[2023-03-18 20:13:32,199] [INFO] DFAST_QC pipeline started.
[2023-03-18 20:13:32,200] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 20:13:32,200] [INFO] DQC Reference Directory: /var/lib/cwl/stg8fbcec6f-2613-4131-9061-c22d4c61a46f/dqc_reference
[2023-03-18 20:13:33,403] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 20:13:33,430] [INFO] Task started: Prodigal
[2023-03-18 20:13:33,430] [INFO] Running command: cat /var/lib/cwl/stg61d56677-652b-4d7c-a66b-0b011462aca4/OceanDNA-b36307.fa | prodigal -d OceanDNA-b36307/cds.fna -a OceanDNA-b36307/protein.faa -g 11 -q > /dev/null
[2023-03-18 20:13:49,870] [INFO] Task succeeded: Prodigal
[2023-03-18 20:13:49,870] [INFO] Task started: HMMsearch
[2023-03-18 20:13:49,870] [INFO] Running command: hmmsearch --tblout OceanDNA-b36307/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8fbcec6f-2613-4131-9061-c22d4c61a46f/dqc_reference/reference_markers.hmm OceanDNA-b36307/protein.faa > /dev/null
[2023-03-18 20:13:50,098] [INFO] Task succeeded: HMMsearch
[2023-03-18 20:13:50,099] [INFO] Found 6/6 markers.
[2023-03-18 20:13:50,118] [INFO] Query marker FASTA was written to OceanDNA-b36307/markers.fasta
[2023-03-18 20:13:50,119] [INFO] Task started: Blastn
[2023-03-18 20:13:50,119] [INFO] Running command: blastn -query OceanDNA-b36307/markers.fasta -db /var/lib/cwl/stg8fbcec6f-2613-4131-9061-c22d4c61a46f/dqc_reference/reference_markers.fasta -out OceanDNA-b36307/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 20:13:50,722] [INFO] Task succeeded: Blastn
[2023-03-18 20:13:50,723] [INFO] Selected 22 target genomes.
[2023-03-18 20:13:50,723] [INFO] Target genome list was writen to OceanDNA-b36307/target_genomes.txt
[2023-03-18 20:13:50,735] [INFO] Task started: fastANI
[2023-03-18 20:13:50,735] [INFO] Running command: fastANI --query /var/lib/cwl/stg61d56677-652b-4d7c-a66b-0b011462aca4/OceanDNA-b36307.fa --refList OceanDNA-b36307/target_genomes.txt --output OceanDNA-b36307/fastani_result.tsv --threads 1
[2023-03-18 20:14:04,270] [INFO] Task succeeded: fastANI
[2023-03-18 20:14:04,270] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8fbcec6f-2613-4131-9061-c22d4c61a46f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 20:14:04,270] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8fbcec6f-2613-4131-9061-c22d4c61a46f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 20:14:04,275] [INFO] Found 6 fastANI hits (1 hits with ANI > threshold)
[2023-03-18 20:14:04,276] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-18 20:14:04,276] [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
Methylophaga aminisulfidivorans	strain=MP	GCA_000214595.2	230105	230105	type	True	97.9705	903	969	95	conclusive
Methylophaga sulfidovorans	strain=DSM 11578	GCA_900114205.1	45496	45496	type	True	87.0807	789	969	95	below_threshold
Methylophaga thiooxydans	strain=DMS010	GCA_000156355.1	392484	392484	type	True	78.2248	230	969	95	below_threshold
Methylophaga pinxianii	strain=TMB456	GCA_020447225.1	2881052	2881052	type	True	77.0064	124	969	95	below_threshold
Methylophaga nitratireducenticrescens	strain=JAM1	GCA_000260985.3	754476	754476	type	True	76.9641	120	969	95	below_threshold
Methylophaga lonarensis	strain=MPL	GCA_000349205.1	999151	999151	type	True	76.8281	85	969	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 20:14:04,276] [INFO] DFAST Taxonomy check result was written to OceanDNA-b36307/tc_result.tsv
[2023-03-18 20:14:04,276] [INFO] ===== Taxonomy check completed =====
[2023-03-18 20:14:04,276] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 20:14:04,276] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8fbcec6f-2613-4131-9061-c22d4c61a46f/dqc_reference/checkm_data
[2023-03-18 20:14:04,277] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 20:14:04,282] [INFO] Task started: CheckM
[2023-03-18 20:14:04,282] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b36307/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b36307/checkm_input OceanDNA-b36307/checkm_result
[2023-03-18 20:14:48,021] [INFO] Task succeeded: CheckM
[2023-03-18 20:14:48,022] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 62.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 20:14:48,024] [INFO] ===== Completeness check finished =====
[2023-03-18 20:14:48,024] [INFO] ===== Start GTDB Search =====
[2023-03-18 20:14:48,025] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b36307/markers.fasta)
[2023-03-18 20:14:48,025] [INFO] Task started: Blastn
[2023-03-18 20:14:48,025] [INFO] Running command: blastn -query OceanDNA-b36307/markers.fasta -db /var/lib/cwl/stg8fbcec6f-2613-4131-9061-c22d4c61a46f/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b36307/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 20:14:49,006] [INFO] Task succeeded: Blastn
[2023-03-18 20:14:49,007] [INFO] Selected 11 target genomes.
[2023-03-18 20:14:49,007] [INFO] Target genome list was writen to OceanDNA-b36307/target_genomes_gtdb.txt
[2023-03-18 20:14:49,189] [INFO] Task started: fastANI
[2023-03-18 20:14:49,189] [INFO] Running command: fastANI --query /var/lib/cwl/stg61d56677-652b-4d7c-a66b-0b011462aca4/OceanDNA-b36307.fa --refList OceanDNA-b36307/target_genomes_gtdb.txt --output OceanDNA-b36307/fastani_result_gtdb.tsv --threads 1
[2023-03-18 20:14:55,135] [INFO] Task succeeded: fastANI
[2023-03-18 20:14:55,141] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 20:14:55,141] [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
GCF_000214595.1	s__Methylophaga aminisulfidivorans	97.9705	903	969	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__Methylophaga	95.0	97.12	97.07	0.93	0.92	4	conclusive
GCF_900114205.1	s__Methylophaga sulfidovorans	87.0807	789	969	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__Methylophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002706095.1	s__Methylophaga sp002706095	84.066	732	969	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__Methylophaga	95.0	98.12	97.28	0.92	0.89	8	-
GCA_011052985.1	s__Methylophaga aminisulfidivorans_A	78.8704	221	969	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__Methylophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000156355.1	s__Methylophaga thiooxydans	78.2314	229	969	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__Methylophaga	95.0	96.48	96.37	0.89	0.88	3	-
GCA_014859375.1	s__GCA-002733105 sp014859375	77.1935	89	969	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__GCA-002733105	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002163115.1	s__41-12-T18 sp002163115	76.3319	86	969	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__41-12-T18	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002400805.1	s__41-12-T18 sp002400805	76.2233	52	969	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__41-12-T18	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905479985.1	s__GCA-002733105 sp905479985	75.9534	57	969	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__GCA-002733105	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 20:14:55,141] [INFO] GTDB search result was written to OceanDNA-b36307/result_gtdb.tsv
[2023-03-18 20:14:55,141] [INFO] ===== GTDB Search completed =====
[2023-03-18 20:14:55,142] [INFO] DFAST_QC result json was written to OceanDNA-b36307/dqc_result.json
[2023-03-18 20:14:55,142] [INFO] DFAST_QC completed!
[2023-03-18 20:14:55,142] [INFO] Total running time: 0h1m23s