[2023-03-16 16:53:43,355] [INFO] DFAST_QC pipeline started.
[2023-03-16 16:53:43,355] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 16:53:43,356] [INFO] DQC Reference Directory: /var/lib/cwl/stg8366e46f-caed-4a04-9666-4343086983c8/dqc_reference
[2023-03-16 16:53:44,473] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 16:53:44,473] [INFO] Task started: Prodigal
[2023-03-16 16:53:44,473] [INFO] Running command: cat /var/lib/cwl/stgad6d79ef-41a6-4612-b525-ff1ada90a774/OceanDNA-b36288.fa | prodigal -d OceanDNA-b36288/cds.fna -a OceanDNA-b36288/protein.faa -g 11 -q > /dev/null
[2023-03-16 16:53:59,872] [INFO] Task succeeded: Prodigal
[2023-03-16 16:53:59,873] [INFO] Task started: HMMsearch
[2023-03-16 16:53:59,873] [INFO] Running command: hmmsearch --tblout OceanDNA-b36288/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8366e46f-caed-4a04-9666-4343086983c8/dqc_reference/reference_markers.hmm OceanDNA-b36288/protein.faa > /dev/null
[2023-03-16 16:54:00,048] [INFO] Task succeeded: HMMsearch
[2023-03-16 16:54:00,049] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgad6d79ef-41a6-4612-b525-ff1ada90a774/OceanDNA-b36288.fa]
[2023-03-16 16:54:00,063] [INFO] Query marker FASTA was written to OceanDNA-b36288/markers.fasta
[2023-03-16 16:54:00,064] [INFO] Task started: Blastn
[2023-03-16 16:54:00,064] [INFO] Running command: blastn -query OceanDNA-b36288/markers.fasta -db /var/lib/cwl/stg8366e46f-caed-4a04-9666-4343086983c8/dqc_reference/reference_markers.fasta -out OceanDNA-b36288/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 16:54:00,638] [INFO] Task succeeded: Blastn
[2023-03-16 16:54:00,639] [INFO] Selected 22 target genomes.
[2023-03-16 16:54:00,639] [INFO] Target genome list was writen to OceanDNA-b36288/target_genomes.txt
[2023-03-16 16:54:00,656] [INFO] Task started: fastANI
[2023-03-16 16:54:00,657] [INFO] Running command: fastANI --query /var/lib/cwl/stgad6d79ef-41a6-4612-b525-ff1ada90a774/OceanDNA-b36288.fa --refList OceanDNA-b36288/target_genomes.txt --output OceanDNA-b36288/fastani_result.tsv --threads 1
[2023-03-16 16:54:20,743] [INFO] Task succeeded: fastANI
[2023-03-16 16:54:20,744] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8366e46f-caed-4a04-9666-4343086983c8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 16:54:20,744] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8366e46f-caed-4a04-9666-4343086983c8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 16:54:20,756] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 16:54:20,756] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 16:54:20,756] [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 pinxianii	strain=TMB456	GCA_020447225.1	2881052	2881052	type	True	75.9604	55	755	95	below_threshold
Methylophaga thiooxydans	strain=DMS010	GCA_000156355.1	392484	392484	type	True	75.929	66	755	95	below_threshold
Methylophaga nitratireducenticrescens	strain=JAM1	GCA_000260985.3	754476	754476	type	True	75.8213	57	755	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 16:54:20,756] [INFO] DFAST Taxonomy check result was written to OceanDNA-b36288/tc_result.tsv
[2023-03-16 16:54:20,756] [INFO] ===== Taxonomy check completed =====
[2023-03-16 16:54:20,756] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 16:54:20,757] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8366e46f-caed-4a04-9666-4343086983c8/dqc_reference/checkm_data
[2023-03-16 16:54:20,757] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 16:54:20,761] [INFO] Task started: CheckM
[2023-03-16 16:54:20,761] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b36288/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b36288/checkm_input OceanDNA-b36288/checkm_result
[2023-03-16 16:54:55,469] [INFO] Task succeeded: CheckM
[2023-03-16 16:54:55,469] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 54.17%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 16:54:55,471] [INFO] ===== Completeness check finished =====
[2023-03-16 16:54:55,471] [INFO] ===== Start GTDB Search =====
[2023-03-16 16:54:55,471] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b36288/markers.fasta)
[2023-03-16 16:54:55,473] [INFO] Task started: Blastn
[2023-03-16 16:54:55,473] [INFO] Running command: blastn -query OceanDNA-b36288/markers.fasta -db /var/lib/cwl/stg8366e46f-caed-4a04-9666-4343086983c8/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b36288/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 16:54:56,525] [INFO] Task succeeded: Blastn
[2023-03-16 16:54:56,526] [INFO] Selected 14 target genomes.
[2023-03-16 16:54:56,526] [INFO] Target genome list was writen to OceanDNA-b36288/target_genomes_gtdb.txt
[2023-03-16 16:54:56,538] [INFO] Task started: fastANI
[2023-03-16 16:54:56,538] [INFO] Running command: fastANI --query /var/lib/cwl/stgad6d79ef-41a6-4612-b525-ff1ada90a774/OceanDNA-b36288.fa --refList OceanDNA-b36288/target_genomes_gtdb.txt --output OceanDNA-b36288/fastani_result_gtdb.tsv --threads 1
[2023-03-16 16:55:02,324] [INFO] Task succeeded: fastANI
[2023-03-16 16:55:02,333] [INFO] Found 14 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 16:55:02,333] [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_011053005.1	s__GCA-002733105 sp011053005	81.4856	489	755	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_013139345.1	s__GCA-002733105 sp013139345	77.534	117	755	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_013215825.1	s__GCA-002733105 sp013215825	77.1901	170	755	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_002163085.1	s__41-12-T18 sp002163085	77.1761	122	755	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_002733335.1	s__GCA-002733105 sp002733335	77.1509	146	755	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_002402245.1	s__GCA-002733105 sp002402245	77.0864	139	755	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_014859375.1	s__GCA-002733105 sp014859375	77.0787	145	755	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_013215775.1	s__GCA-002733105 sp013215775	77.0005	150	755	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_002733505.1	s__GCA-002733105 sp002733505	76.9894	131	755	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	76.9808	125	755	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_002733105.1	s__GCA-002733105 sp002733105	76.9575	97	755	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_905479075.1	s__GCA-002733105 sp905479075	76.9177	85	755	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__GCA-002733105	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001720165.1	s__Methylophaga muralis	76.1173	64	755	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__Methylophaga	95.0	97.83	97.83	0.96	0.96	2	-
GCF_000260985.4	s__Methylophaga nitratireducenticrescens	75.8213	57	755	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__Methylophaga	95.0	99.21	99.21	0.92	0.92	2	-
--------------------------------------------------------------------------------
[2023-03-16 16:55:02,333] [INFO] GTDB search result was written to OceanDNA-b36288/result_gtdb.tsv
[2023-03-16 16:55:02,333] [INFO] ===== GTDB Search completed =====
[2023-03-16 16:55:02,334] [INFO] DFAST_QC result json was written to OceanDNA-b36288/dqc_result.json
[2023-03-16 16:55:02,335] [INFO] DFAST_QC completed!
[2023-03-16 16:55:02,335] [INFO] Total running time: 0h1m19s