Release test 21.05

[bernt-matthias]

/run-all-tool-tests branch=release_21.05

[gxydevbot]

Summary:

4 failure 3410 success

Find all tool test results here

[mvdbeek]

That looks pretty good, I suppose those 4 are likely also flaky on 21.01:

• ❌ meryl (Test #9)

  **Problems**: * ``` Output read_db: different than expected Expected file size was 60531, actual file size was 60841 (difference of 300 accepted) ``` **Command Line:** * ```console mkdir -p ./temp_db/ && tar -zxf /tmp/tmpirj2mate/files/7/b/5/dataset_7b5d131f-647e-4720-8bd7-40ed5bf72f29.dat -C ./temp_db/ && mv ./temp_db/* tmp.meryl && meryl multiply 3 tmp.meryl output read-db.meryl && tar -zcf read-db.meryldb read-db.meryl ``` **Exit Code:** * ```console 0 ``` **Standard Error:** * ```console Found 1 command tree. PROCESSING TREE #1 using 2 threads. opMultiply constant=3 tmp.meryl output to read-db.meryl Cleaning up. Bye. ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | \_\_input\_ext | ` "input" ` | | chromInfo | ` "/tmp/tmpirj2mate/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | dbkey | ` "?" ` | | operation\_type | ` {"X": "3", "__current_case__": 2, "arithmetic_operations": "multiply", "command_type": "arithmetic-kmers", "input_meryldb_02": {"values": [{"id": 374, "src": "hda"}]}} ` |
• ❌ rdavidwebservice (Test #1)

