Hello,
I am having issues with running cactus on 3 fish genomes, two of reference quality and one not. I am not sure if this is simply a disk space error (which if so I am unsure where to indicate I want it to increase) or some other error (see below for error). It looks like it tried at least three times to get through this step and failed every time. Any help would be greatly appreciated.
Thank you!
Log from job "'CactusConsolidated' kind-CactusConsolidated/instance-vl35k8j6 v6" follows:
=========>
[2021-12-14T12:21:43-0500] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG---
[2021-12-14T12:21:43-0500] [MainThread] [I] [toil] Running Toil version 5.5.0-b0ff5be051f2fd55352e00450b7848dcf8354a3b on host system76-pc.
[2021-12-14T12:21:43-0500] [MainThread] [I] [toil.worker] Working on job 'CactusConsolidated' kind-CactusConsolidated/instance-vl35k8j6 v4
[2021-12-14T12:21:43-0500] [MainThread] [I] [toil.worker] Loaded body Job('CactusConsolidated' kind-CactusConsolidated/instance-vl35k8j6 v4) from description 'CactusConsolidated' kind-CactusConsolidated/instance-vl35k8j6 v4
[2021-12-14T12:21:43-0500] [MainThread] [I] [toil.statsAndLogging] Alignments file: /home/aquaomics/cactus/3fish_run/e320d40a100a568eabe29e71c9c4efaf/7de3/d060/tmpsvvzcvll.tmp
[2021-12-14T12:21:43-0500] [MainThread] [W] [root] Deprecated toil method. Please call "logging.getLevelName" directly.
[2021-12-14T12:21:43-0500] [MainThread] [I] [cactus.shared.common] Running the command ['cactus_consolidated', '--sequences', 'FL_Pompano /home/aquaomics/cactus/3fish_run/e320d40a100a568eabe29e71c9c4efaf/7de3/d060/tmpak16ww9l.tmp golden_pompano /home/aquaomics/cactus/3fish_run/e320d40a100a568eabe29e71c9c4efaf/7de3/d060/tmp_jbaa3wk.tmp greater_amberjack /home/aquaomics/cactus/3fish_run/e320d40a100a568eabe29e71c9c4efaf/7de3/d060/tmpneqsvhfc.tmp', '--speciesTree', '(golden_pompano:1.0,greater_amberjack:1.0,FL_Pompano:1.0)Anc0;', '--logLevel', 'INFO', '--alignments', '/home/aquaomics/cactus/3fish_run/e320d40a100a568eabe29e71c9c4efaf/7de3/d060/tmpsvvzcvll.tmp', '--params', '/home/aquaomics/cactus/3fish_run/e320d40a100a568eabe29e71c9c4efaf/7de3/d060/tmpjca9th52.tmp', '--outputFile', '/home/aquaomics/cactus/3fish_run/e320d40a100a568eabe29e71c9c4efaf/7de3/d060/tmphfnm_0mv.tmp', '--outputHalFastaFile', '/home/aquaomics/cactus/3fish_run/e320d40a100a568eabe29e71c9c4efaf/7de3/d060/tmpibx8tq6t.tmp', '--outputReferenceFile', '/home/aquaomics/cactus/3fish_run/e320d40a100a568eabe29e71c9c4efaf/7de3/d060/tmpu8kh8rfw.tmp', '--referenceEvent', 'Anc0', '--secondaryAlignments', '/home/aquaomics/cactus/3fish_run/e320d40a100a568eabe29e71c9c4efaf/7de3/d060/tmpcc7xy8b9.tmp', '--threads', '32']
[2021-12-14T13:03:15-0500] [MainThread] [W] [toil.fileStores.abstractFileStore] Failed job accessed files:
[2021-12-14T13:03:15-0500] [MainThread] [W] [toil.fileStores.abstractFileStore] Downloaded file 'files/for-job/kind-CactusBlastPhase/instance-29c33t1m/cleanup/file-3ae2935258d64b848e8c3fc70db9656a/tmp4pmx7xtr.tmp' to path '/home/aquaomics/cactus/3fish_run/e320d40a100a568eabe29e71c9c4efaf/7de3/d060/tmpak16ww9l.tmp'
