[2023-07-01 02:13:02,904] [INFO] DFAST_QC pipeline started.
[2023-07-01 02:13:02,907] [INFO] DFAST_QC version: 0.5.7
[2023-07-01 02:13:02,908] [INFO] DQC Reference Directory: /var/lib/cwl/stgee58f089-6ba1-4578-a67f-1a986438a2c5/dqc_reference
[2023-07-01 02:13:04,836] [INFO] ===== Start taxonomy check using ANI =====
[2023-07-01 02:13:04,837] [INFO] Task started: Prodigal
[2023-07-01 02:13:04,837] [INFO] Running command: gunzip -c /var/lib/cwl/stgca539687-709d-4839-9856-7388c33fbd50/GCA_903913135.1_freshwater_MAG_---_MJ130820A_bin-041_genomic.fna.gz | prodigal -d GCA_903913135.1_freshwater_MAG_---_MJ130820A_bin-041_genomic.fna/cds.fna -a GCA_903913135.1_freshwater_MAG_---_MJ130820A_bin-041_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-07-01 02:13:07,320] [INFO] Task succeeded: Prodigal
[2023-07-01 02:13:07,320] [INFO] Task started: HMMsearch
[2023-07-01 02:13:07,321] [INFO] Running command: hmmsearch --tblout GCA_903913135.1_freshwater_MAG_---_MJ130820A_bin-041_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgee58f089-6ba1-4578-a67f-1a986438a2c5/dqc_reference/reference_markers.hmm GCA_903913135.1_freshwater_MAG_---_MJ130820A_bin-041_genomic.fna/protein.faa > /dev/null
[2023-07-01 02:13:07,605] [INFO] Task succeeded: HMMsearch
[2023-07-01 02:13:07,606] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgca539687-709d-4839-9856-7388c33fbd50/GCA_903913135.1_freshwater_MAG_---_MJ130820A_bin-041_genomic.fna.gz]
[2023-07-01 02:13:07,630] [INFO] Query marker FASTA was written to GCA_903913135.1_freshwater_MAG_---_MJ130820A_bin-041_genomic.fna/markers.fasta
[2023-07-01 02:13:07,630] [INFO] Task started: Blastn
[2023-07-01 02:13:07,630] [INFO] Running command: blastn -query GCA_903913135.1_freshwater_MAG_---_MJ130820A_bin-041_genomic.fna/markers.fasta -db /var/lib/cwl/stgee58f089-6ba1-4578-a67f-1a986438a2c5/dqc_reference/reference_markers.fasta -out GCA_903913135.1_freshwater_MAG_---_MJ130820A_bin-041_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-07-01 02:13:09,220] [INFO] Task succeeded: Blastn
[2023-07-01 02:13:09,224] [INFO] Selected 16 target genomes.
[2023-07-01 02:13:09,224] [INFO] Target genome list was writen to GCA_903913135.1_freshwater_MAG_---_MJ130820A_bin-041_genomic.fna/target_genomes.txt
[2023-07-01 02:13:09,233] [INFO] Task started: fastANI
[2023-07-01 02:13:09,233] [INFO] Running command: fastANI --query /var/lib/cwl/stgca539687-709d-4839-9856-7388c33fbd50/GCA_903913135.1_freshwater_MAG_---_MJ130820A_bin-041_genomic.fna.gz --refList GCA_903913135.1_freshwater_MAG_---_MJ130820A_bin-041_genomic.fna/target_genomes.txt --output GCA_903913135.1_freshwater_MAG_---_MJ130820A_bin-041_genomic.fna/fastani_result.tsv --threads 1
[2023-07-01 02:13:14,289] [INFO] Task succeeded: fastANI
[2023-07-01 02:13:14,289] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgee58f089-6ba1-4578-a67f-1a986438a2c5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-07-01 02:13:14,290] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgee58f089-6ba1-4578-a67f-1a986438a2c5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-07-01 02:13:14,306] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2023-07-01 02:13:14,306] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-07-01 02:13:14,306] [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
Polynucleobacter finlandensis	strain=MWH-Mekk-B1	GCA_018881755.1	1855894	1855894	type	True	98.589	152	158	95	conclusive
Polynucleobacter hirudinilacicola	strain=MWH-EgelM1-30-B4	GCA_002192535.1	1743166	1743166	type	True	81.3073	80	158	95	below_threshold
