[2023-07-01 04:39:32,411] [INFO] DFAST_QC pipeline started.
[2023-07-01 04:39:32,413] [INFO] DFAST_QC version: 0.5.7
[2023-07-01 04:39:32,414] [INFO] DQC Reference Directory: /var/lib/cwl/stg4ee1a651-bc96-46ba-ad00-1a9db4f8a270/dqc_reference
[2023-07-01 04:39:33,636] [INFO] ===== Start taxonomy check using ANI =====
[2023-07-01 04:39:33,637] [INFO] Task started: Prodigal
[2023-07-01 04:39:33,638] [INFO] Running command: gunzip -c /var/lib/cwl/stg575cf2ff-6ac8-4aaa-a6c7-7d736408bcac/GCA_903941075.1_freshwater_MAG_---_E-3_bin-042_genomic.fna.gz | prodigal -d GCA_903941075.1_freshwater_MAG_---_E-3_bin-042_genomic.fna/cds.fna -a GCA_903941075.1_freshwater_MAG_---_E-3_bin-042_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-07-01 04:39:37,486] [INFO] Task succeeded: Prodigal
[2023-07-01 04:39:37,486] [INFO] Task started: HMMsearch
[2023-07-01 04:39:37,486] [INFO] Running command: hmmsearch --tblout GCA_903941075.1_freshwater_MAG_---_E-3_bin-042_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4ee1a651-bc96-46ba-ad00-1a9db4f8a270/dqc_reference/reference_markers.hmm GCA_903941075.1_freshwater_MAG_---_E-3_bin-042_genomic.fna/protein.faa > /dev/null
[2023-07-01 04:39:37,662] [INFO] Task succeeded: HMMsearch
[2023-07-01 04:39:37,663] [INFO] Found 6/6 markers.
[2023-07-01 04:39:37,683] [INFO] Query marker FASTA was written to GCA_903941075.1_freshwater_MAG_---_E-3_bin-042_genomic.fna/markers.fasta
[2023-07-01 04:39:37,684] [INFO] Task started: Blastn
[2023-07-01 04:39:37,684] [INFO] Running command: blastn -query GCA_903941075.1_freshwater_MAG_---_E-3_bin-042_genomic.fna/markers.fasta -db /var/lib/cwl/stg4ee1a651-bc96-46ba-ad00-1a9db4f8a270/dqc_reference/reference_markers.fasta -out GCA_903941075.1_freshwater_MAG_---_E-3_bin-042_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-07-01 04:39:38,247] [INFO] Task succeeded: Blastn
[2023-07-01 04:39:38,250] [INFO] Selected 14 target genomes.
[2023-07-01 04:39:38,251] [INFO] Target genome list was writen to GCA_903941075.1_freshwater_MAG_---_E-3_bin-042_genomic.fna/target_genomes.txt
[2023-07-01 04:39:38,251] [INFO] Task started: fastANI
[2023-07-01 04:39:38,252] [INFO] Running command: fastANI --query /var/lib/cwl/stg575cf2ff-6ac8-4aaa-a6c7-7d736408bcac/GCA_903941075.1_freshwater_MAG_---_E-3_bin-042_genomic.fna.gz --refList GCA_903941075.1_freshwater_MAG_---_E-3_bin-042_genomic.fna/target_genomes.txt --output GCA_903941075.1_freshwater_MAG_---_E-3_bin-042_genomic.fna/fastani_result.tsv --threads 1
[2023-07-01 04:39:43,231] [INFO] Task succeeded: fastANI
[2023-07-01 04:39:43,231] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4ee1a651-bc96-46ba-ad00-1a9db4f8a270/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-07-01 04:39:43,232] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4ee1a651-bc96-46ba-ad00-1a9db4f8a270/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-07-01 04:39:43,243] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2023-07-01 04:39:43,243] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-07-01 04:39:43,243] [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	97.9331	381	397	95	conclusive
Polynucleobacter parvulilacunae	strain=Ross1-W9	GCA_018881715.1	1855631	1855631	type	True	80.1525	214	397	95	below_threshold
Polynucleobacter corsicus	strain=AP-Melu-1000-A1	GCA_018688255.1	2081042	2081042	type	True	79.9151	216	397	95	below_threshold
Polynucleobacter duraquae	strain=MWH-MoK4	GCA_000973625.1	1835254	1835254	type	True	79.8137	199	397	95	below_threshold
Polynucleobacter hallstattensis	strain=MWH-Hall10	GCA_018881835.1	1855586	1855586	type	True	79.7708	212	397	95	below_threshold
Polynucleobacter bastaniensis	strain=AP-Basta-1000A-D1	GCA_018882205.1	2081039	2081039	type	True	79.7088	201	397	95	below_threshold
Polynucleobacter alcilacus	strain=UK-Pondora-W15	GCA_018881545.1	1819739	1819739	type	True	79.6858	200	397	95	below_threshold
Polynucleobacter nymphae	strain=AP-Mumm-500A-B3	GCA_018882155.1	2081043	2081043	type	True	79.6563	205	397	95	below_threshold
Polynucleobacter wuianus	strain=QLW-P1FAT50C-4	GCA_001659725.1	1743168	1743168	type	True	79.6431	203	397	95	below_threshold
Polynucleobacter arcticus	strain=UK-Long2-W17	GCA_013307205.1	1743165	1743165	type	True	79.6074	197	397	95	below_threshold
Polynucleobacter asymbioticus	strain=QLW-P1DMWA-1	GCA_000016345.1	576611	576611	type	True	79.5882	198	397	95	below_threshold
Polynucleobacter campilacus	strain=MWH-Feld-100	GCA_002206625.1	1743163	1743163	type	True	79.5101	201	397	95	below_threshold
Polynucleobacter tropicus	strain=MWH-UH21B	GCA_013307225.1	1743174	1743174	type	True	79.2232	191	397	95	below_threshold
--------------------------------------------------------------------------------
[2023-07-01 04:39:43,245] [INFO] DFAST Taxonomy check result was written to GCA_903941075.1_freshwater_MAG_---_E-3_bin-042_genomic.fna/tc_result.tsv
[2023-07-01 04:39:43,246] [INFO] ===== Taxonomy check completed =====
[2023-07-01 04:39:43,246] [INFO] ===== Start completeness check using CheckM =====
