change.@gq1: The update looks fine to me. I have added rounding of the buffer memory in bamtobed_sort module.
This error can be seen randomly. Re-running should work:
Failed to pull singularity image
command: singularity pull --name ghcr.io-nbisweden-fastk_genescopefk_merquryfk-1.2.img.pulling.1715092918304 docker://ghcr.io/nbisweden/fastk_genescopefk_merquryfk:1.2 > /dev/null
status : 255
message:
INFO: Converting OCI blobs to SIF format
INFO: Starting build...
Getting image source signatures
Copying blob sha256:b56b35773cdcbd2913e4d4b4c8deeb38a4f3ff4abf1e22c1f66d7e561739bc3f
Copying blob sha256:ac77672a979829fb237e3b2bf02d933da8f1419de36efc0e902fdb2c60bf521c
Copying blob sha256:83eeaff6d4af9433f22fc60ba62bc851474157f4433388e17b76f05f7badb9a8
Copying blob sha256:8cc533bc8a27c6fa8d5d4ca6804f553f8be9fdd74bd99e5ecfebef9416078cf6
Copying blob sha256:7b303595d9b321a9020d0ddbf1dea4c83237e2367117606a8d5466c446714ba1
Copying blob sha256:38a8fd9de21eaee23a103dc924054d05dc4c4bc06334e7930f06871b17fca606
Copying blob sha256:8faa8459fed85f8afdba73a54844c4e5fd34779577afd8be3d9a38a2e[70](https://github.com/sanger-tol/genomeassembly/actions/runs/8987250188/job/24685687775?pr=42#step:9:71)2e849
Copying blob sha256:84463ad43d8de19d0f07ae43c081868ab61f920766b8e593ecf87d4cfb6a34fc
Copying blob sha256:09db92fad269c5e2ffb9526eb8613884f68ea277b173f65cd029bd5fc3d36f6d
Copying blob sha256:4f4fb700ef54461cfa025[71](https://github.com/sanger-tol/genomeassembly/actions/runs/8987250188/job/24685687775?pr=42#step:9:72)ae0db9a0dc1e0cdb5577484a6d75e68dc38e8acc1
Copying blob sha256:307f67c1539cc9a801e3126a462c953404bee7e831909a332cd0c2de897[74](https://github.com/sanger-tol/genomeassembly/actions/runs/8987250188/job/24685687775?pr=42#step:9:75)928
Copying config sha256:af05a1a95bc1bb513db1c2d166970e2ff5[75](https://github.com/sanger-tol/genomeassembly/actions/runs/8987250188/job/24685687775?pr=42#step:9:76)d6de8e80635987a09b74a617f1dd
Writing manifest to image destination
FATAL: While making image from oci registry: error fetching image to cache: while building SIF from layers: conveyor failed to get: while getting config: no descriptor found for reference "60da47b6[76](https://github.com/sanger-tol/genomeassembly/actions/runs/8987250188/job/24685687775?pr=42#step:9:77)ee2b52be5b774a9b65e54edc2bb2fd319876efd09efd8d99d39ada"
Another error message:
Command output:
Looking for mitochondrion for Caradrina clavipalpis
Command error:
INFO: Environment variable SINGULARITYENV_NXF_DEBUG is set, but APPTAINERENV_NXF_DEBUG is preferred
INFO: Environment variable SINGULARITYENV_NCBI_API_KEY is set, but APPTAINERENV_NCBI_API_KEY is preferred
Looking for mitochondrion for Caradrina clavipalpis
Traceback (most recent call last):
File "/opt/MitoHiFi/src/findMitoReference.py", line 96, in <module>
for g in [args.species] + list(get_lineage(args.species)):
File "/opt/MitoHiFi/src/findMitoReference.py", line 29, in get_lineage
record = Entrez.read(handle)
File "/usr/local/lib/python3.6/dist-packages/Bio/Entrez/__init__.py", line 508, in read
record = handler.read(handle)
File "/usr/local/lib/python3.6/dist-packages/Bio/Entrez/Parser.py", line 335, in read
self.parser.ParseFile(handle)
File "../Modules/pyexpat.c", line 473, in EndElement
File "/usr/local/lib/python3.6/dist-packages/Bio/Entrez/Parser.py", line 704, in endErrorElementHandler
raise RuntimeError(value)
RuntimeError: Search Backend failed:
PR checklist
nf-core lint
).nextflow run . -profile test,docker --outdir <OUTDIR>
).docs/usage.md
is updated.docs/output.md
is updated.CHANGELOG.md
is updated.README.md
is updated (including new tool citations and authors/contributors).