[2023-03-18 09:26:42,702] [INFO] DFAST_QC pipeline started.
[2023-03-18 09:26:42,702] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 09:26:42,702] [INFO] DQC Reference Directory: /var/lib/cwl/stgdc2f1285-2ba8-4031-ba55-75f28509cc78/dqc_reference
[2023-03-18 09:26:43,798] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 09:26:43,799] [INFO] Task started: Prodigal
[2023-03-18 09:26:43,799] [INFO] Running command: cat /var/lib/cwl/stg3505df15-d3ca-4027-99c8-2321fbf2e765/OceanDNA-a4964.fa | prodigal -d OceanDNA-a4964/cds.fna -a OceanDNA-a4964/protein.faa -g 11 -q > /dev/null
[2023-03-18 09:26:50,007] [INFO] Task succeeded: Prodigal
[2023-03-18 09:26:50,008] [INFO] Task started: HMMsearch
[2023-03-18 09:26:50,008] [INFO] Running command: hmmsearch --tblout OceanDNA-a4964/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdc2f1285-2ba8-4031-ba55-75f28509cc78/dqc_reference/reference_markers.hmm OceanDNA-a4964/protein.faa > /dev/null
[2023-03-18 09:26:50,142] [INFO] Task succeeded: HMMsearch
[2023-03-18 09:26:50,142] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg3505df15-d3ca-4027-99c8-2321fbf2e765/OceanDNA-a4964.fa]
[2023-03-18 09:26:50,150] [INFO] Query marker FASTA was written to OceanDNA-a4964/markers.fasta
[2023-03-18 09:26:50,150] [INFO] Task started: Blastn
[2023-03-18 09:26:50,150] [INFO] Running command: blastn -query OceanDNA-a4964/markers.fasta -db /var/lib/cwl/stgdc2f1285-2ba8-4031-ba55-75f28509cc78/dqc_reference/reference_markers.fasta -out OceanDNA-a4964/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 09:26:50,614] [INFO] Task succeeded: Blastn
[2023-03-18 09:26:50,614] [INFO] Selected 6 target genomes.
[2023-03-18 09:26:50,615] [INFO] Target genome list was writen to OceanDNA-a4964/target_genomes.txt
[2023-03-18 09:26:50,618] [INFO] Task started: fastANI
[2023-03-18 09:26:50,618] [INFO] Running command: fastANI --query /var/lib/cwl/stg3505df15-d3ca-4027-99c8-2321fbf2e765/OceanDNA-a4964.fa --refList OceanDNA-a4964/target_genomes.txt --output OceanDNA-a4964/fastani_result.tsv --threads 1
[2023-03-18 09:26:54,038] [INFO] Task succeeded: fastANI
[2023-03-18 09:26:54,038] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdc2f1285-2ba8-4031-ba55-75f28509cc78/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 09:26:54,038] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdc2f1285-2ba8-4031-ba55-75f28509cc78/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 09:26:54,038] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 09:26:54,038] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 09:26:54,039] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
--------------------------------------------------------------------------------
[2023-03-18 09:26:54,039] [INFO] DFAST Taxonomy check result was written to OceanDNA-a4964/tc_result.tsv
[2023-03-18 09:26:54,039] [INFO] ===== Taxonomy check completed =====
[2023-03-18 09:26:54,039] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 09:26:54,039] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdc2f1285-2ba8-4031-ba55-75f28509cc78/dqc_reference/checkm_data
[2023-03-18 09:26:54,042] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 09:26:54,044] [INFO] Task started: CheckM
[2023-03-18 09:26:54,044] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a4964/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a4964/checkm_input OceanDNA-a4964/checkm_result
[2023-03-18 09:27:15,491] [INFO] Task succeeded: CheckM
[2023-03-18 09:27:15,492] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 65.01%
Contamintation: 6.11%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-03-18 09:27:15,493] [INFO] ===== Completeness check finished =====
[2023-03-18 09:27:15,493] [INFO] ===== Start GTDB Search =====
[2023-03-18 09:27:15,494] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a4964/markers.fasta)
[2023-03-18 09:27:15,494] [INFO] Task started: Blastn
[2023-03-18 09:27:15,494] [INFO] Running command: blastn -query OceanDNA-a4964/markers.fasta -db /var/lib/cwl/stgdc2f1285-2ba8-4031-ba55-75f28509cc78/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a4964/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 09:27:16,070] [INFO] Task succeeded: Blastn
[2023-03-18 09:27:16,071] [INFO] Selected 8 target genomes.
[2023-03-18 09:27:16,071] [INFO] Target genome list was writen to OceanDNA-a4964/target_genomes_gtdb.txt
[2023-03-18 09:27:16,088] [INFO] Task started: fastANI
[2023-03-18 09:27:16,088] [INFO] Running command: fastANI --query /var/lib/cwl/stg3505df15-d3ca-4027-99c8-2321fbf2e765/OceanDNA-a4964.fa --refList OceanDNA-a4964/target_genomes_gtdb.txt --output OceanDNA-a4964/fastani_result_gtdb.tsv --threads 1
[2023-03-18 09:27:18,146] [INFO] Task succeeded: fastANI
[2023-03-18 09:27:18,150] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 09:27:18,150] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCA_004195715.1	s__Thalassarchaeum sp004195715	85.53	168	177	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__Thalassarchaeum	95.0	99.87	99.86	0.95	0.94	3	-
GCA_014240285.1	s__Thalassarchaeum sp014240285	85.1749	159	177	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__Thalassarchaeum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002495735.1	s__Thalassarchaeum sp002495735	85.1216	145	177	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__Thalassarchaeum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002457605.1	s__Thalassarchaeum sp002457605	82.9135	129	177	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__Thalassarchaeum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002505325.1	s__Thalassarchaeum sp002505325	82.783	140	177	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__Thalassarchaeum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003193925.1	s__Thalassarchaeum betae	79.763	137	177	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__Thalassarchaeum	95.0	99.52	98.11	0.96	0.90	6	-
--------------------------------------------------------------------------------
[2023-03-18 09:27:18,150] [INFO] GTDB search result was written to OceanDNA-a4964/result_gtdb.tsv
[2023-03-18 09:27:18,151] [INFO] ===== GTDB Search completed =====
[2023-03-18 09:27:18,151] [INFO] DFAST_QC result json was written to OceanDNA-a4964/dqc_result.json
[2023-03-18 09:27:18,151] [INFO] DFAST_QC completed!
[2023-03-18 09:27:18,151] [INFO] Total running time: 0h0m35s