[2023-03-18 00:35:04,573] [INFO] DFAST_QC pipeline started.
[2023-03-18 00:35:04,573] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 00:35:04,573] [INFO] DQC Reference Directory: /var/lib/cwl/stg9084499c-5d7b-4584-88af-33a514c5aa55/dqc_reference
[2023-03-18 00:35:05,664] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 00:35:05,664] [INFO] Task started: Prodigal
[2023-03-18 00:35:05,664] [INFO] Running command: cat /var/lib/cwl/stg1a673f7c-8e11-484e-86ef-299cf3b8f84c/OceanDNA-b7551.fa | prodigal -d OceanDNA-b7551/cds.fna -a OceanDNA-b7551/protein.faa -g 11 -q > /dev/null
[2023-03-18 00:35:16,145] [INFO] Task succeeded: Prodigal
[2023-03-18 00:35:16,145] [INFO] Task started: HMMsearch
[2023-03-18 00:35:16,145] [INFO] Running command: hmmsearch --tblout OceanDNA-b7551/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9084499c-5d7b-4584-88af-33a514c5aa55/dqc_reference/reference_markers.hmm OceanDNA-b7551/protein.faa > /dev/null
[2023-03-18 00:35:16,361] [INFO] Task succeeded: HMMsearch
[2023-03-18 00:35:16,362] [INFO] Found 6/6 markers.
[2023-03-18 00:35:16,374] [INFO] Query marker FASTA was written to OceanDNA-b7551/markers.fasta
[2023-03-18 00:35:16,374] [INFO] Task started: Blastn
[2023-03-18 00:35:16,374] [INFO] Running command: blastn -query OceanDNA-b7551/markers.fasta -db /var/lib/cwl/stg9084499c-5d7b-4584-88af-33a514c5aa55/dqc_reference/reference_markers.fasta -out OceanDNA-b7551/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 00:35:16,938] [INFO] Task succeeded: Blastn
[2023-03-18 00:35:16,939] [INFO] Selected 33 target genomes.
[2023-03-18 00:35:16,939] [INFO] Target genome list was writen to OceanDNA-b7551/target_genomes.txt
[2023-03-18 00:35:16,950] [INFO] Task started: fastANI
[2023-03-18 00:35:16,950] [INFO] Running command: fastANI --query /var/lib/cwl/stg1a673f7c-8e11-484e-86ef-299cf3b8f84c/OceanDNA-b7551.fa --refList OceanDNA-b7551/target_genomes.txt --output OceanDNA-b7551/fastani_result.tsv --threads 1
[2023-03-18 00:35:39,098] [INFO] Task succeeded: fastANI
[2023-03-18 00:35:39,098] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9084499c-5d7b-4584-88af-33a514c5aa55/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 00:35:39,098] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9084499c-5d7b-4584-88af-33a514c5aa55/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 00:35:39,103] [INFO] Found 5 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 00:35:39,103] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 00:35:39,103] [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
Cellulophaga fucicola	strain=DSM 24786	GCA_900119145.1	76595	76595	type	True	76.4267	70	525	95	below_threshold
Cellulophaga algicola	strain=DSM 14237	GCA_000186265.1	59600	59600	type	True	76.0619	68	525	95	below_threshold
Cellulophaga tyrosinoxydans	strain=DSM 21164	GCA_900176415.1	504486	504486	type	True	75.9225	64	525	95	below_threshold
Maribacter spongiicola	strain=DSM 25233	GCA_004364165.1	1206753	1206753	type	True	75.8591	51	525	95	below_threshold
Cellulophaga baltica	strain=DSM 24729	GCA_900102165.1	76594	76594	type	True	75.6266	55	525	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 00:35:39,103] [INFO] DFAST Taxonomy check result was written to OceanDNA-b7551/tc_result.tsv
[2023-03-18 00:35:39,103] [INFO] ===== Taxonomy check completed =====
[2023-03-18 00:35:39,104] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 00:35:39,104] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9084499c-5d7b-4584-88af-33a514c5aa55/dqc_reference/checkm_data
[2023-03-18 00:35:39,104] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 00:35:39,108] [INFO] Task started: CheckM
[2023-03-18 00:35:39,108] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b7551/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b7551/checkm_input OceanDNA-b7551/checkm_result
[2023-03-18 00:36:09,309] [INFO] Task succeeded: CheckM
[2023-03-18 00:36:09,310] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 68.75%
Contamintation: 2.08%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-18 00:36:09,312] [INFO] ===== Completeness check finished =====
[2023-03-18 00:36:09,312] [INFO] ===== Start GTDB Search =====
[2023-03-18 00:36:09,312] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b7551/markers.fasta)
[2023-03-18 00:36:09,312] [INFO] Task started: Blastn
[2023-03-18 00:36:09,312] [INFO] Running command: blastn -query OceanDNA-b7551/markers.fasta -db /var/lib/cwl/stg9084499c-5d7b-4584-88af-33a514c5aa55/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b7551/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 00:36:10,087] [INFO] Task succeeded: Blastn
[2023-03-18 00:36:10,088] [INFO] Selected 23 target genomes.
[2023-03-18 00:36:10,088] [INFO] Target genome list was writen to OceanDNA-b7551/target_genomes_gtdb.txt
[2023-03-18 00:36:10,111] [INFO] Task started: fastANI
[2023-03-18 00:36:10,111] [INFO] Running command: fastANI --query /var/lib/cwl/stg1a673f7c-8e11-484e-86ef-299cf3b8f84c/OceanDNA-b7551.fa --refList OceanDNA-b7551/target_genomes_gtdb.txt --output OceanDNA-b7551/fastani_result_gtdb.tsv --threads 1
[2023-03-18 00:36:22,133] [INFO] Task succeeded: fastANI
[2023-03-18 00:36:22,138] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 00:36:22,138] [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_905182295.1	s__MAG-120531 sp905182295	78.3425	147	525	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-120531	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000173115.1	s__MAG-120531 sp000173115	78.1847	166	525	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-120531	95.0	99.02	98.72	0.73	0.67	33	-
GCA_018500065.1	s__MAG-120531 sp018500065	77.9203	187	525	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-120531	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018401115.1	s__MAG-120531 sp018401115	77.8837	219	525	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-120531	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900119145.1	s__Cellulophaga fucicola	76.4267	70	525	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Cellulophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000186265.1	s__Cellulophaga algicola	76.0619	68	525	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Cellulophaga	95.0	98.35	98.34	0.88	0.87	3	-
GCF_018861125.1	s__Cellulophaga baltica_A	76.0375	53	525	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Cellulophaga	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 00:36:22,138] [INFO] GTDB search result was written to OceanDNA-b7551/result_gtdb.tsv
[2023-03-18 00:36:22,138] [INFO] ===== GTDB Search completed =====
[2023-03-18 00:36:22,139] [INFO] DFAST_QC result json was written to OceanDNA-b7551/dqc_result.json
[2023-03-18 00:36:22,139] [INFO] DFAST_QC completed!
[2023-03-18 00:36:22,139] [INFO] Total running time: 0h1m18s