  **Problems**: * ``` Job in error state.. tool_id: rdavidwebservice, exit_code: 1, stderr: Warning message: In Sys.setlocale("LC_MESSAGES", "C.UTF-8") : OS reports request to set locale to "C.UTF-8" cannot be honored Loading required package: graph Loading required package: BiocGenerics Loading required package: parallel Attaching package: 'BiocGenerics' The following objects are masked from 'package:parallel': clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, append, as.data.frame, basename, cbind, colMeans, colSums, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which, which.max, which.min Loading required package: GOstats Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Loading required package: Category Loading required package: stats4 Loading required package: AnnotationDbi Loading required package: IRanges Loading required package: S4Vectors Attaching package: 'S4Vectors' The following object is masked from 'package:base': expand.grid Loading required package: Matrix Attaching package: 'Matrix' The following object is masked from 'package:S4Vectors': expand Attaching package: 'GOstats' The following object is masked from 'package:AnnotationDbi': makeGOGraph Loading required package: ggplot2 Attaching package: 'RDAVIDWebService' The following object is masked from 'package:AnnotationDbi': species The following object is masked from 'package:IRanges': members The following objects are masked from 'package:BiocGenerics': counts, species Read 164 items Error in .jcall("RJavaTools", "Ljava/lang/Object;", "invokeMethod", cl, : org.apache.axis2.AxisFault: Transport error: 403 Error: Forbidden Calls: addList ... strsplit -> -> .jrcall -> .jcall -> .jcheck . ``` * ``` Job in error state.. tool_id: rdavidwebservice, exit_code: 1, stderr: Warning message: In Sys.setlocale("LC_MESSAGES", "C.UTF-8") : OS reports request to set locale to "C.UTF-8" cannot be honored Loading required package: graph Loading required package: BiocGenerics Loading required package: parallel Attaching package: 'BiocGenerics' The following objects are masked from 'package:parallel': clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, append, as.data.frame, basename, cbind, colMeans, colSums, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which, which.max, which.min Loading required package: GOstats Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Loading required package: Category Loading required package: stats4 Loading required package: AnnotationDbi Loading required package: IRanges Loading required package: S4Vectors Attaching package: 'S4Vectors' The following object is masked from 'package:base': expand.grid Loading required package: Matrix Attaching package: 'Matrix' The following object is masked from 'package:S4Vectors': expand Attaching package: 'GOstats' The following object is masked from 'package:AnnotationDbi': makeGOGraph Loading required package: ggplot2 Attaching package: 'RDAVIDWebService' The following object is masked from 'package:AnnotationDbi': species The following object is masked from 'package:IRanges': members The following objects are masked from 'package:BiocGenerics': counts, species Read 164 items Error in .jcall("RJavaTools", "Ljava/lang/Object;", "invokeMethod", cl, : org.apache.axis2.AxisFault: Transport error: 403 Error: Forbidden Calls: addList ... strsplit -> -> .jrcall -> .jcall -> .jcheck . ``` * ``` Job in error state.. tool_id: rdavidwebservice, exit_code: 1, stderr: Warning message: In Sys.setlocale("LC_MESSAGES", "C.UTF-8") : OS reports request to set locale to "C.UTF-8" cannot be honored Loading required package: graph Loading required package: BiocGenerics Loading required package: parallel Attaching package: 'BiocGenerics' The following objects are masked from 'package:parallel': clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, append, as.data.frame, basename, cbind, colMeans, colSums, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which, which.max, which.min Loading required package: GOstats Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Loading required package: Category Loading required package: stats4 Loading required package: AnnotationDbi Loading required package: IRanges Loading required package: S4Vectors Attaching package: 'S4Vectors' The following object is masked from 'package:base': expand.grid Loading required package: Matrix Attaching package: 'Matrix' The following object is masked from 'package:S4Vectors': expand Attaching package: 'GOstats' The following object is masked from 'package:AnnotationDbi': makeGOGraph Loading required package: ggplot2 Attaching package: 'RDAVIDWebService' The following object is masked from 'package:AnnotationDbi': species