[2021-12-14T13:03:15-0500] [MainThread] [W] [toil.fileStores.abstractFileStore] Downloaded file 'files/for-job/kind-CactusBlastPhase/instance-29c33t1m/cleanup/file-be3bc3ed684743fe85f9d0f4d02ade2b/tmpyr4ykh18.tmp' to path '/home/aquaomics/cactus/3fish_run/e320d40a100a568eabe29e71c9c4efaf/7de3/d060/tmp_jbaa3wk.tmp'
[2021-12-14T13:03:15-0500] [MainThread] [W] [toil.fileStores.abstractFileStore] Downloaded file 'files/for-job/kind-CactusBlastPhase/instance-29c33t1m/cleanup/file-e8cba6b2d0bf4be1a90a99ac6f73bd0f/tmp96d9evi3.tmp' to path '/home/aquaomics/cactus/3fish_run/e320d40a100a568eabe29e71c9c4efaf/7de3/d060/tmpneqsvhfc.tmp'
[2021-12-14T13:03:15-0500] [MainThread] [W] [toil.fileStores.abstractFileStore] Downloaded file 'files/for-job/kind-JobFunctionWrappingJob/instance-b75ky_8l/file-75363ef775394a6da30cc47682705f92/tmpcvrwutl5.tmp' to path '/home/aquaomics/cactus/3fish_run/e320d40a100a568eabe29e71c9c4efaf/7de3/d060/tmpsvvzcvll.tmp'
[2021-12-14T13:03:15-0500] [MainThread] [W] [toil.fileStores.abstractFileStore] Downloaded file 'files/for-job/kind-JobFunctionWrappingJob/instance-b75ky_8l/file-7f096e282b684cdd9b93081c1be5580c/tmpk3txh68w.tmp' to path '/home/aquaomics/cactus/3fish_run/e320d40a100a568eabe29e71c9c4efaf/7de3/d060/tmpcc7xy8b9.tmp'
[2021-12-14T13:03:15-0500] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-MASTER: Job used more disk than requested. For CWL, consider increasing the outdirMin requirement, otherwise, consider increasing the disk requirement. Job files/for-job/kind-CactusConsolidated/instance-vl35k8j6/cleanup/file-ed1326ee87bb427ba8e4f29d7f299f91/stream used 1780.10% disk (102.5 GiB [110012878848B] used, 5.8 GiB [6180166866B] requested).
Traceback (most recent call last):
File "/home/aquaomics/cactus_env/lib/python3.8/site-packages/toil/worker.py", line 402, in workerScript
job._runner(jobGraph=None, jobStore=jobStore, fileStore=fileStore, defer=defer)
File "/home/aquaomics/cactus_env/lib/python3.8/site-packages/cactus/shared/common.py", line 932, in _runner
super(RoundedJob, self)._runner(*args, jobStore=jobStore,
File "/home/aquaomics/cactus_env/lib/python3.8/site-packages/toil/job.py", line 2362, in _runner
returnValues = self._run(jobGraph=None, fileStore=fileStore)
File "/home/aquaomics/cactus_env/lib/python3.8/site-packages/toil/job.py", line 2283, in _run
return self.run(fileStore)
File "/home/aquaomics/cactus_env/lib/python3.8/site-packages/cactus/pipeline/cactus_workflow.py", line 408, in run
messages = runCactusConsolidated(seqMap=seqMap,
File "/home/aquaomics/cactus_env/lib/python3.8/site-packages/cactus/shared/common.py", line 197, in runCactusConsolidated
masterMessages = cactus_call(check_output=True, returnStdErr=True, realtimeStderrPrefix='cactus_consolidated({})'.format(referenceEvent),
File "/home/aquaomics/cactus_env/lib/python3.8/site-packages/cactus/shared/common.py", line 868, in cactus_call
raise RuntimeError("Command {} signaled {}: {}".format(call, signal.Signals(-process.returncode).name, out))
