 _____ ______                                   
| ____|__  / |_ _ __ __ _ _ __ ___  _ __   ___  
|  _|   / /| __| '__/ _` | '_ ` _ \| '_ \ / _ \ 
| |___ / /_| |_| | | (_| | | | | | | |_) | (_) |
|_____/____|\__|_|  \__,_|_| |_| |_| .__/ \___/ 
                                   |_|


Starting EZtrampo run
FASTA: ['/home/labadmin/Ezmito/uploaded_jobs/claudio_20260319_154613_120123_406726a2/atp6.fas', '/home/labadmin/Ezmito/uploaded_jobs/claudio_20260319_154613_120123_406726a2/atp8.fas', '/home/labadmin/Ezmito/uploaded_jobs/claudio_20260319_154613_120123_406726a2/cob.fas', '/home/labadmin/Ezmito/uploaded_jobs/claudio_20260319_154613_120123_406726a2/cox1.fas', '/home/labadmin/Ezmito/uploaded_jobs/claudio_20260319_154613_120123_406726a2/cox2.fas', '/home/labadmin/Ezmito/uploaded_jobs/claudio_20260319_154613_120123_406726a2/cox3.fas', '/home/labadmin/Ezmito/uploaded_jobs/claudio_20260319_154613_120123_406726a2/nad1.fas', '/home/labadmin/Ezmito/uploaded_jobs/claudio_20260319_154613_120123_406726a2/nad2.fas', '/home/labadmin/Ezmito/uploaded_jobs/claudio_20260319_154613_120123_406726a2/nad3.fas', '/home/labadmin/Ezmito/uploaded_jobs/claudio_20260319_154613_120123_406726a2/nad4.fas', '/home/labadmin/Ezmito/uploaded_jobs/claudio_20260319_154613_120123_406726a2/nad4L.fas', '/home/labadmin/Ezmito/uploaded_jobs/claudio_20260319_154613_120123_406726a2/nad5.fas', '/home/labadmin/Ezmito/uploaded_jobs/claudio_20260319_154613_120123_406726a2/nad6.fas']
Genetic code: 5
Model organism: dme
Gene order: panc
Custom sequence: None
Custom THMM tables: None
Outdir: /home/labadmin/Ezmito/complete_jobs/claudio_20260319_154613_120123_406726a2

Warning: the length of CTE in atp6 differs more than three standard deviation
Warning: the length of CAN in atp6 differs more than three standard deviation
Warning: the length of FOC in atp6 differs more than three standard deviation
Warning: the length of FGR_AP in atp6 differs more than three standard deviation
Warning: the length of FGR_VL in atp6 differs more than three standard deviation
Warning: the length of BAU in atp6 differs more than three standard deviation
Warning: the length of GHO in atp6 differs more than three standard deviation
Warning: the length of PAQ in atp6 differs more than three standard deviation
Warning: the length of OOR in atp6 differs more than three standard deviation
Warning: the length of TBI in atp6 differs more than three standard deviation
Warning: the length of OVI in atp6 differs more than three standard deviation
Warning: the length of OCI in atp6 differs more than three standard deviation
Warning: the length of SVI in atp6 differs more than three standard deviation


The original alignment of atp6_checked_translated_ali_aa_ref.nexus lost 5/228 - 2.19% of nucleotide characters
The original alignment of atp6_checked_translated_ali_nt_ref.nexus lost 13/684 - 1.9% of nucleotide characters
Warning: the length of CTE in atp8 differs more than three standard deviation
Warning: the length of CAN in atp8 differs more than three standard deviation
Warning: the length of FOC in atp8 differs more than three standard deviation
Warning: the length of FGR_AP in atp8 differs more than three standard deviation
Warning: the length of FGR_VL in atp8 differs more than three standard deviation
Warning: the length of BAU in atp8 differs more than three standard deviation
Warning: the length of GHO in atp8 differs more than three standard deviation
Warning: the length of PAQ in atp8 differs more than three standard deviation
Warning: the length of OOR in atp8 differs more than three standard deviation
Warning: the length of TBI in atp8 differs more than three standard deviation
Warning: the length of OVI in atp8 differs more than three standard deviation
Warning: the length of OCI in atp8 differs more than three standard deviation
Warning: the length of SVI in atp8 differs more than three standard deviation


