profile
viewpoint

Riptides/auto-gdrive-folder-share 0

Automate the sharing of a google drive folder via form submission

Riptides/setup-simple-openvpn 0

Setup Simple OpenVPN server for Amazon Linux and Centos

issue commenttrinityrnaseq/trinityrnaseq

Exception in thread "main" java.lang.RuntimeException: Error, graph contains at least one cycle and is not a DAG!

Getting a similar error but the assembly fails and cannot continue to completion. Using the v2.13.2 singularity image.

ERROR: after topo sort, still have edge unaccounted for: Edge(9047->9048,w:1.0)
ERROR: after topo sort, still have edge unaccounted for: Edge(12041->12027,w:1.0)
ERROR: after topo sort, still have edge unaccounted for: Edge(7997->7998,w:1.0)
ERROR: after topo sort, still have edge unaccounted for: Edge(8556->8557,w:1.0)
ERROR: after topo sort, still have edge unaccounted for: Edge(8561->8562,w:1.0)
ERROR: after topo sort, still have edge unaccounted for: Edge(8952->8953,w:1.0)
ERROR: after topo sort, still have edge unaccounted for: Edge(8943->7996,w:1.0)
ERROR: after topo sort, still have edge unaccounted for: Edge(9046->9047,w:1.0)
ERROR: after topo sort, still have edge unaccounted for: Edge(8013->8014,w:1.0)
ERROR: after topo sort, still have edge unaccounted for: Edge(9165->9166,w:1.0)
ERROR: after topo sort, still have edge unaccounted for: Edge(9045->9046,w:1.0)
ERROR: after topo sort, still have edge unaccounted for: Edge(9048->9049,w:1.0)
ERROR: after topo sort, still have edge unaccounted for: Edge(9048->8939,w:1.0)
ERROR: after topo sort, still have edge unaccounted for: Edge(11955->11940,w:1.0)
ERROR: after topo sort, still have edge unaccounted for: Edge(9168->9169,w:1.0)
ERROR: after topo sort, still have edge unaccounted for: Edge(8546->8003,w:1.0)
ERROR: after topo sort, still have edge unaccounted for: Edge(8008->8009,w:1.0)
ERROR: after topo sort, still have edge unaccounted for: Edge(12056->12041,w:1.0)
ERROR: after topo sort, still have edge unaccounted for: Edge(8560->8561,w:1.0)
ERROR: after topo sort, still have edge unaccounted for: Edge(8010->8011,w:1.0)
ERROR: after topo sort, still have edge unaccounted for: Edge(8004->8005,w:1.0)
ERROR: after topo sort, still have edge unaccounted for: Edge(8551->8552,w:1.0)
ERROR: after topo sort, still have edge unaccounted for: Edge(8948->8949,w:1.0)
ERROR: after topo sort, still have edge unaccounted for: Edge(12027->12012,w:1.0)
ERROR: after topo sort, still have edge unaccounted for: Edge(8001->8546,w:1.0)
ERROR: after topo sort, still have edge unaccounted for: Edge(8940->8941,w:1.0)
Exception in thread "main" java.lang.RuntimeException: Error, graph contains at least one cycle and is not a DAG!
	at TopologicalSort.topoSortSeqVerticesDAG(TopologicalSort.java:112)
	at TransAssembly_allProbPaths.ZipMergeRounds(TransAssembly_allProbPaths.java:2612)
	at TransAssembly_allProbPaths.link_residual_INTER_component_unique_nodes(TransAssembly_allProbPaths.java:2868)
	at TransAssembly_allProbPaths.convert_path_DAG_to_SeqVertex_DAG(TransAssembly_allProbPaths.java:2515)
	at TransAssembly_allProbPaths.create_DAG_from_OverlapLayout(TransAssembly_allProbPaths.java:1797)
	at TransAssembly_allProbPaths.main(TransAssembly_allProbPaths.java:967)
warning, cmd: java -Xmx10G -Xms1G -Xss1G   -XX:ParallelGCThreads=2  -jar /usr/local/bin/Butterfly/Butterfly.jar -N 100000 -L 200 -F 500 -C /ddn/bric/genome_scratch/stingray_rna/trinity_temp/trinity_out_50p/read_partitions/Fb_0/CBin_94/c9453.trinity.reads.fa.out/chrysalis/Component_bins/Cbin0/c0.graph  --path_reinforcement_distance=25  --NO_EM_REDUCE  failed with ret: 256, going to retry.

--->

Trinity run failed. Must investigate error above.
warning, cmd: /usr/local/bin/util/support_scripts/../../Trinity --single "/ddn/bric/genome_scratch/stingray_rna/trinity_temp/trinity_out_50p/read_partitions/Fb_0/CBin_94/c9453.trinity.reads.fa" --output "/ddn/bric/genome_scratch/stingray_rna/trinity_temp/trinity_out_50p/read_partitions/Fb_0/CBin_94/c9453.trinity.reads.fa.out" --CPU 1 --max_memory 1G --run_as_paired --seqType fa --trinity_complete --full_cleanup --no_salmon   failed with ret: 65280, going to retry.
nicolasalexandre21

comment created time in 19 days

more