The following object is masked from 'package:IRanges': members The following objects are masked from 'package:BiocGenerics': counts, species Read 164 items Error in .jcall("RJavaTools", "Ljava/lang/Object;", "invokeMethod", cl, : org.apache.axis2.AxisFault: Transport error: 403 Error: Forbidden Calls: addList ... strsplit -> -> .jrcall -> .jcall -> .jcheck . ``` * ``` Job in error state.. tool_id: rdavidwebservice, exit_code: 1, stderr: Warning message: In Sys.setlocale("LC_MESSAGES", "C.UTF-8") : OS reports request to set locale to "C.UTF-8" cannot be honored Loading required package: graph Loading required package: BiocGenerics Loading required package: parallel Attaching package: 'BiocGenerics' The following objects are masked from 'package:parallel': clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, append, as.data.frame, basename, cbind, colMeans, colSums, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which, which.max, which.min Loading required package: GOstats Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Loading required package: Category Loading required package: stats4 Loading required package: AnnotationDbi Loading required package: IRanges Loading required package: S4Vectors Attaching package: 'S4Vectors' The following object is masked from 'package:base': expand.grid Loading required package: Matrix Attaching package: 'Matrix' The following object is masked from 'package:S4Vectors': expand Attaching package: 'GOstats' The following object is masked from 'package:AnnotationDbi': makeGOGraph Loading required package: ggplot2 Attaching package: 'RDAVIDWebService' The following object is masked from 'package:AnnotationDbi': species The following object is masked from 'package:IRanges': members The following objects are masked from 'package:BiocGenerics': counts, species Read 164 items Error in .jcall("RJavaTools", "Ljava/lang/Object;", "invokeMethod", cl, : org.apache.axis2.AxisFault: Transport error: 403 Error: Forbidden Calls: addList ... strsplit -> -> .jrcall -> .jcall -> .jcheck . ``` * ``` Job in error state.. tool_id: rdavidwebservice, exit_code: 1, stderr: Warning message: In Sys.setlocale("LC_MESSAGES", "C.UTF-8") : OS reports request to set locale to "C.UTF-8" cannot be honored Loading required package: graph Loading required package: BiocGenerics Loading required package: parallel Attaching package: 'BiocGenerics' The following objects are masked from 'package:parallel': clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, append, as.data.frame, basename, cbind, colMeans, colSums, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which, which.max, which.min Loading required package: GOstats Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Loading required package: Category Loading required package: stats4 Loading required package: AnnotationDbi Loading required package: IRanges Loading required package: S4Vectors Attaching package: 'S4Vectors' The following object is masked from 'package:base': expand.grid Loading required package: Matrix Attaching package: 'Matrix' The following object is masked from 'package:S4Vectors': expand Attaching package: 'GOstats' The following object is masked from 'package:AnnotationDbi': makeGOGraph Loading required package: ggplot2 Attaching package: 'RDAVIDWebService' The following object is masked from 'package:AnnotationDbi': species The following object is masked from 'package:IRanges': members The following objects are masked from 'package:BiocGenerics': counts, species Read 164 items Error in .jcall("RJavaTools", "Ljava/lang/Object;", "invokeMethod", cl, : org.apache.axis2.AxisFault: Transport error: 403 Error: Forbidden Calls: addList ... strsplit -> -> .jrcall -> .jcall -> .jcheck . ``` **Command Line:** * ```console cat '/tmp/tmpvx2xlv7b/job_working_directory/000/231/configs/tmp1hncwwuq' && Rscript '/tmp/tmpvx2xlv7b/job_working_directory/000/231/configs/tmp1hncwwuq' ``` **Exit Code:** * ```console 1 ``` **Standard Error:** * ```console Warning message: In Sys.setlocale("LC_MESSAGES", "C.UTF-8") : OS reports request to set locale to "C.UTF-8" cannot be honored Loading required package: graph Loading required package: BiocGenerics Loading required package: parallel Attaching package: 'BiocGenerics' The following objects are masked from 'package:parallel': clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, append, as.data.frame, basename, cbind, colMeans, colSums, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which, which.max, which.min Loading required package: GOstats Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Loading required package: Category Loading required package: stats4 Loading required package: AnnotationDbi