The original alignment of atp8_checked_translated_ali_aa_ref.nexus lost 20/72 - 27.78% of nucleotide characters
The original alignment of atp8_checked_translated_ali_nt_ref.nexus lost 58/216 - 26.85% of nucleotide characters
Warning: the length of CTE in cob differs more than three standard deviation
Warning: the length of CAN in cob differs more than three standard deviation
Warning: the length of FOC in cob differs more than three standard deviation
Warning: the length of FGR_AP in cob differs more than three standard deviation
Warning: the length of FGR_VL in cob differs more than three standard deviation
Warning: the length of BAU in cob differs more than three standard deviation
Warning: the length of GHO in cob differs more than three standard deviation
Warning: the length of PAQ in cob differs more than three standard deviation
Warning: the length of OOR in cob differs more than three standard deviation
Warning: the length of TBI in cob differs more than three standard deviation
Warning: the length of OVI in cob differs more than three standard deviation
Warning: the length of OCI in cob differs more than three standard deviation
Warning: the length of SVI in cob differs more than three standard deviation


The original alignment of cob_checked_translated_ali_aa_ref.nexus lost 13/390 - 3.33% of nucleotide characters
The original alignment of cob_checked_translated_ali_nt_ref.nexus lost 37/1170 - 3.16% of nucleotide characters
Warning: the length of CTE in cox1 differs more than three standard deviation
Warning: the length of CAN in cox1 differs more than three standard deviation
Warning: the length of FOC in cox1 differs more than three standard deviation
Warning: the length of FGR_AP in cox1 differs more than three standard deviation
Warning: the length of FGR_VL in cox1 differs more than three standard deviation
Warning: the length of BAU in cox1 differs more than three standard deviation
Warning: the length of GHO in cox1 differs more than three standard deviation
Warning: the length of PAQ in cox1 differs more than three standard deviation
Warning: the length of OOR in cox1 differs more than three standard deviation
Warning: the length of TBI in cox1 differs more than three standard deviation
Warning: the length of OVI in cox1 differs more than three standard deviation
Warning: the length of OCI in cox1 differs more than three standard deviation
Warning: the length of SVI in cox1 differs more than three standard deviation


The original alignment of cox1_checked_translated_ali_aa_ref.nexus lost 11/521 - 2.11% of nucleotide characters
The original alignment of cox1_checked_translated_ali_nt_ref.nexus lost 31/1563 - 1.98% of nucleotide characters


Warning: Found gap (-) in OCI. Removing gap...
Warning: Found gap (-) in PAQ. Removing gap...
Warning: Found gap (-) in BAU. Removing gap...
Warning: Found gap (-) in SVI. Removing gap...
Warning: Found gap (-) in FOC. Removing gap...
Warning: Found gap (-) in FGR_AP. Removing gap...
Warning: Found gap (-) in FGR_VL. Removing gap...
Warning: Found gap (-) in CTE. Removing gap...
Warning: Found gap (-) in CAN. Removing gap...
Warning: Found gap (-) in OOR. Removing gap...
Warning: Found gap (-) in OVI. Removing gap...
Warning: Found gap (-) in TBI. Removing gap...
Warning: Found gap (-) in GHO. Removing gap...
The original alignment of cox2_checked_translated_ali_aa_ref.nexus lost 13/240 - 5.42% of nucleotide characters
The original alignment of cox2_checked_translated_ali_nt_ref.nexus lost 37/720 - 5.14% of nucleotide characters
Warning: the length of CTE in cox3 differs more than three standard deviation
Warning: the length of CAN in cox3 differs more than three standard deviation
Warning: the length of FOC in cox3 differs more than three standard deviation
Warning: the length of FGR_AP in cox3 differs more than three standard deviation
Warning: the length of FGR_VL in cox3 differs more than three standard deviation
Warning: the length of BAU in cox3 differs more than three standard deviation
Warning: the length of GHO in cox3 differs more than three standard deviation
Warning: the length of PAQ in cox3 differs more than three standard deviation
Warning: the length of OOR in cox3 differs more than three standard deviation
Warning: the length of TBI in cox3 differs more than three standard deviation
Warning: the length of OVI in cox3 differs more than three standard deviation
Warning: the length of OCI in cox3 differs more than three standard deviation
Warning: the length of SVI in cox3 differs more than three standard deviation


