[2023-03-17 10:16:56,372] [INFO] DFAST_QC pipeline started.
[2023-03-17 10:16:56,372] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 10:16:56,372] [INFO] DQC Reference Directory: /var/lib/cwl/stg0fa8d37e-d0aa-49bd-8ef7-0ec5a674cfd8/dqc_reference
[2023-03-17 10:16:57,516] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 10:16:57,517] [INFO] Task started: Prodigal
[2023-03-17 10:16:57,518] [INFO] Running command: cat /var/lib/cwl/stg18957611-4bae-4b01-9c87-4a3dc960a225/OceanDNA-a3625.fa | prodigal -d OceanDNA-a3625/cds.fna -a OceanDNA-a3625/protein.faa -g 11 -q > /dev/null
[2023-03-17 10:17:06,529] [INFO] Task succeeded: Prodigal
[2023-03-17 10:17:06,529] [INFO] Task started: HMMsearch
[2023-03-17 10:17:06,530] [INFO] Running command: hmmsearch --tblout OceanDNA-a3625/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0fa8d37e-d0aa-49bd-8ef7-0ec5a674cfd8/dqc_reference/reference_markers.hmm OceanDNA-a3625/protein.faa > /dev/null
[2023-03-17 10:17:06,685] [INFO] Task succeeded: HMMsearch
[2023-03-17 10:17:06,686] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg18957611-4bae-4b01-9c87-4a3dc960a225/OceanDNA-a3625.fa]
[2023-03-17 10:17:06,743] [INFO] Query marker FASTA was written to OceanDNA-a3625/markers.fasta
[2023-03-17 10:17:06,744] [INFO] Task started: Blastn
[2023-03-17 10:17:06,744] [INFO] Running command: blastn -query OceanDNA-a3625/markers.fasta -db /var/lib/cwl/stg0fa8d37e-d0aa-49bd-8ef7-0ec5a674cfd8/dqc_reference/reference_markers.fasta -out OceanDNA-a3625/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 10:17:07,185] [INFO] Task succeeded: Blastn
[2023-03-17 10:17:07,186] [INFO] Selected 5 target genomes.
[2023-03-17 10:17:07,187] [INFO] Target genome list was writen to OceanDNA-a3625/target_genomes.txt
[2023-03-17 10:17:07,190] [INFO] Task started: fastANI
[2023-03-17 10:17:07,190] [INFO] Running command: fastANI --query /var/lib/cwl/stg18957611-4bae-4b01-9c87-4a3dc960a225/OceanDNA-a3625.fa --refList OceanDNA-a3625/target_genomes.txt --output OceanDNA-a3625/fastani_result.tsv --threads 1
[2023-03-17 10:17:12,347] [INFO] Task succeeded: fastANI
[2023-03-17 10:17:12,348] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0fa8d37e-d0aa-49bd-8ef7-0ec5a674cfd8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 10:17:12,348] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0fa8d37e-d0aa-49bd-8ef7-0ec5a674cfd8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 10:17:12,348] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 10:17:12,348] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 10:17:12,348] [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
--------------------------------------------------------------------------------
[2023-03-17 10:17:12,349] [INFO] DFAST Taxonomy check result was written to OceanDNA-a3625/tc_result.tsv
[2023-03-17 10:17:12,349] [INFO] ===== Taxonomy check completed =====
[2023-03-17 10:17:12,349] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 10:17:12,349] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0fa8d37e-d0aa-49bd-8ef7-0ec5a674cfd8/dqc_reference/checkm_data
[2023-03-17 10:17:12,352] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 10:17:12,356] [INFO] Task started: CheckM
[2023-03-17 10:17:12,356] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a3625/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a3625/checkm_input OceanDNA-a3625/checkm_result
[2023-03-17 10:17:40,079] [INFO] Task succeeded: CheckM
[2023-03-17 10:17:40,079] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 94.07%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 10:17:40,107] [INFO] ===== Completeness check finished =====
[2023-03-17 10:17:40,107] [INFO] ===== Start GTDB Search =====
[2023-03-17 10:17:40,108] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a3625/markers.fasta)
[2023-03-17 10:17:40,109] [INFO] Task started: Blastn
[2023-03-17 10:17:40,109] [INFO] Running command: blastn -query OceanDNA-a3625/markers.fasta -db /var/lib/cwl/stg0fa8d37e-d0aa-49bd-8ef7-0ec5a674cfd8/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a3625/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 10:17:40,565] [INFO] Task succeeded: Blastn
[2023-03-17 10:17:40,568] [INFO] Selected 9 target genomes.
[2023-03-17 10:17:40,568] [INFO] Target genome list was writen to OceanDNA-a3625/target_genomes_gtdb.txt
[2023-03-17 10:17:40,576] [INFO] Task started: fastANI
[2023-03-17 10:17:40,576] [INFO] Running command: fastANI --query /var/lib/cwl/stg18957611-4bae-4b01-9c87-4a3dc960a225/OceanDNA-a3625.fa --refList OceanDNA-a3625/target_genomes_gtdb.txt --output OceanDNA-a3625/fastani_result_gtdb.tsv --threads 1
[2023-03-17 10:17:42,955] [INFO] Task succeeded: fastANI
[2023-03-17 10:17:42,960] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 10:17:42,960] [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_002498525.1	s__MGIIb-O1 sp002498525	97.6115	461	483	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O1	95.0	98.43	97.35	0.95	0.89	6	conclusive
GCA_004195715.1	s__Thalassarchaeum sp004195715	78.8217	68	483	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__Thalassarchaeum	95.0	99.87	99.86	0.95	0.94	3	-
GCA_003193925.1	s__Thalassarchaeum betae	78.1866	98	483	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__Thalassarchaeum	95.0	99.52	98.11	0.96	0.90	6	-
GCA_013329905.1	s__MGIIb-O1 sp8684u	77.8561	153	483	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O1	95.0	99.67	99.41	0.91	0.86	4	-
GCA_014240285.1	s__Thalassarchaeum sp014240285	77.4977	62	483	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__Thalassarchaeum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002497895.1	s__MGIIb-O1 sp002497895	77.3286	122	483	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O1	95.0	99.30	99.27	0.83	0.71	4	-
--------------------------------------------------------------------------------
[2023-03-17 10:17:42,962] [INFO] GTDB search result was written to OceanDNA-a3625/result_gtdb.tsv
[2023-03-17 10:17:42,965] [INFO] ===== GTDB Search completed =====
[2023-03-17 10:17:42,967] [INFO] DFAST_QC result json was written to OceanDNA-a3625/dqc_result.json
[2023-03-17 10:17:42,967] [INFO] DFAST_QC completed!
[2023-03-17 10:17:42,968] [INFO] Total running time: 0h0m47s