[2023-07-01 04:39:43,246] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4ee1a651-bc96-46ba-ad00-1a9db4f8a270/dqc_reference/checkm_data
[2023-07-01 04:39:43,247] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-07-01 04:39:43,268] [INFO] Task started: CheckM
[2023-07-01 04:39:43,269] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903941075.1_freshwater_MAG_---_E-3_bin-042_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903941075.1_freshwater_MAG_---_E-3_bin-042_genomic.fna/checkm_input GCA_903941075.1_freshwater_MAG_---_E-3_bin-042_genomic.fna/checkm_result
[2023-07-01 04:40:01,334] [INFO] Task succeeded: CheckM
[2023-07-01 04:40:01,335] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 64.58%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-07-01 04:40:01,350] [INFO] ===== Completeness check finished =====
[2023-07-01 04:40:01,351] [INFO] ===== Start GTDB Search =====
[2023-07-01 04:40:01,351] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903941075.1_freshwater_MAG_---_E-3_bin-042_genomic.fna/markers.fasta)
[2023-07-01 04:40:01,351] [INFO] Task started: Blastn
[2023-07-01 04:40:01,351] [INFO] Running command: blastn -query GCA_903941075.1_freshwater_MAG_---_E-3_bin-042_genomic.fna/markers.fasta -db /var/lib/cwl/stg4ee1a651-bc96-46ba-ad00-1a9db4f8a270/dqc_reference/reference_markers_gtdb.fasta -out GCA_903941075.1_freshwater_MAG_---_E-3_bin-042_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-07-01 04:40:02,153] [INFO] Task succeeded: Blastn
[2023-07-01 04:40:02,157] [INFO] Selected 21 target genomes.
[2023-07-01 04:40:02,157] [INFO] Target genome list was writen to GCA_903941075.1_freshwater_MAG_---_E-3_bin-042_genomic.fna/target_genomes_gtdb.txt
[2023-07-01 04:40:02,158] [INFO] Task started: fastANI
[2023-07-01 04:40:02,158] [INFO] Running command: fastANI --query /var/lib/cwl/stg575cf2ff-6ac8-4aaa-a6c7-7d736408bcac/GCA_903941075.1_freshwater_MAG_---_E-3_bin-042_genomic.fna.gz --refList GCA_903941075.1_freshwater_MAG_---_E-3_bin-042_genomic.fna/target_genomes_gtdb.txt --output GCA_903941075.1_freshwater_MAG_---_E-3_bin-042_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-07-01 04:40:10,296] [INFO] Task succeeded: fastANI
[2023-07-01 04:40:10,313] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2023-07-01 04:40:10,313] [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	97.9331	381	397	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	88.8336	301	397	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	83.7503	290	397	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	82.8089	308	397	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	99.13	99.10	0.89	0.87	4	-
GCA_903858445.1	s__Polynucleobacter sp903858445	81.8083	285	397	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018882295.1	s__Polynucleobacter sp018882295	80.5248	218	397	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018882415.1	s__Polynucleobacter sp018882415	80.3809	213	397	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	80.2351	219	397	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018882325.1	s__Polynucleobacter sp018882325	80.2286	218	397	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018687355.1	s__Polynucleobacter sp018687355	80.1808	206	397	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018687275.1	s__Polynucleobacter sp018687275	80.1238	209	397	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018881795.1	s__Polynucleobacter sp018881795	80.0872	210	397	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001830325.1	s__Polynucleobacter sp001830325	80.0581	205	397	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	99.99	99.99	1.00	1.00	2	-
GCA_000342265.1	s__Polynucleobacter sp000342265	80.0564	221	397	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018688355.1	s__Polynucleobacter sp018688355	80.0032	206	397	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	79.93	226	397	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	79.7126	194	397	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	99.13	99.03	0.84	0.82	6	-
GCF_001659725.1	s__Polynucleobacter wuianus	79.6431	203	397	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	98.91	97.82	0.95	0.89	3	-
GCF_018687975.1	s__Polynucleobacter sp018687975	79.5689	194	397	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002206625.1	s__Polynucleobacter campilacus	79.5101	201	397	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	79.1379	175	397	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 04:40:10,314] [INFO] GTDB search result was written to GCA_903941075.1_freshwater_MAG_---_E-3_bin-042_genomic.fna/result_gtdb.tsv
[2023-07-01 04:40:10,315] [INFO] ===== GTDB Search completed =====
[2023-07-01 04:40:10,319] [INFO] DFAST_QC result json was written to GCA_903941075.1_freshwater_MAG_---_E-3_bin-042_genomic.fna/dqc_result.json
[2023-07-01 04:40:10,319] [INFO] DFAST_QC completed!
[2023-07-01 04:40:10,319] [INFO] Total running time: 0h0m38s