RuntimeError: Command ['cactus_consolidated', '--sequences', 'FL_Pompano /home/aquaomics/cactus/3fish_run/e320d40a100a568eabe29e71c9c4efaf/7de3/d060/tmpak16ww9l.tmp golden_pompano /home/aquaomics/cactus/3fish_run/e320d40a100a568eabe29e71c9c4efaf/7de3/d060/tmp_jbaa3wk.tmp greater_amberjack /home/aquaomics/cactus/3fish_run/e320d40a100a568eabe29e71c9c4efaf/7de3/d060/tmpneqsvhfc.tmp', '--speciesTree', '(golden_pompano:1.0,greater_amberjack:1.0,FL_Pompano:1.0)Anc0;', '--logLevel', 'INFO', '--alignments', '/home/aquaomics/cactus/3fish_run/e320d40a100a568eabe29e71c9c4efaf/7de3/d060/tmpsvvzcvll.tmp', '--params', '/home/aquaomics/cactus/3fish_run/e320d40a100a568eabe29e71c9c4efaf/7de3/d060/tmpjca9th52.tmp', '--outputFile', '/home/aquaomics/cactus/3fish_run/e320d40a100a568eabe29e71c9c4efaf/7de3/d060/tmphfnm_0mv.tmp', '--outputHalFastaFile', '/home/aquaomics/cactus/3fish_run/e320d40a100a568eabe29e71c9c4efaf/7de3/d060/tmpibx8tq6t.tmp', '--outputReferenceFile', '/home/aquaomics/cactus/3fish_run/e320d40a100a568eabe29e71c9c4efaf/7de3/d060/tmpu8kh8rfw.tmp', '--referenceEvent', 'Anc0', '--secondaryAlignments', '/home/aquaomics/cactus/3fish_run/e320d40a100a568eabe29e71c9c4efaf/7de3/d060/tmpcc7xy8b9.tmp', '--threads', '32'] signaled SIGKILL: stdout=, stderr=Params file: /home/aquaomics/cactus/3fish_run/e320d40a100a568eabe29e71c9c4efaf/7de3/d060/tmpjca9th52.tmp
Output file string : /home/aquaomics/cactus/3fish_run/e320d40a100a568eabe29e71c9c4efaf/7de3/d060/tmphfnm_0mv.tmp
Output hal fasta file string : /home/aquaomics/cactus/3fish_run/e320d40a100a568eabe29e71c9c4efaf/7de3/d060/tmpibx8tq6t.tmp
Output reference fasta file string : /home/aquaomics/cactus/3fish_run/e320d40a100a568eabe29e71c9c4efaf/7de3/d060/tmpu8kh8rfw.tmp
Sequence files and events: FL_Pompano /home/aquaomics/cactus/3fish_run/e320d40a100a568eabe29e71c9c4efaf/7de3/d060/tmpak16ww9l.tmp golden_pompano /home/aquaomics/cactus/3fish_run/e320d40a100a568eabe29e71c9c4efaf/7de3/d060/tmp_jbaa3wk.tmp greater_amberjack /home/aquaomics/cactus/3fish_run/e320d40a100a568eabe29e71c9c4efaf/7de3/d060/tmpneqsvhfc.tmp
Alignments file: /home/aquaomics/cactus/3fish_run/e320d40a100a568eabe29e71c9c4efaf/7de3/d060/tmpsvvzcvll.tmp
Secondary alignments file: /home/aquaomics/cactus/3fish_run/e320d40a100a568eabe29e71c9c4efaf/7de3/d060/tmpcc7xy8b9.tmp
Constraint alignments file: (null)
Species tree: (golden_pompano:1.0,greater_amberjack:1.0,FL_Pompano:1.0)Anc0;
Outgroup events: (null)
Reference event: Anc0
Loaded the parameters files, 0 seconds have elapsed
Set up the cactus disk, 0 seconds have elapsed
Constructed the first flower
Going to build the event tree with newick string: (golden_pompano:1.0,greater_amberjack:1.0,FL_Pompano:1.0)Anc0;
Parsed the tree
Constructed the basic event tree
Assigning sequence /home/aquaomics/cactus/3fish_run/e320d40a100a568eabe29e71c9c4efaf/7de3/d060/tmpak16ww9l.tmp to FL_Pompano
Processing file: /home/aquaomics/cactus/3fish_run/e320d40a100a568eabe29e71c9c4efaf/7de3/d060/tmpak16ww9l.tmp
The file /home/aquaomics/cactus/3fish_run/e320d40a100a568eabe29e71c9c4efaf/7de3/d060/tmpak16ww9l.tmp is specified incomplete, the sequences will not be attached
