I'm running cactus on a HPC server and get the following error. I'm quit new to cactus and struggle to understand the meaning of errors written on the log file. any help would be much appreciated.
Find bellow the content of the error file
[2023-03-20T14:10:35+0200] [MainThread] [I] [toil.statsAndLogging] Enabling realtime logging in Toil
[2023-03-20T14:10:35+0200] [MainThread] [I] [toil.statsAndLogging] Cactus Command: /apps/chpc/bio/python/3.9.6/bin/cactus ./js14 seqfile_procellariiformes_2.txt procellariiformes.hal
[2023-03-20T14:10:35+0200] [MainThread] [I] [toil.statsAndLogging] Cactus Commit: 2d6c076af80c66f4948dade61043e68c6bec5a47
[2023-03-20T14:10:35+0200] [MainThread] [W] [toil.statsAndLogging] No branch length for Rissa_tridactyla_GCA_013401015.1_ASM1340101v1_genomic: setting to 1
[2023-03-20T14:10:35+0200] [MainThread] [W] [toil.statsAndLogging] No branch length for Sula_dactylatra_GCA_013389905.1_ASM1338990v1_genomic: setting to 1
[2023-03-20T14:10:35+0200] [MainThread] [W] [toil.statsAndLogging] No branch length for Fregata_magnificens_GCA_013389945.1_ASM1338994v1_genomic: setting to 1
[2023-03-20T14:10:35+0200] [MainThread] [W] [toil.statsAndLogging] No branch length for Spheniscus_magellanicus_GCA_010076225.1_BGI_Smag.V1_genomic: setting to 1
[2023-03-20T14:10:35+0200] [MainThread] [W] [toil.statsAndLogging] No branch length for Phoebastria_albatrus_GCA_014363385.1_P_albatrus_scaffold_01_genomic: setting to 1
[2023-03-20T14:10:35+0200] [MainThread] [W] [toil.statsAndLogging] No branch length for Thalassarche_chlororhynchos_GCA_013400895.1_ASM1340089v1_genomic: setting to 1
[2023-03-20T14:10:35+0200] [MainThread] [W] [toil.statsAndLogging] No branch length for : setting to 1
[2023-03-20T14:10:35+0200] [MainThread] [W] [toil.statsAndLogging] No branch length for Oceanites_oceanicus_GCA_013396615.1_ASM1339661v1_genomic: setting to 1
[2023-03-20T14:10:35+0200] [MainThread] [W] [toil.statsAndLogging] No branch length for Fregetta_grallaria_GCA_013399335.1_ASM1339933v1_genomic: setting to 1
[2023-03-20T14:10:35+0200] [MainThread] [W] [toil.statsAndLogging] No branch length for : setting to 1
[2023-03-20T14:10:35+0200] [MainThread] [W] [toil.statsAndLogging] No branch length for Oceanodroma_tethys_GCA_013397025.1_ASM1339702v1_genomic: setting to 1
[2023-03-20T14:10:35+0200] [MainThread] [W] [toil.statsAndLogging] No branch length for Fulmarus_glacialis_GCA_000690835.1_ASM69083v1_genomic: setting to 1
[2023-03-20T14:10:35+0200] [MainThread] [W] [toil.statsAndLogging] No branch length for Pelecanoides_urinatrix_GCA_013400755.1_ASM1340075v1_genomic: setting to 1
[2023-03-20T14:10:35+0200] [MainThread] [W] [toil.statsAndLogging] No branch length for Puffinus_mauretanicus_GCA_023333565.1_ASM2333356v1_genomic: setting to 1
[2023-03-20T14:10:35+0200] [MainThread] [W] [toil.statsAndLogging] No branch length for Calonectris_borelis_GCA_013401115.1_ASM1340111v1_genomic: setting to 1
[2023-03-20T14:10:35+0200] [MainThread] [W] [toil.statsAndLogging] No branch length for : setting to 1
[2023-03-20T14:10:35+0200] [MainThread] [W] [toil.statsAndLogging] No branch length for : setting to 1
[2023-03-20T14:10:35+0200] [MainThread] [W] [toil.statsAndLogging] No branch length for : setting to 1
[2023-03-20T14:10:35+0200] [MainThread] [W] [toil.statsAndLogging] No branch length for : setting to 1