Loading required package: IRanges Loading required package: S4Vectors Attaching package: 'S4Vectors' The following object is masked from 'package:base': expand.grid Loading required package: Matrix Attaching package: 'Matrix' The following object is masked from 'package:S4Vectors': expand Attaching package: 'GOstats' The following object is masked from 'package:AnnotationDbi': makeGOGraph Loading required package: ggplot2 Attaching package: 'RDAVIDWebService' The following object is masked from 'package:AnnotationDbi': species The following object is masked from 'package:IRanges': members The following objects are masked from 'package:BiocGenerics': counts, species Read 164 items Error in .jcall("RJavaTools", "Ljava/lang/Object;", "invokeMethod", cl, : org.apache.axis2.AxisFault: Transport error: 403 Error: Forbidden Calls: addList ... strsplit -> -> .jrcall -> .jcall -> .jcheck ``` **Standard Output:** * ```console options(show.error.messages=F, error=function(){cat(geterrmessage(), file=stderr()); q("no",1,F)}) loc <- Sys.setlocale("LC_MESSAGES", "C.UTF-8") library(RDAVIDWebService) gene_list <- scan('/tmp/tmpvx2xlv7b/files/b/a/3/dataset_ba3c503a-1b2c-45c0-8b9a-29b045f272af.dat', what="character") gene_identifier_type <- 'AFFYMETRIX_3PRIME_IVT_ID' email <- 'test@bx.psu.edu' david <- DAVIDWebService(email=email, url="https://david.ncifcrf.gov/webservice/services/DAVIDWebService.DAVIDWebServiceHttpSoap12Endpoint/") geneList <- addList(david, gene_list, idType=gene_identifier_type, listName="genelist", listType="Gene") getClusterReportFile(david, '/tmp/tmpvx2xlv7b/files/3/6/3/dataset_3639ca69-fcb5-4a8a-aa40-ec023a5fde52.dat', kappa = as.integer('50'), overlap = as.integer('3'), initialSeed = as.integer('3'), finalSeed = as.integer('3'), linkage = as.double('0.50')) getFunctionalAnnotationChartFile(david, '/tmp/tmpvx2xlv7b/files/f/4/0/dataset_f407c6eb-4b8c-42a7-88a1-9285983c5f72.dat', count = as.integer('2'), threshold = as.double('0.1')) getFunctionalAnnotationTableFile(david, '/tmp/tmpvx2xlv7b/files/5/f/8/dataset_5f808039-f67a-47d1-8ab1-a3abf0ebe7b7.dat') getGeneListReportFile(david, '/tmp/tmpvx2xlv7b/files/1/3/7/dataset_1379dbb2-0c85-45fa-bfa3-89596f1b2b39.dat') [INFO] Unable to sendViaPost to url[https://david.ncifcrf.gov/webservice/services/DAVIDWebService.DAVIDWebServiceHttpSoap12Endpoint/] org.apache.axis2.AxisFault: Transport error: 403 Error: Forbidden at org.apache.axis2.transport.http.HTTPSender.handleResponse(HTTPSender.java:310) at org.apache.axis2.transport.http.HTTPSender.sendViaPost(HTTPSender.java:200) at org.apache.axis2.transport.http.HTTPSender.send(HTTPSender.java:76) at org.apache.axis2.transport.http.CommonsHTTPTransportSender.writeMessageWithCommons(CommonsHTTPTransportSender.java:400) at org.apache.axis2.transport.http.CommonsHTTPTransportSender.invoke(CommonsHTTPTransportSender.java:225) at org.apache.axis2.engine.AxisEngine.send(AxisEngine.java:435) at org.apache.axis2.description.OutInAxisOperationClient.send(OutInAxisOperation.java:402) at org.apache.axis2.description.OutInAxisOperationClient.executeImpl(OutInAxisOperation.java:229) at org.apache.axis2.client.OperationClient.execute(OperationClient.java:165) at sample.session.client.stub.DAVIDWebServiceStub.getAllListNames(DAVIDWebServiceStub.java:2533) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:498) at RJavaTools.invokeMethod(RJavaTools.java:386) ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | AnnotationCategories | ` {"Disease": ["GAD_DISEASE", "GAD_DISEASE_CLASS", "OMIM_DISEASE"], "Functional_Categories": null, "Gene_Ontology": ["GOTERM_MF_FAT", "GOTERM_CC_FAT", "GOTERM_BP_FAT"], "General_Annotations": null, "Literature": null, "Main_Accessions": null, "Pathways": "KEGG_PATHWAY", "Protein_Domains": null, "Protein_Interactions": null, "Tissue_Expression": null, "__current_case__": 0, "setAnnotationCategories": "with_AnnotationCategories"} ` | | FunctionalAnnotationChart | ` {"__current_case__": 0, "count": "2", "set_FAChart_params": "Yes", "threshold": "0.1"} ` | | FunctionalAnnotationCluster | ` {"__current_case__": 0, "finalSeed": "3", "initialSeed": "3", "kappa": "50", "linkage": "0.50", "overlap": "3", "set_FACluster_params": "Yes"} ` | | FunctionalAnnotationTable | ` {"__current_case__": 0, "set_FATable_params": "Yes"} ` | | GeneListReport | ` {"__current_case__": 0, "set_GLReport_params": "Yes"} ` | | \_\_input\_ext | ` "tabular" ` | | background | ` {"__current_case__": 1, "background_selector": "without_background"} ` | | chromInfo | ` "/tmp/tmpvx2xlv7b/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | dbkey | ` "?" ` | | email | ` "yes" ` | | identifier1 | ` "AFFYMETRIX_3PRIME_IVT_ID" ` |
• ❌ sarscov2formatter (Test #1)