Assigning sequence /home/aquaomics/cactus/3fish_run/e320d40a100a568eabe29e71c9c4efaf/7de3/d060/tmp_jbaa3wk.tmp to golden_pompano
Processing file: /home/aquaomics/cactus/3fish_run/e320d40a100a568eabe29e71c9c4efaf/7de3/d060/tmp_jbaa3wk.tmp
The file /home/aquaomics/cactus/3fish_run/e320d40a100a568eabe29e71c9c4efaf/7de3/d060/tmp_jbaa3wk.tmp is specified incomplete, the sequences will not be attached
Assigning sequence /home/aquaomics/cactus/3fish_run/e320d40a100a568eabe29e71c9c4efaf/7de3/d060/tmpneqsvhfc.tmp to greater_amberjack
Processing file: /home/aquaomics/cactus/3fish_run/e320d40a100a568eabe29e71c9c4efaf/7de3/d060/tmpneqsvhfc.tmp
The file /home/aquaomics/cactus/3fish_run/e320d40a100a568eabe29e71c9c4efaf/7de3/d060/tmpneqsvhfc.tmp is specified incomplete, the sequences will not be attached
Constructed the initial flower with 43109 sequences and 5 events with string: ((golden_pompano:1,greater_amberjack:1,FL_Pompano:1)Anc0:9.22337e+18)ROOT:9.22337e+18;
Established the first Flower in the hierarchy, 13 seconds have elapsed
Converted alignment coordinates, 1017 seconds have elapsed
Stripped the unique IDs, 1017 seconds have elapsed
Starting annealing round with a minimum chain length of 64 and an alignment trim of 3
There were 63279373 blocks in the sequence graph, representing 1731233415 total aligned bases
Block degree stats: min 1, avg 4.658805, median 3, max 177187
Block support stats: min 0.000000, avg 0.438768, median 0.333333, max 3.500000
Starting melting round with a minimum chain length of 2
[2021-12-14T13:03:15-0500] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host system76-pc
<=========
Hello,
I am having issues with running cactus on 3 fish genomes, two of reference quality and one not. I am not sure if this is simply a disk space error (which if so I am unsure where to indicate I want it to increase) or some other error (see below for error). It looks like it tried at least three times to get through this step and failed every time. Any help would be greatly appreciated.
Thank you!
Log from job "'CactusConsolidated' kind-CactusConsolidated/instance-vl35k8j6 v6" follows:
=========>
[2021-12-14T12:21:43-0500] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG---
[2021-12-14T12:21:43-0500] [MainThread] [I] [toil] Running Toil version 5.5.0-b0ff5be051f2fd55352e00450b7848dcf8354a3b on host system76-pc.
[2021-12-14T12:21:43-0500] [MainThread] [I] [toil.worker] Working on job 'CactusConsolidated' kind-CactusConsolidated/instance-vl35k8j6 v4
[2021-12-14T12:21:43-0500] [MainThread] [I] [toil.worker] Loaded body Job('CactusConsolidated' kind-CactusConsolidated/instance-vl35k8j6 v4) from description 'CactusConsolidated' kind-CactusConsolidated/instance-vl35k8j6 v4
[2021-12-14T12:21:43-0500] [MainThread] [I] [toil.statsAndLogging] Alignments file: /home/aquaomics/cactus/3fish_run/e320d40a100a568eabe29e71c9c4efaf/7de3/d060/tmpsvvzcvll.tmp
[2021-12-14T12:21:43-0500] [MainThread] [W] [root] Deprecated toil method. Please call "logging.getLevelName" directly.