[2023-03-20T14:10:35+0200] [MainThread] [W] [toil.statsAndLogging] No branch length for : setting to 1
[2023-03-20T14:10:35+0200] [MainThread] [W] [toil.statsAndLogging] No branch length for : setting to 1
[2023-03-20T14:10:35+0200] [MainThread] [W] [toil.statsAndLogging] No branch length for : setting to 1
[2023-03-20T14:10:35+0200] [MainThread] [W] [toil.statsAndLogging] No branch length for : setting to 1
[2023-03-20T14:10:35+0200] [MainThread] [W] [toil.statsAndLogging] No branch length for : setting to 1
[2023-03-20T14:10:35+0200] [MainThread] [I] [toil.statsAndLogging] Tree: (Rissa_tridactyla_GCA_013401015.1_ASM1340101v1_genomic:1.0,(Sula_dactylatra_GCA_013389905.1_ASM1338990v1_genomic:1.0,(Fregata_magnificens_GCA_013389945.1_ASM1338994v1_genomic:1.0,(Spheniscus_magellanicus_GCA_010076225.1_BGI_Smag.V1_genomic:1.0,((Phoebastria_albatrus_GCA_014363385.1_P_albatrus_scaffold_01_genomic:1.0,Thalassarche_chlororhynchos_GCA_013400895.1_ASM1340089v1_genomic:1.0)Anc05:1.0,((Oceanites_oceanicus_GCA_013396615.1_ASM1339661v1_genomic:1.0,Fregetta_grallaria_GCA_013399335.1_ASM1339933v1_genomic:1.0)Anc07:1.0,(Oceanodroma_tethys_GCA_013397025.1_ASM1339702v1_genomic:1.0,(Fulmarus_glacialis_GCA_000690835.1_ASM69083v1_genomic:1.0,(Pelecanoides_urinatrix_GCA_013400755.1_ASM1340075v1_genomic:1.0,(Puffinus_mauretanicus_GCA_023333565.1_ASM2333356v1_genomic:1.0,Calonectris_borelis_GCA_013401115.1_ASM1340111v1_genomic:1.0)Anc11:1.0)Anc10:1.0)Anc09:1.0)Anc08:1.0)Anc06:1.0)Anc04:1.0)Anc03:1.0)Anc02:1.0)Anc01:1.0)Anc00;
[2023-03-20T14:10:35+0200] [MainThread] [W] [toil.statsAndLogging] Deprecated toil method. Please use "toil.test.get_temp_file()" instead."
[2023-03-20T14:10:35+0200] [MainThread] [W] [toil.statsAndLogging] Deprecated toil method that will be moved/replaced in a future release."
[2023-03-20T14:11:06+0200] [MainThread] [I] [toil.statsAndLogging] Importing file:///var/tmp/pbs.4773853.sched01/tmp43rrsn69
[2023-03-20T14:11:12+0200] [MainThread] [W] [toil.statsAndLogging] Deprecated toil method. Please use "toil.test.get_temp_file()" instead."
[2023-03-20T14:11:12+0200] [MainThread] [W] [toil.statsAndLogging] Deprecated toil method that will be moved/replaced in a future release."
[2023-03-20T14:11:21+0200] [MainThread] [I] [toil.statsAndLogging] Importing file:///var/tmp/pbs.4773853.sched01/tmp5phj4jv7
[2023-03-20T14:11:21+0200] [MainThread] [W] [toil.statsAndLogging] Deprecated toil method. Please use "toil.test.get_temp_file()" instead."
[2023-03-20T14:11:21+0200] [MainThread] [W] [toil.statsAndLogging] Deprecated toil method that will be moved/replaced in a future release."
[2023-03-20T14:11:30+0200] [MainThread] [I] [toil.statsAndLogging] Importing file:///var/tmp/pbs.4773853.sched01/tmpmee8gvtc
[2023-03-20T14:11:30+0200] [MainThread] [W] [toil.statsAndLogging] Deprecated toil method. Please use "toil.test.get_temp_file()" instead."
[2023-03-20T14:11:30+0200] [MainThread] [W] [toil.statsAndLogging] Deprecated toil method that will be moved/replaced in a future release."
[2023-03-20T14:11:40+0200] [MainThread] [I] [toil.statsAndLogging] Importing file:///var/tmp/pbs.4773853.sched01/tmpxkjqasau
[2023-03-20T14:11:40+0200] [MainThread] [W] [toil.statsAndLogging] Deprecated toil method. Please use "toil.test.get_temp_file()" instead."