The original alignment of cox3_checked_translated_ali_aa_ref.nexus lost 4/265 - 1.51% of nucleotide characters
The original alignment of cox3_checked_translated_ali_nt_ref.nexus lost 10/795 - 1.26% of nucleotide characters
Warning: the length of CTE in nd1 differs more than three standard deviation
Warning: the length of CAN in nd1 differs more than three standard deviation
Warning: the length of FOC in nd1 differs more than three standard deviation
Warning: the length of FGR_AP in nd1 differs more than three standard deviation
Warning: the length of FGR_VL in nd1 differs more than three standard deviation
Warning: the length of BAU in nd1 differs more than three standard deviation
Warning: the length of GHO in nd1 differs more than three standard deviation
Warning: the length of PAQ in nd1 differs more than three standard deviation
Warning: the length of OOR in nd1 differs more than three standard deviation
Warning: the length of TBI in nd1 differs more than three standard deviation
Warning: the length of OVI in nd1 differs more than three standard deviation
Warning: the length of OCI in nd1 differs more than three standard deviation
Warning: the length of SVI in nd1 differs more than three standard deviation


The original alignment of nd1_checked_translated_ali_aa_ref.nexus lost 16/327 - 4.89% of nucleotide characters
The original alignment of nd1_checked_translated_ali_nt_ref.nexus lost 46/981 - 4.69% of nucleotide characters
Warning: the length of CTE in nd2 differs more than three standard deviation
Warning: the length of CAN in nd2 differs more than three standard deviation
Warning: the length of FOC in nd2 differs more than three standard deviation
Warning: the length of FGR_AP in nd2 differs more than three standard deviation
Warning: the length of FGR_VL in nd2 differs more than three standard deviation
Warning: the length of BAU in nd2 differs more than three standard deviation
Warning: the length of GHO in nd2 differs more than three standard deviation
Warning: the length of PAQ in nd2 differs more than three standard deviation
Warning: the length of OOR in nd2 differs more than three standard deviation
Warning: the length of TBI in nd2 differs more than three standard deviation
Warning: the length of OVI in nd2 differs more than three standard deviation
Warning: the length of OCI in nd2 differs more than three standard deviation
Warning: the length of SVI in nd2 differs more than three standard deviation


The original alignment of nd2_checked_translated_ali_aa_ref.nexus lost 17/357 - 4.76% of nucleotide characters
The original alignment of nd2_checked_translated_ali_nt_ref.nexus lost 58/1071 - 5.42% of nucleotide characters
Warning: the length of CTE in nd3 differs more than three standard deviation
Warning: the length of CAN in nd3 differs more than three standard deviation
Warning: the length of FOC in nd3 differs more than three standard deviation
Warning: the length of FGR_AP in nd3 differs more than three standard deviation
Warning: the length of FGR_VL in nd3 differs more than three standard deviation
Warning: the length of BAU in nd3 differs more than three standard deviation
Warning: the length of GHO in nd3 differs more than three standard deviation
Warning: the length of PAQ in nd3 differs more than three standard deviation
Warning: the length of OOR in nd3 differs more than three standard deviation
Warning: the length of TBI in nd3 differs more than three standard deviation
Warning: the length of OVI in nd3 differs more than three standard deviation
Warning: the length of OCI in nd3 differs more than three standard deviation
Warning: the length of SVI in nd3 differs more than three standard deviation


Warning: Found a truncated sequence: SVI of /home/labadmin/Ezmito/complete_jobs/claudio_20260319_154613_120123_406726a2/tmp/nd3_degapped.fasta. It will be automatically adjusted and the analysis is continuing...
The original alignment of nd3_checked_translated_ali_aa_ref.nexus lost 52/168 - 30.95% of nucleotide characters
The original alignment of nd3_checked_translated_ali_nt_ref.nexus lost 157/504 - 31.15% of nucleotide characters
Warning: the length of CTE in nd4 differs more than three standard deviation
Warning: the length of CAN in nd4 differs more than three standard deviation
Warning: the length of FOC in nd4 differs more than three standard deviation
Warning: the length of FGR_AP in nd4 differs more than three standard deviation
Warning: the length of FGR_VL in nd4 differs more than three standard deviation
Warning: the length of BAU in nd4 differs more than three standard deviation
Warning: the length of GHO in nd4 differs more than three standard deviation
Warning: the length of PAQ in nd4 differs more than three standard deviation
Warning: the length of OOR in nd4 differs more than three standard deviation
Warning: the length of TBI in nd4 differs more than three standard deviation
Warning: the length of OVI in nd4 differs more than three standard deviation
Warning: the length of OCI in nd4 differs more than three standard deviation
Warning: the length of SVI in nd4 differs more than three standard deviation