[2021-12-14T12:21:43-0500] [MainThread] [I] [cactus.shared.common] Running the command ['cactus_consolidated', '--sequences', 'FL_Pompano /home/aquaomics/cactus/3fish_run/e320d40a100a568eabe29e71c9c4efaf/7de3/d060/tmpak16ww9l.tmp golden_pompano /home/aquaomics/cactus/3fish_run/e320d40a100a568eabe29e71c9c4efaf/7de3/d060/tmp_jbaa3wk.tmp greater_amberjack /home/aquaomics/cactus/3fish_run/e320d40a100a568eabe29e71c9c4efaf/7de3/d060/tmpneqsvhfc.tmp', '--speciesTree', '(golden_pompano:1.0,greater_amberjack:1.0,FL_Pompano:1.0)Anc0;', '--logLevel', 'INFO', '--alignments', '/home/aquaomics/cactus/3fish_run/e320d40a100a568eabe29e71c9c4efaf/7de3/d060/tmpsvvzcvll.tmp', '--params', '/home/aquaomics/cactus/3fish_run/e320d40a100a568eabe29e71c9c4efaf/7de3/d060/tmpjca9th52.tmp', '--outputFile', '/home/aquaomics/cactus/3fish_run/e320d40a100a568eabe29e71c9c4efaf/7de3/d060/tmphfnm_0mv.tmp', '--outputHalFastaFile', '/home/aquaomics/cactus/3fish_run/e320d40a100a568eabe29e71c9c4efaf/7de3/d060/tmpibx8tq6t.tmp', '--outputReferenceFile', '/home/aquaomics/cactus/3fish_run/e320d40a100a568eabe29e71c9c4efaf/7de3/d060/tmpu8kh8rfw.tmp', '--referenceEvent', 'Anc0', '--secondaryAlignments', '/home/aquaomics/cactus/3fish_run/e320d40a100a568eabe29e71c9c4efaf/7de3/d060/tmpcc7xy8b9.tmp', '--threads', '32']
[2021-12-14T13:03:15-0500] [MainThread] [W] [toil.fileStores.abstractFileStore] Failed job accessed files:
[2021-12-14T13:03:15-0500] [MainThread] [W] [toil.fileStores.abstractFileStore] Downloaded file 'files/for-job/kind-CactusBlastPhase/instance-29c33t1m/cleanup/file-3ae2935258d64b848e8c3fc70db9656a/tmp4pmx7xtr.tmp' to path '/home/aquaomics/cactus/3fish_run/e320d40a100a568eabe29e71c9c4efaf/7de3/d060/tmpak16ww9l.tmp'
[2021-12-14T13:03:15-0500] [MainThread] [W] [toil.fileStores.abstractFileStore] Downloaded file 'files/for-job/kind-CactusBlastPhase/instance-29c33t1m/cleanup/file-be3bc3ed684743fe85f9d0f4d02ade2b/tmpyr4ykh18.tmp' to path '/home/aquaomics/cactus/3fish_run/e320d40a100a568eabe29e71c9c4efaf/7de3/d060/tmp_jbaa3wk.tmp'
[2021-12-14T13:03:15-0500] [MainThread] [W] [toil.fileStores.abstractFileStore] Downloaded file 'files/for-job/kind-CactusBlastPhase/instance-29c33t1m/cleanup/file-e8cba6b2d0bf4be1a90a99ac6f73bd0f/tmp96d9evi3.tmp' to path '/home/aquaomics/cactus/3fish_run/e320d40a100a568eabe29e71c9c4efaf/7de3/d060/tmpneqsvhfc.tmp'
[2021-12-14T13:03:15-0500] [MainThread] [W] [toil.fileStores.abstractFileStore] Downloaded file 'files/for-job/kind-JobFunctionWrappingJob/instance-b75ky_8l/file-75363ef775394a6da30cc47682705f92/tmpcvrwutl5.tmp' to path '/home/aquaomics/cactus/3fish_run/e320d40a100a568eabe29e71c9c4efaf/7de3/d060/tmpsvvzcvll.tmp'
[2021-12-14T13:03:15-0500] [MainThread] [W] [toil.fileStores.abstractFileStore] Downloaded file 'files/for-job/kind-JobFunctionWrappingJob/instance-b75ky_8l/file-7f096e282b684cdd9b93081c1be5580c/tmpk3txh68w.tmp' to path '/home/aquaomics/cactus/3fish_run/e320d40a100a568eabe29e71c9c4efaf/7de3/d060/tmpcc7xy8b9.tmp'
[2021-12-14T13:03:15-0500] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-MASTER: Job used more disk than requested. For CWL, consider increasing the outdirMin requirement, otherwise, consider increasing the disk requirement. Job files/for-job/kind-CactusConsolidated/instance-vl35k8j6/cleanup/file-ed1326ee87bb427ba8e4f29d7f299f91/stream used 1780.10% disk (102.5 GiB [110012878848B] used, 5.8 GiB [6180166866B] requested).