[2023-03-20T14:11:40+0200] [MainThread] [W] [toil.statsAndLogging] Deprecated toil method that will be moved/replaced in a future release."
[2023-03-20T14:11:48+0200] [MainThread] [I] [toil.statsAndLogging] Importing file:///var/tmp/pbs.4773853.sched01/tmp_ufl64jw
[2023-03-20T14:11:48+0200] [MainThread] [W] [toil.statsAndLogging] Deprecated toil method. Please use "toil.test.get_temp_file()" instead."
[2023-03-20T14:11:48+0200] [MainThread] [W] [toil.statsAndLogging] Deprecated toil method that will be moved/replaced in a future release."
[2023-03-20T14:11:58+0200] [MainThread] [I] [toil.statsAndLogging] Importing file:///var/tmp/pbs.4773853.sched01/tmpac5envln
[2023-03-20T14:11:58+0200] [MainThread] [W] [toil.statsAndLogging] Deprecated toil method. Please use "toil.test.get_temp_file()" instead."
[2023-03-20T14:11:58+0200] [MainThread] [W] [toil.statsAndLogging] Deprecated toil method that will be moved/replaced in a future release."
[2023-03-20T14:12:10+0200] [MainThread] [I] [toil.statsAndLogging] Importing file:///var/tmp/pbs.4773853.sched01/tmp58jwl9qs
[2023-03-20T14:12:10+0200] [MainThread] [W] [toil.statsAndLogging] Deprecated toil method. Please use "toil.test.get_temp_file()" instead."
[2023-03-20T14:12:10+0200] [MainThread] [W] [toil.statsAndLogging] Deprecated toil method that will be moved/replaced in a future release."
cat: write error: No space left on device
Traceback (most recent call last):
File "/apps/chpc/bio/python/3.9.6/bin/cactus", line 8, in
sys.exit(main())
File "/apps/chpc/bio/python/3.9.6/lib/python3.9/site-packages/cactus/progressive/cactus_progressive.py", line 390, in main
catFiles([os.path.join(seq, subSeq) for subSeq in os.listdir(seq)], tmpSeq)
File "/apps/chpc/bio/python/3.9.6/lib/p
I'm running cactus on a HPC server and get the following error. I'm quit new to cactus and struggle to understand the meaning of errors written on the log file. any help would be much appreciated.
Find bellow the content of the error file
[2023-03-20T14:10:35+0200] [MainThread] [I] [toil.statsAndLogging] Enabling realtime logging in Toil [2023-03-20T14:10:35+0200] [MainThread] [I] [toil.statsAndLogging] Cactus Command: /apps/chpc/bio/python/3.9.6/bin/cactus ./js14 seqfile_procellariiformes_2.txt procellariiformes.hal [2023-03-20T14:10:35+0200] [MainThread] [I] [toil.statsAndLogging] Cactus Commit: 2d6c076af80c66f4948dade61043e68c6bec5a47 [2023-03-20T14:10:35+0200] [MainThread] [W] [toil.statsAndLogging] No branch length for Rissa_tridactyla_GCA_013401015.1_ASM1340101v1_genomic: setting to 1
[2023-03-20T14:10:35+0200] [MainThread] [W] [toil.statsAndLogging] No branch length for Sula_dactylatra_GCA_013389905.1_ASM1338990v1_genomic: setting to 1
[2023-03-20T14:10:35+0200] [MainThread] [W] [toil.statsAndLogging] No branch length for Fregata_magnificens_GCA_013389945.1_ASM1338994v1_genomic: setting to 1
[2023-03-20T14:10:35+0200] [MainThread] [W] [toil.statsAndLogging] No branch length for Spheniscus_magellanicus_GCA_010076225.1_BGI_Smag.V1_genomic: setting to 1
[2023-03-20T14:10:35+0200] [MainThread] [W] [toil.statsAndLogging] No branch length for Phoebastria_albatrus_GCA_014363385.1_P_albatrus_scaffold_01_genomic: setting to 1
[2023-03-20T14:10:35+0200] [MainThread] [W] [toil.statsAndLogging] No branch length for Thalassarche_chlororhynchos_GCA_013400895.1_ASM1340089v1_genomic: setting to 1