Polynucleobacter corsicus	strain=AP-Melu-1000-A1	GCA_018688255.1	2081042	2081042	type	True	81.1006	82	158	95	below_threshold
Polynucleobacter hallstattensis	strain=MWH-Hall10	GCA_018881835.1	1855586	1855586	type	True	80.9839	78	158	95	below_threshold
Polynucleobacter yangtzensis	strain=MWH-JaK3	GCA_001595965.1	1743159	1743159	type	True	80.9781	83	158	95	below_threshold
Polynucleobacter ibericus	strain=es-MAR-2	GCA_018687955.1	1819725	1819725	type	True	80.9474	86	158	95	below_threshold
Polynucleobacter parvulilacunae	strain=Ross1-W9	GCA_018881715.1	1855631	1855631	type	True	80.8837	93	158	95	below_threshold
Polynucleobacter duraquae	strain=MWH-MoK4	GCA_000973625.1	1835254	1835254	type	True	80.8421	80	158	95	below_threshold
Polynucleobacter nymphae	strain=AP-Mumm-500A-B3	GCA_018882155.1	2081043	2081043	type	True	80.7704	81	158	95	below_threshold
Polynucleobacter aenigmaticus	strain=MWH-K35W1	GCA_002206635.1	1743164	1743164	type	True	80.6879	86	158	95	below_threshold
Polynucleobacter bastaniensis	strain=AP-Basta-1000A-D1	GCA_018882205.1	2081039	2081039	type	True	80.6555	77	158	95	below_threshold
Polynucleobacter alcilacus	strain=UK-Pondora-W15	GCA_018881545.1	1819739	1819739	type	True	80.5083	84	158	95	below_threshold
Polynucleobacter campilacus	strain=MWH-Feld-100	GCA_002206625.1	1743163	1743163	type	True	80.4874	88	158	95	below_threshold
Polynucleobacter wuianus	strain=QLW-P1FAT50C-4	GCA_001659725.1	1743168	1743168	type	True	80.4447	89	158	95	below_threshold
Polynucleobacter arcticus	strain=UK-Long2-W17	GCA_013307205.1	1743165	1743165	type	True	80.361	78	158	95	below_threshold
Polynucleobacter tropicus	strain=MWH-UH21B	GCA_013307225.1	1743174	1743174	type	True	79.8427	81	158	95	below_threshold
--------------------------------------------------------------------------------
[2023-07-01 02:13:14,326] [INFO] DFAST Taxonomy check result was written to GCA_903913135.1_freshwater_MAG_---_MJ130820A_bin-041_genomic.fna/tc_result.tsv
[2023-07-01 02:13:14,327] [INFO] ===== Taxonomy check completed =====
[2023-07-01 02:13:14,327] [INFO] ===== Start completeness check using CheckM =====
[2023-07-01 02:13:14,328] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgee58f089-6ba1-4578-a67f-1a986438a2c5/dqc_reference/checkm_data
[2023-07-01 02:13:14,330] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-07-01 02:13:14,346] [INFO] Task started: CheckM
[2023-07-01 02:13:14,347] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903913135.1_freshwater_MAG_---_MJ130820A_bin-041_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903913135.1_freshwater_MAG_---_MJ130820A_bin-041_genomic.fna/checkm_input GCA_903913135.1_freshwater_MAG_---_MJ130820A_bin-041_genomic.fna/checkm_result
[2023-07-01 02:13:30,799] [INFO] Task succeeded: CheckM
[2023-07-01 02:13:30,800] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-07-01 02:13:30,821] [INFO] ===== Completeness check finished =====
[2023-07-01 02:13:30,821] [INFO] ===== Start GTDB Search =====
[2023-07-01 02:13:30,822] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903913135.1_freshwater_MAG_---_MJ130820A_bin-041_genomic.fna/markers.fasta)
[2023-07-01 02:13:30,822] [INFO] Task started: Blastn
[2023-07-01 02:13:30,822] [INFO] Running command: blastn -query GCA_903913135.1_freshwater_MAG_---_MJ130820A_bin-041_genomic.fna/markers.fasta -db /var/lib/cwl/stgee58f089-6ba1-4578-a67f-1a986438a2c5/dqc_reference/reference_markers_gtdb.fasta -out GCA_903913135.1_freshwater_MAG_---_MJ130820A_bin-041_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-07-01 02:13:31,678] [INFO] Task succeeded: Blastn
[2023-07-01 02:13:31,682] [INFO] Selected 20 target genomes.