Traceback (most recent call last):
File "/home/aquaomics/cactus_env/lib/python3.8/site-packages/toil/worker.py", line 402, in workerScript
job._runner(jobGraph=None, jobStore=jobStore, fileStore=fileStore, defer=defer)
File "/home/aquaomics/cactus_env/lib/python3.8/site-packages/cactus/shared/common.py", line 932, in _runner
super(RoundedJob, self)._runner(*args, jobStore=jobStore,
File "/home/aquaomics/cactus_env/lib/python3.8/site-packages/toil/job.py", line 2362, in _runner
returnValues = self._run(jobGraph=None, fileStore=fileStore)
File "/home/aquaomics/cactus_env/lib/python3.8/site-packages/toil/job.py", line 2283, in _run
return self.run(fileStore)
File "/home/aquaomics/cactus_env/lib/python3.8/site-packages/cactus/pipeline/cactus_workflow.py", line 408, in run
messages = runCactusConsolidated(seqMap=seqMap,
File "/home/aquaomics/cactus_env/lib/python3.8/site-packages/cactus/shared/common.py", line 197, in runCactusConsolidated
masterMessages = cactus_call(check_output=True, returnStdErr=True, realtimeStderrPrefix='cactus_consolidated({})'.format(referenceEvent),
File "/home/aquaomics/cactus_env/lib/python3.8/site-packages/cactus/shared/common.py", line 868, in cactus_call
raise RuntimeError("Command {} signaled {}: {}".format(call, signal.Signals(-process.returncode).name, out))
RuntimeError: Command ['cactus_consolidated', '--sequences', 'FL_Pompano /home/aquaomics/cactus/3fish_run/e320d40a100a568eabe29e71c9c4efaf/7de3/d060/tmpak16ww9l.tmp golden_pompano /home/aquaomics/cactus/3fish_run/e320d40a100a568eabe29e71c9c4efaf/7de3/d060/tmp_jbaa3wk.tmp greater_amberjack /home/aquaomics/cactus/3fish_run/e320d40a100a568eabe29e71c9c4efaf/7de3/d060/tmpneqsvhfc.tmp', '--speciesTree', '(golden_pompano:1.0,greater_amberjack:1.0,FL_Pompano:1.0)Anc0;', '--logLevel', 'INFO', '--alignments', '/home/aquaomics/cactus/3fish_run/e320d40a100a568eabe29e71c9c4efaf/7de3/d060/tmpsvvzcvll.tmp', '--params', '/home/aquaomics/cactus/3fish_run/e320d40a100a568eabe29e71c9c4efaf/7de3/d060/tmpjca9th52.tmp', '--outputFile', '/home/aquaomics/cactus/3fish_run/e320d40a100a568eabe29e71c9c4efaf/7de3/d060/tmphfnm_0mv.tmp', '--outputHalFastaFile', '/home/aquaomics/cactus/3fish_run/e320d40a100a568eabe29e71c9c4efaf/7de3/d060/tmpibx8tq6t.tmp', '--outputReferenceFile', '/home/aquaomics/cactus/3fish_run/e320d40a100a568eabe29e71c9c4efaf/7de3/d060/tmpu8kh8rfw.tmp', '--referenceEvent', 'Anc0', '--secondaryAlignments', '/home/aquaomics/cactus/3fish_run/e320d40a100a568eabe29e71c9c4efaf/7de3/d060/tmpcc7xy8b9.tmp', '--threads', '32'] signaled SIGKILL: stdout=, stderr=Params file: /home/aquaomics/cactus/3fish_run/e320d40a100a568eabe29e71c9c4efaf/7de3/d060/tmpjca9th52.tmp
Output file string : /home/aquaomics/cactus/3fish_run/e320d40a100a568eabe29e71c9c4efaf/7de3/d060/tmphfnm_0mv.tmp
Output hal fasta file string : /home/aquaomics/cactus/3fish_run/e320d40a100a568eabe29e71c9c4efaf/7de3/d060/tmpibx8tq6t.tmp
Output reference fasta file string : /home/aquaomics/cactus/3fish_run/e320d40a100a568eabe29e71c9c4efaf/7de3/d060/tmpu8kh8rfw.tmp