  **Problems**: * ``` Job in error state.. tool_id: sarscov2formatter, exit_code: 137, stderr: /tmp/tmpa5vwoor0/job_working_directory/000/153/tool_script.sh: line 22: 8 Killed sarscov2formatter -a '/tmp/tmpa5vwoor0/files/0/f/c/dataset_0fc1e267-8c53-43d9-b564-ba1be18316d1.dat' -m ncbi . ``` * ``` Job in error state.. tool_id: sarscov2formatter, exit_code: 137, stderr: /tmp/tmpa5vwoor0/job_working_directory/000/153/tool_script.sh: line 22: 8 Killed sarscov2formatter -a '/tmp/tmpa5vwoor0/files/0/f/c/dataset_0fc1e267-8c53-43d9-b564-ba1be18316d1.dat' -m ncbi . ``` * ``` Job in error state.. tool_id: sarscov2formatter, exit_code: 137, stderr: /tmp/tmpa5vwoor0/job_working_directory/000/153/tool_script.sh: line 22: 8 Killed sarscov2formatter -a '/tmp/tmpa5vwoor0/files/0/f/c/dataset_0fc1e267-8c53-43d9-b564-ba1be18316d1.dat' -m ncbi . ``` * ``` Job in error state.. tool_id: sarscov2formatter, exit_code: 137, stderr: /tmp/tmpa5vwoor0/job_working_directory/000/153/tool_script.sh: line 22: 8 Killed sarscov2formatter -a '/tmp/tmpa5vwoor0/files/0/f/c/dataset_0fc1e267-8c53-43d9-b564-ba1be18316d1.dat' -m ncbi . ``` **Command Line:** * ```console sarscov2formatter -a '/tmp/tmpa5vwoor0/files/0/f/c/dataset_0fc1e267-8c53-43d9-b564-ba1be18316d1.dat' -m ncbi ``` **Exit Code:** * ```console 137 ``` **Standard Error:** * ```console /tmp/tmpa5vwoor0/job_working_directory/000/153/tool_script.sh: line 22: 8 Killed sarscov2formatter -a '/tmp/tmpa5vwoor0/files/0/f/c/dataset_0fc1e267-8c53-43d9-b564-ba1be18316d1.dat' -m ncbi ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | \_\_input\_ext | ` "input" ` | | chromInfo | ` "/tmp/tmpa5vwoor0/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | dbkey | ` "?" ` | | source | ` {"__current_case__": 0, "source_choice": "ncbi"} ` |
• ❌ scpipe (Test #4)