Warning: Found a not recognized amino acid in file /home/labadmin/Ezmito/complete_jobs/claudio_20260319_154613_120123_406726a2/tmp/nd4_checked_translated.fasta, sequence ID OOR. It will be switched to X to continue the analysis. Otherwise, check it and re-submit a new job.

The original alignment of nd4_checked_translated_ali_aa_ref.nexus lost 40/485 - 8.25% of nucleotide characters
The original alignment of nd4_checked_translated_ali_nt_ref.nexus lost 118/1455 - 8.11% of nucleotide characters
Warning: the length of CTE in ndl differs more than three standard deviation
Warning: the length of CAN in ndl differs more than three standard deviation
Warning: the length of FOC in ndl differs more than three standard deviation
Warning: the length of FGR_AP in ndl differs more than three standard deviation
Warning: the length of FGR_VL in ndl differs more than three standard deviation
Warning: the length of BAU in ndl differs more than three standard deviation
Warning: the length of GHO in ndl differs more than three standard deviation
Warning: the length of PAQ in ndl differs more than three standard deviation
Warning: the length of OOR in ndl differs more than three standard deviation
Warning: the length of TBI in ndl differs more than three standard deviation
Warning: the length of OVI in ndl differs more than three standard deviation
Warning: the length of OCI in ndl differs more than three standard deviation
Warning: the length of SVI in ndl differs more than three standard deviation


The original alignment of ndl_checked_translated_ali_aa_ref.nexus lost 14/109 - 12.84% of nucleotide characters
The original alignment of ndl_checked_translated_ali_nt_ref.nexus lost 52/327 - 15.9% of nucleotide characters
Warning: the length of CTE in nd5 differs more than three standard deviation
Warning: the length of CAN in nd5 differs more than three standard deviation
Warning: the length of FOC in nd5 differs more than three standard deviation
Warning: the length of FGR_AP in nd5 differs more than three standard deviation
Warning: the length of FGR_VL in nd5 differs more than three standard deviation
Warning: the length of BAU in nd5 differs more than three standard deviation
Warning: the length of GHO in nd5 differs more than three standard deviation
Warning: the length of PAQ in nd5 differs more than three standard deviation
Warning: the length of OOR in nd5 differs more than three standard deviation
Warning: the length of TBI in nd5 differs more than three standard deviation
Warning: the length of OVI in nd5 differs more than three standard deviation
Warning: the length of OCI in nd5 differs more than three standard deviation
Warning: the length of SVI in nd5 differs more than three standard deviation


The original alignment of nd5_checked_translated_ali_aa_ref.nexus lost 55/626 - 8.79% of nucleotide characters
The original alignment of nd5_checked_translated_ali_nt_ref.nexus lost 187/1878 - 9.96% of nucleotide characters
Warning: the length of CTE in nd6 differs more than three standard deviation
Warning: the length of CAN in nd6 differs more than three standard deviation
Warning: the length of FOC in nd6 differs more than three standard deviation
Warning: the length of FGR_AP in nd6 differs more than three standard deviation
Warning: the length of FGR_VL in nd6 differs more than three standard deviation
Warning: the length of BAU in nd6 differs more than three standard deviation
Warning: the length of GHO in nd6 differs more than three standard deviation
Warning: the length of PAQ in nd6 differs more than three standard deviation
Warning: the length of OOR in nd6 differs more than three standard deviation
Warning: the length of TBI in nd6 differs more than three standard deviation
Warning: the length of OVI in nd6 differs more than three standard deviation
Warning: the length of OCI in nd6 differs more than three standard deviation
Warning: the length of SVI in nd6 differs more than three standard deviation


The original alignment of nd6_checked_translated_ali_aa_ref.nexus lost 26/199 - 13.07% of nucleotide characters
The original alignment of nd6_checked_translated_ali_nt_ref.nexus lost 97/597 - 16.25% of nucleotide characters

Total runtime: 93.74 seconds