[2023-07-01 02:13:31,682] [INFO] Target genome list was writen to GCA_903913135.1_freshwater_MAG_---_MJ130820A_bin-041_genomic.fna/target_genomes_gtdb.txt
[2023-07-01 02:13:31,689] [INFO] Task started: fastANI
[2023-07-01 02:13:31,689] [INFO] Running command: fastANI --query /var/lib/cwl/stgca539687-709d-4839-9856-7388c33fbd50/GCA_903913135.1_freshwater_MAG_---_MJ130820A_bin-041_genomic.fna.gz --refList GCA_903913135.1_freshwater_MAG_---_MJ130820A_bin-041_genomic.fna/target_genomes_gtdb.txt --output GCA_903913135.1_freshwater_MAG_---_MJ130820A_bin-041_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-07-01 02:13:37,920] [INFO] Task succeeded: fastANI
[2023-07-01 02:13:37,940] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2023-07-01 02:13:37,941] [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_018881755.1	s__Polynucleobacter sp903953215	98.589	152	158	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	98.19	97.38	0.93	0.86	15	conclusive
GCA_903843235.1	s__Polynucleobacter sp903843235	88.4442	121	158	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	99.64	99.31	0.88	0.84	5	-
GCA_903845455.1	s__Polynucleobacter sp903845455	83.7622	117	158	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	98.50	98.25	0.75	0.69	7	-
GCF_018881925.1	s__Polynucleobacter sp903880555	83.1907	124	158	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	99.13	99.10	0.89	0.87	4	-
GCF_018882295.1	s__Polynucleobacter sp018882295	81.6877	85	158	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018688095.1	s__Polynucleobacter sp018688095	81.3264	76	158	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002192535.1	s__Polynucleobacter hirudinilacicola	81.3073	80	158	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903858445.1	s__Polynucleobacter sp903858445	81.1933	121	158	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000342265.1	s__Polynucleobacter sp000342265	81.1603	84	158	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018688155.1	s__Polynucleobacter sp018688155	80.9648	81	158	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018687075.1	s__Polynucleobacter sp018687075	80.9077	84	158	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018687975.1	s__Polynucleobacter sp018687975	80.8426	78	158	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018882335.1	s__Polynucleobacter sp018882335	80.7911	86	158	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018687575.1	s__Polynucleobacter asymbioticus_C	80.7883	85	158	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018688315.1	s__Polynucleobacter sp018688315	80.7708	89	158	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018687735.1	s__Polynucleobacter sp018687735	80.4904	89	158	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	98.63	98.63	0.93	0.93	2	-
GCF_002206625.1	s__Polynucleobacter campilacus	80.4874	88	158	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903827075.1	s__Polynucleobacter sp903827075	80.2458	77	158	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	99.13	99.03	0.84	0.82	6	-
GCF_013307225.1	s__Polynucleobacter sp013307225	79.8427	81	158	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903900805.1	s__Polynucleobacter sp903900805	79.7803	75	158	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-07-01 02:13:37,943] [INFO] GTDB search result was written to GCA_903913135.1_freshwater_MAG_---_MJ130820A_bin-041_genomic.fna/result_gtdb.tsv
[2023-07-01 02:13:37,944] [INFO] ===== GTDB Search completed =====
[2023-07-01 02:13:37,949] [INFO] DFAST_QC result json was written to GCA_903913135.1_freshwater_MAG_---_MJ130820A_bin-041_genomic.fna/dqc_result.json
[2023-07-01 02:13:37,949] [INFO] DFAST_QC completed!
[2023-07-01 02:13:37,949] [INFO] Total running time: 0h0m35s