  **Problems**: * ``` Output out_plots: different than expected, difference (using sim_size): ( /tmp/tmp3hwnwrrqplots.pdf v. /tmp/tmpt8hrcu1eplots.pdf ) Files /tmp/tmp3hwnwrrqplots.pdf=29923b but /tmp/tmpt8hrcu1eplots.pdf=46876b - compare by size (delta=10000) failed ``` **Command Line:** * ```console ln -s '/tmp/tmp81b_mcez/files/1/4/9/dataset_149296c1-d516-4dcc-a769-bba245254724.dat' 'aligned_mapped_bam' && ln -s '/tmp/tmp81b_mcez/files/_metadata_files/f/a/6/metadata_fa6a68ff-1fef-4a10-af6f-9a7834438926.dat' 'aligned_mapped_bam.bai' && ln -s '/tmp/tmp81b_mcez/files/3/6/6/dataset_3660661b-ab0f-432b-b8ca-9e1400314606.dat' 'mm10_MT19_gff3 uncompressed.gff3' && TAB=$(printf '\t') && sed -e "s/${TAB}/,/g" '/tmp/tmp81b_mcez/files/3/5/d/dataset_35dd3f88-ab9a-4472-93b9-d88112fd189c.dat' > samples.barcodes && Rscript '/home/runner/.planemo/planemo_tmp_1y9wjywt/scpipe.R' --bam 'aligned_mapped_bam' --samplename 'aligned_mapped_bam' --barcodes 'samples.barcodes' --exons 'mm10_MT19_gff3 uncompressed.gff3' --organism 'mmusculus_gene_ensembl' --bs1 -1 --bl1 0 --bs2 6 --bl2 8 --us -1 --ul 6 --metrics_matrix 'TRUE' --rmlow True --rmN True --minq 20 --numbq 2 --max_mis 1 --max_reads 1000000 --min_count 10 --UMI_cor 1 --stnd True --gene_fl False --nthreads ${GALAXY_SLOTS:-2} ``` **Exit Code:** * ```console 0 ``` **Standard Error:** * ```console Warning message: In Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") : OS reports request to set locale to "en_US.UTF-8" cannot be honored Warning message: Removed 6 rows containing missing values (position_stack). `stat_bin()` using `bins = 30`. Pick better value with `binwidth`. `stat_bin()` using `bins = 30`. Pick better value with `binwidth`. `stat_bin()` using `bins = 30`. Pick better value with `binwidth`. ``` **Standard Output:** * ```console [1] "Assigning reads to exons" add gff3 annotation: mm10_MT19_gff3 uncompressed.gff3 unique map to exon:27351 ambiguous map to multiple exon:261 map to intron:112 not mapped:988 unaligned:0 [1] "De-multiplexing data" [1] "Counting genes" [1] "Performing QC" [1] "organism/gene_id_type not provided. make a guess: mmusculus_gene_ensembl / ensembl_gene_id" [1] "spikeNames(sce)==NULL, no spike-in information." [1] "the following QC metrics not find in colData from sce:" [1] "non_ERCC_percent" null device 1 [1] "Removing outliers" R version 3.4.1 (2017-06-30) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Buildroot 2014.02 Matrix products: default BLAS: /usr/local/lib/R/lib/libRblas.so LAPACK: /usr/local/lib/R/lib/libRlapack.so locale: [1] C attached base packages: [1] parallel stats4 methods stats graphics grDevices utils [8] datasets base other attached packages: [1] Rtsne_0.13 scales_1.0.0 [3] scran_1.6.2 scater_1.6.0 [5] DT_0.4 plotly_4.7.1 [7] readr_1.1.1 optparse_1.6.0 [9] scPipe_1.0.0 SingleCellExperiment_1.0.0 [11] SummarizedExperiment_1.10.1 DelayedArray_0.6.6 [13] BiocParallel_1.14.2 matrixStats_0.54.0 [15] Biobase_2.40.0 GenomicRanges_1.32.7 [17] GenomeInfoDb_1.16.0 IRanges_2.14.12 [19] S4Vectors_0.18.3 BiocGenerics_0.26.0 [21] ggplot2_2.2.1 loaded via a namespace (and not attached): [1] bitops_1.0-6 bit64_0.9-7 RColorBrewer_1.1-2 [4] progress_1.2.0 httr_1.3.1 dynamicTreeCut_1.63-1 [7] tools_3.4.1 R6_2.2.2 vipor_0.4.5 [10] DBI_1.0.0 lazyeval_0.2.1 colorspace_1.3-2 [13] tidyselect_0.2.4 gridExtra_2.3 prettyunits_1.0.2 [16] GGally_1.4.0 curl_3.2 bit_1.1-12 [19] compiler_3.4.1 labeling_0.3 DEoptimR_1.0-8 [22] robustbase_0.93-2 stringr_1.3.1 digest_0.6.18 [25] XVector_0.20.0 pkgconfig_2.0.2 htmltools_0.3.6 [28] limma_3.36.5 htmlwidgets_1.2 rlang_0.3.0.1 [31] RSQLite_2.1.1 FNN_1.1.2.1 shiny_1.2.0 [34] bindr_0.1.1 zoo_1.8-3 jsonlite_1.5 [37] mclust_5.4.1 dplyr_0.7.6 RCurl_1.95-4.11 [40] magrittr_1.5 GenomeInfoDbData_1.1.0 Matrix_1.2-14 [43] Rhdf5lib_1.2.1 Rcpp_1.0.0 ggbeeswarm_0.6.0 [46] munsell_0.5.0 viridis_0.5.1 stringi_1.2.4 [49] edgeR_3.22.5 MASS_7.3-50 zlibbioc_1.26.0 [52] rhdf5_2.24.0 plyr_1.8.4 grid_3.4.1 [55] blob_1.1.1 promises_1.0.1 shinydashboard_0.7.1 [58] crayon_1.3.4 lattice_0.20-35 splines_3.4.1 [61] hms_0.4.2 locfit_1.5-9.1 pillar_1.3.0 [64] igraph_1.2.2 rjson_0.2.20 reshape2_1.4.3 [67] biomaRt_2.36.1 XML_3.98-1.16 glue_1.3.0 [70] data.table_1.11.4 httpuv_1.4.5 gtable_0.2.0 [73] getopt_1.20.2 purrr_0.2.5 tidyr_0.8.1 [76] reshape_0.8.7 assertthat_0.2.0 mime_0.5 [79] xtable_1.8-3 later_0.7.3 viridisLite_0.3.0 [82] tibble_1.4.2 AnnotationDbi_1.42.1 beeswarm_0.2.3 [85] memoise_1.1.0 tximport_1.8.0 bindrcpp_0.2.2 [88] statmod_1.4.30 Rhtslib_1.10.0 ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | \_\_input\_ext | ` "input" ` | | adv | ` {"UMI_cor": "1", "f": {"max_mis": "1", "max_reads": "1000000", "min_count": "10", "minq": "20", "numbq": "2", "rmN": "true", "rmlow": "true"}, "gene_fl": "false", "stnd": "true"} ` | | bl1 | ` "0" ` | | bl2 | ` "8" ` | | bs1 | ` "-1" ` | | bs2 | ` "6" ` | | chromInfo | ` "/tmp/tmp81b_mcez/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | dbkey | ` "?" ` | | keep\_outliers | ` "false" ` | | organism | ` "mmusculus_gene_ensembl" ` | | out | ` {"metrics_matrix": "true", "plots": "true", "rdata": "false", "report": "false", "rscript": "false"} ` | | samples | ` {"__current_case__": 0, "bam": {"values": [{"id": 285, "src": "hda"}]}, "barcodes": {"values": [{"id": 286, "src": "hda"}]}, "format_select": "bam"} ` | | ul | ` "6" ` | | us | ` "-1" ` |

[bernt-matthias]

Yes, but I remember that last week only pyega3 failed.. Odd

[davelopez]

In the last Weekly global Tool Linting and Tests run, there are some more tests failing. They appear to be all related to temporal service unavailability or connectivity issues. I tracked them in #3688 and #3689 just in case, but probably another run will make them pass.

[bernt-matthias]

We are back to 5 failing tests.

❌ ncbi_eutils_elink (Test #3) ❌ rdavidwebservice (Test #1) ❌ sarscov2formatter (Test #1) ❌ scpipe (Test #4) ❌ simple_weather (Test #1)

Should we close the 2 issues again? Or is there anything we could improve in the wrappers?

[bernt-matthias]

I guess simple_weather could need pipefail and should not redirect stderr.

[davelopez]

Should we close the 2 issues again?

Sure, I will close the issues now. Thanks for checking again!