[2023-03-14 11:06:15,078] [INFO] DFAST_QC pipeline started.
[2023-03-14 11:06:15,078] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 11:06:15,078] [INFO] DQC Reference Directory: /var/lib/cwl/stgaf1970be-5302-4ceb-b931-2b3a704426c6/dqc_reference
[2023-03-14 11:06:16,185] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 11:06:16,187] [INFO] Task started: Prodigal
[2023-03-14 11:06:16,187] [INFO] Running command: cat /var/lib/cwl/stgbcc9b3ab-7adf-425d-a8dd-46d48a39b6b9/OceanDNA-a4981.fa | prodigal -d OceanDNA-a4981/cds.fna -a OceanDNA-a4981/protein.faa -g 11 -q > /dev/null
[2023-03-14 11:06:24,109] [INFO] Task succeeded: Prodigal
[2023-03-14 11:06:24,109] [INFO] Task started: HMMsearch
[2023-03-14 11:06:24,109] [INFO] Running command: hmmsearch --tblout OceanDNA-a4981/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgaf1970be-5302-4ceb-b931-2b3a704426c6/dqc_reference/reference_markers.hmm OceanDNA-a4981/protein.faa > /dev/null
[2023-03-14 11:06:24,429] [INFO] Task succeeded: HMMsearch
[2023-03-14 11:06:24,429] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgbcc9b3ab-7adf-425d-a8dd-46d48a39b6b9/OceanDNA-a4981.fa]
[2023-03-14 11:06:24,439] [INFO] Query marker FASTA was written to OceanDNA-a4981/markers.fasta
[2023-03-14 11:06:24,441] [INFO] Task started: Blastn
[2023-03-14 11:06:24,441] [INFO] Running command: blastn -query OceanDNA-a4981/markers.fasta -db /var/lib/cwl/stgaf1970be-5302-4ceb-b931-2b3a704426c6/dqc_reference/reference_markers.fasta -out OceanDNA-a4981/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 11:06:27,102] [INFO] Task succeeded: Blastn
[2023-03-14 11:06:27,103] [INFO] Selected 6 target genomes.
[2023-03-14 11:06:27,103] [INFO] Target genome list was writen to OceanDNA-a4981/target_genomes.txt
[2023-03-14 11:06:27,108] [INFO] Task started: fastANI
[2023-03-14 11:06:27,108] [INFO] Running command: fastANI --query /var/lib/cwl/stgbcc9b3ab-7adf-425d-a8dd-46d48a39b6b9/OceanDNA-a4981.fa --refList OceanDNA-a4981/target_genomes.txt --output OceanDNA-a4981/fastani_result.tsv --threads 1
[2023-03-14 11:06:30,307] [INFO] Task succeeded: fastANI
[2023-03-14 11:06:30,307] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgaf1970be-5302-4ceb-b931-2b3a704426c6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 11:06:30,308] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgaf1970be-5302-4ceb-b931-2b3a704426c6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 11:06:30,308] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 11:06:30,308] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-14 11:06:30,308] [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
--------------------------------------------------------------------------------
[2023-03-14 11:06:30,308] [INFO] DFAST Taxonomy check result was written to OceanDNA-a4981/tc_result.tsv
[2023-03-14 11:06:30,308] [INFO] ===== Taxonomy check completed =====
[2023-03-14 11:06:30,308] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 11:06:30,308] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgaf1970be-5302-4ceb-b931-2b3a704426c6/dqc_reference/checkm_data
[2023-03-14 11:06:30,468] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 11:06:30,472] [INFO] Task started: CheckM
[2023-03-14 11:06:30,473] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a4981/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a4981/checkm_input OceanDNA-a4981/checkm_result
[2023-03-14 11:06:59,636] [INFO] Task succeeded: CheckM
[2023-03-14 11:06:59,636] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 88.72%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 11:06:59,638] [INFO] ===== Completeness check finished =====
[2023-03-14 11:06:59,638] [INFO] ===== Start GTDB Search =====
[2023-03-14 11:06:59,638] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a4981/markers.fasta)
[2023-03-14 11:06:59,640] [INFO] Task started: Blastn
[2023-03-14 11:06:59,640] [INFO] Running command: blastn -query OceanDNA-a4981/markers.fasta -db /var/lib/cwl/stgaf1970be-5302-4ceb-b931-2b3a704426c6/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a4981/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 11:07:00,317] [INFO] Task succeeded: Blastn
[2023-03-14 11:07:00,318] [INFO] Selected 9 target genomes.
[2023-03-14 11:07:00,318] [INFO] Target genome list was writen to OceanDNA-a4981/target_genomes_gtdb.txt
[2023-03-14 11:07:00,332] [INFO] Task started: fastANI
[2023-03-14 11:07:00,332] [INFO] Running command: fastANI --query /var/lib/cwl/stgbcc9b3ab-7adf-425d-a8dd-46d48a39b6b9/OceanDNA-a4981.fa --refList OceanDNA-a4981/target_genomes_gtdb.txt --output OceanDNA-a4981/fastani_result_gtdb.tsv --threads 1
[2023-03-14 11:07:02,680] [INFO] Task succeeded: fastANI
[2023-03-14 11:07:02,686] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-14 11:07:02,686] [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_003193925.1	s__Thalassarchaeum betae	97.9727	410	425	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__Thalassarchaeum	95.0	99.52	98.11	0.96	0.90	6	conclusive
GCA_002507125.1	s__Thalassarchaeum sp002507125	84.9541	267	425	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__Thalassarchaeum	95.0	98.54	98.42	0.77	0.74	3	-
GCA_014240285.1	s__Thalassarchaeum sp014240285	78.8171	195	425	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__Thalassarchaeum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004195715.1	s__Thalassarchaeum sp004195715	78.7569	225	425	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__Thalassarchaeum	95.0	99.87	99.86	0.95	0.94	3	-
GCA_002457605.1	s__Thalassarchaeum sp002457605	77.9971	143	425	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__Thalassarchaeum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002498525.1	s__MGIIb-O1 sp002498525	77.9914	93	425	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O1	95.0	98.43	97.35	0.95	0.89	6	-
GCA_016845365.1	s__MGIIb-O1 sp016845365	76.669	56	425	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002725315.1	s__MGIIb-O3 sp002725315	76.5199	52	425	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O3	95.0	99.12	98.81	0.90	0.86	5	-
--------------------------------------------------------------------------------
[2023-03-14 11:07:02,686] [INFO] GTDB search result was written to OceanDNA-a4981/result_gtdb.tsv
[2023-03-14 11:07:02,686] [INFO] ===== GTDB Search completed =====
[2023-03-14 11:07:02,687] [INFO] DFAST_QC result json was written to OceanDNA-a4981/dqc_result.json
[2023-03-14 11:07:02,687] [INFO] DFAST_QC completed!
[2023-03-14 11:07:02,687] [INFO] Total running time: 0h0m48s