Sequence files and events: FL_Pompano /home/aquaomics/cactus/3fish_run/e320d40a100a568eabe29e71c9c4efaf/7de3/d060/tmpak16ww9l.tmp golden_pompano /home/aquaomics/cactus/3fish_run/e320d40a100a568eabe29e71c9c4efaf/7de3/d060/tmp_jbaa3wk.tmp greater_amberjack /home/aquaomics/cactus/3fish_run/e320d40a100a568eabe29e71c9c4efaf/7de3/d060/tmpneqsvhfc.tmp
Alignments file: /home/aquaomics/cactus/3fish_run/e320d40a100a568eabe29e71c9c4efaf/7de3/d060/tmpsvvzcvll.tmp
Secondary alignments file: /home/aquaomics/cactus/3fish_run/e320d40a100a568eabe29e71c9c4efaf/7de3/d060/tmpcc7xy8b9.tmp
Constraint alignments file: (null)
Species tree: (golden_pompano:1.0,greater_amberjack:1.0,FL_Pompano:1.0)Anc0;
Outgroup events: (null)
Reference event: Anc0
Loaded the parameters files, 0 seconds have elapsed
Set up the cactus disk, 0 seconds have elapsed
Constructed the first flower
Going to build the event tree with newick string: (golden_pompano:1.0,greater_amberjack:1.0,FL_Pompano:1.0)Anc0;
Parsed the tree
Constructed the basic event tree
Assigning sequence /home/aquaomics/cactus/3fish_run/e320d40a100a568eabe29e71c9c4efaf/7de3/d060/tmpak16ww9l.tmp to FL_Pompano
Processing file: /home/aquaomics/cactus/3fish_run/e320d40a100a568eabe29e71c9c4efaf/7de3/d060/tmpak16ww9l.tmp
The file /home/aquaomics/cactus/3fish_run/e320d40a100a568eabe29e71c9c4efaf/7de3/d060/tmpak16ww9l.tmp is specified incomplete, the sequences will not be attached
Assigning sequence /home/aquaomics/cactus/3fish_run/e320d40a100a568eabe29e71c9c4efaf/7de3/d060/tmp_jbaa3wk.tmp to golden_pompano
Processing file: /home/aquaomics/cactus/3fish_run/e320d40a100a568eabe29e71c9c4efaf/7de3/d060/tmp_jbaa3wk.tmp
The file /home/aquaomics/cactus/3fish_run/e320d40a100a568eabe29e71c9c4efaf/7de3/d060/tmp_jbaa3wk.tmp is specified incomplete, the sequences will not be attached
Assigning sequence /home/aquaomics/cactus/3fish_run/e320d40a100a568eabe29e71c9c4efaf/7de3/d060/tmpneqsvhfc.tmp to greater_amberjack
Processing file: /home/aquaomics/cactus/3fish_run/e320d40a100a568eabe29e71c9c4efaf/7de3/d060/tmpneqsvhfc.tmp
The file /home/aquaomics/cactus/3fish_run/e320d40a100a568eabe29e71c9c4efaf/7de3/d060/tmpneqsvhfc.tmp is specified incomplete, the sequences will not be attached
Constructed the initial flower with 43109 sequences and 5 events with string: ((golden_pompano:1,greater_amberjack:1,FL_Pompano:1)Anc0:9.22337e+18)ROOT:9.22337e+18;
Established the first Flower in the hierarchy, 13 seconds have elapsed
Converted alignment coordinates, 1017 seconds have elapsed
Stripped the unique IDs, 1017 seconds have elapsed
Starting annealing round with a minimum chain length of 64 and an alignment trim of 3
There were 63279373 blocks in the sequence graph, representing 1731233415 total aligned bases
Block degree stats: min 1, avg 4.658805, median 3, max 177187
Block support stats: min 0.000000, avg 0.438768, median 0.333333, max 3.500000
Starting melting round with a minimum chain length of 2
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