[2023-03-20T14:10:35+0200] [MainThread] [W] [toil.statsAndLogging] No branch length for : setting to 1
[2023-03-20T14:10:35+0200] [MainThread] [W] [toil.statsAndLogging] No branch length for Oceanites_oceanicus_GCA_013396615.1_ASM1339661v1_genomic: setting to 1
[2023-03-20T14:10:35+0200] [MainThread] [W] [toil.statsAndLogging] No branch length for Fregetta_grallaria_GCA_013399335.1_ASM1339933v1_genomic: setting to 1
[2023-03-20T14:10:35+0200] [MainThread] [W] [toil.statsAndLogging] No branch length for : setting to 1
[2023-03-20T14:10:35+0200] [MainThread] [W] [toil.statsAndLogging] No branch length for Oceanodroma_tethys_GCA_013397025.1_ASM1339702v1_genomic: setting to 1
[2023-03-20T14:10:35+0200] [MainThread] [W] [toil.statsAndLogging] No branch length for Fulmarus_glacialis_GCA_000690835.1_ASM69083v1_genomic: setting to 1
[2023-03-20T14:10:35+0200] [MainThread] [W] [toil.statsAndLogging] No branch length for Pelecanoides_urinatrix_GCA_013400755.1_ASM1340075v1_genomic: setting to 1
[2023-03-20T14:10:35+0200] [MainThread] [W] [toil.statsAndLogging] No branch length for Puffinus_mauretanicus_GCA_023333565.1_ASM2333356v1_genomic: setting to 1
[2023-03-20T14:10:35+0200] [MainThread] [W] [toil.statsAndLogging] No branch length for Calonectris_borelis_GCA_013401115.1_ASM1340111v1_genomic: setting to 1
[2023-03-20T14:10:35+0200] [MainThread] [W] [toil.statsAndLogging] No branch length for : setting to 1
[2023-03-20T14:10:35+0200] [MainThread] [W] [toil.statsAndLogging] No branch length for : setting to 1
[2023-03-20T14:10:35+0200] [MainThread] [W] [toil.statsAndLogging] No branch length for : setting to 1
[2023-03-20T14:10:35+0200] [MainThread] [W] [toil.statsAndLogging] No branch length for : setting to 1
[2023-03-20T14:10:35+0200] [MainThread] [W] [toil.statsAndLogging] No branch length for : setting to 1
[2023-03-20T14:10:35+0200] [MainThread] [W] [toil.statsAndLogging] No branch length for : setting to 1
[2023-03-20T14:10:35+0200] [MainThread] [W] [toil.statsAndLogging] No branch length for : setting to 1
[2023-03-20T14:10:35+0200] [MainThread] [W] [toil.statsAndLogging] No branch length for : setting to 1
[2023-03-20T14:10:35+0200] [MainThread] [W] [toil.statsAndLogging] No branch length for : setting to 1
[2023-03-20T14:10:35+0200] [MainThread] [I] [toil.statsAndLogging] Tree: (Rissa_tridactyla_GCA_013401015.1_ASM1340101v1_genomic:1.0,(Sula_dactylatra_GCA_013389905.1_ASM1338990v1_genomic:1.0,(Fregata_magnificens_GCA_013389945.1_ASM1338994v1_genomic:1.0,(Spheniscus_magellanicus_GCA_010076225.1_BGI_Smag.V1_genomic:1.0,((Phoebastria_albatrus_GCA_014363385.1_P_albatrus_scaffold_01_genomic:1.0,Thalassarche_chlororhynchos_GCA_013400895.1_ASM1340089v1_genomic:1.0)Anc05:1.0,((Oceanites_oceanicus_GCA_013396615.1_ASM1339661v1_genomic:1.0,Fregetta_grallaria_GCA_013399335.1_ASM1339933v1_genomic:1.0)Anc07:1.0,(Oceanodroma_tethys_GCA_013397025.1_ASM1339702v1_genomic:1.0,(Fulmarus_glacialis_GCA_000690835.1_ASM69083v1_genomic:1.0,(Pelecanoides_urinatrix_GCA_013400755.1_ASM1340075v1_genomic:1.0,(Puffinus_mauretanicus_GCA_023333565.1_ASM2333356v1_genomic:1.0,Calonectris_borelis_GCA_013401115.1_ASM1340111v1_genomic:1.0)Anc11:1.0)Anc10:1.0)Anc09:1.0)Anc08:1.0)Anc06:1.0)Anc04:1.0)Anc03:1.0)Anc02:1.0)Anc01:1.0)Anc00; [2023-03-20T14:10:35+0200] [MainThread] [W] [toil.statsAndLogging] Deprecated toil method. Please use "toil.test.get_temp_file()" instead." [2023-03-20T14:10:35+0200] [MainThread] [W] [toil.statsAndLogging] Deprecated toil method that will be moved/replaced in a future release." [2023-03-20T14:11:06+0200] [MainThread] [I] [toil.statsAndLogging] Importing file:///var/tmp/pbs.4773853.sched01/tmp43rrsn69 [2023-03-20T14:11:12+0200] [MainThread] [W] [toil.statsAndLogging] Deprecated toil method. Please use "toil.test.get_temp_file()" instead." [2023-03-20T14:11:12+0200] [MainThread] [W] [toil.statsAndLogging] Deprecated toil method that will be moved/replaced in a future release." [2023-03-20T14:11:21+0200] [MainThread] [I] [toil.statsAndLogging] Importing file:///var/tmp/pbs.4773853.sched01/tmp5phj4jv7 [2023-03-20T14:11:21+0200] [MainThread] [W] [toil.statsAndLogging] Deprecated toil method. Please use "toil.test.get_temp_file()" instead." [2023-03-20T14:11:21+0200] [MainThread] [W] [toil.statsAndLogging] Deprecated toil method that will be moved/replaced in a future release." [2023-03-20T14:11:30+0200] [MainThread] [I] [toil.statsAndLogging] Importing file:///var/tmp/pbs.4773853.sched01/tmpmee8gvtc [2023-03-20T14:11:30+0200] [MainThread] [W] [toil.statsAndLogging] Deprecated toil method. Please use "toil.test.get_temp_file()" instead." [2023-03-20T14:11:30+0200] [MainThread] [W] [toil.statsAndLogging] Deprecated toil method that will be moved/replaced in a future release." [2023-03-20T14:11:40+0200] [MainThread] [I] [toil.statsAndLogging] Importing file:///var/tmp/pbs.4773853.sched01/tmpxkjqasau [2023-03-20T14:11:40+0200] [MainThread] [W] [toil.statsAndLogging] Deprecated toil method. Please use "toil.test.get_temp_file()" instead." [2023-03-20T14:11:40+0200] [MainThread] [W] [toil.statsAndLogging] Deprecated toil method that will be moved/replaced in a future release." [2023-03-20T14:11:48+0200] [MainThread] [I] [toil.statsAndLogging] Importing file:///var/tmp/pbs.4773853.sched01/tmp_ufl64jw [2023-03-20T14:11:48+0200] [MainThread] [W] [toil.statsAndLogging] Deprecated toil method. Please use "toil.test.get_temp_file()" instead." [2023-03-20T14:11:48+0200] [MainThread] [W] [toil.statsAndLogging] Deprecated toil method that will be moved/replaced in a future release." [2023-03-20T14:11:58+0200] [MainThread] [I] [toil.statsAndLogging] Importing file:///var/tmp/pbs.4773853.sched01/tmpac5envln [2023-03-20T14:11:58+0200] [MainThread] [W] [toil.statsAndLogging] Deprecated toil method. Please use "toil.test.get_temp_file()" instead." [2023-03-20T14:11:58+0200] [MainThread] [W] [toil.statsAndLogging] Deprecated toil method that will be moved/replaced in a future release." [2023-03-20T14:12:10+0200] [MainThread] [I] [toil.statsAndLogging] Importing file:///var/tmp/pbs.4773853.sched01/tmp58jwl9qs [2023-03-20T14:12:10+0200] [MainThread] [W] [toil.statsAndLogging] Deprecated toil method. Please use "toil.test.get_temp_file()" instead." [2023-03-20T14:12:10+0200] [MainThread] [W] [toil.statsAndLogging] Deprecated toil method that will be moved/replaced in a future release." cat: write error: No space left on device Traceback (most recent call last): File "/apps/chpc/bio/python/3.9.6/bin/cactus", line 8, in
sys.exit(main())
File "/apps/chpc/bio/python/3.9.6/lib/python3.9/site-packages/cactus/progressive/cactus_progressive.py", line 390, in main
catFiles([os.path.join(seq, subSeq) for subSeq in os.listdir(seq)], tmpSeq)
File "/apps/chpc/bio/python/3.9.6/lib/p