[2023-06-29 21:28:13,845] [INFO] DFAST_QC pipeline started.
[2023-06-29 21:28:13,851] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 21:28:13,851] [INFO] DQC Reference Directory: /var/lib/cwl/stg77acad0b-5908-436f-bb21-cc1e8eee6f76/dqc_reference
[2023-06-29 21:28:15,149] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 21:28:15,150] [INFO] Task started: Prodigal
[2023-06-29 21:28:15,150] [INFO] Running command: gunzip -c /var/lib/cwl/stgca4cc78b-697f-4a81-b6de-2c1592b91b52/GCA_903845455.1_freshwater_MAG_---_Ki2-D4_bin-0267_genomic.fna.gz | prodigal -d GCA_903845455.1_freshwater_MAG_---_Ki2-D4_bin-0267_genomic.fna/cds.fna -a GCA_903845455.1_freshwater_MAG_---_Ki2-D4_bin-0267_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 21:28:19,952] [INFO] Task succeeded: Prodigal
[2023-06-29 21:28:19,952] [INFO] Task started: HMMsearch
[2023-06-29 21:28:19,953] [INFO] Running command: hmmsearch --tblout GCA_903845455.1_freshwater_MAG_---_Ki2-D4_bin-0267_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg77acad0b-5908-436f-bb21-cc1e8eee6f76/dqc_reference/reference_markers.hmm GCA_903845455.1_freshwater_MAG_---_Ki2-D4_bin-0267_genomic.fna/protein.faa > /dev/null
[2023-06-29 21:28:20,201] [INFO] Task succeeded: HMMsearch
[2023-06-29 21:28:20,203] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgca4cc78b-697f-4a81-b6de-2c1592b91b52/GCA_903845455.1_freshwater_MAG_---_Ki2-D4_bin-0267_genomic.fna.gz]
[2023-06-29 21:28:20,230] [INFO] Query marker FASTA was written to GCA_903845455.1_freshwater_MAG_---_Ki2-D4_bin-0267_genomic.fna/markers.fasta
[2023-06-29 21:28:20,231] [INFO] Task started: Blastn
[2023-06-29 21:28:20,231] [INFO] Running command: blastn -query GCA_903845455.1_freshwater_MAG_---_Ki2-D4_bin-0267_genomic.fna/markers.fasta -db /var/lib/cwl/stg77acad0b-5908-436f-bb21-cc1e8eee6f76/dqc_reference/reference_markers.fasta -out GCA_903845455.1_freshwater_MAG_---_Ki2-D4_bin-0267_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 21:28:20,762] [INFO] Task succeeded: Blastn
[2023-06-29 21:28:20,766] [INFO] Selected 19 target genomes.
[2023-06-29 21:28:20,766] [INFO] Target genome list was writen to GCA_903845455.1_freshwater_MAG_---_Ki2-D4_bin-0267_genomic.fna/target_genomes.txt
[2023-06-29 21:28:20,769] [INFO] Task started: fastANI
[2023-06-29 21:28:20,769] [INFO] Running command: fastANI --query /var/lib/cwl/stgca4cc78b-697f-4a81-b6de-2c1592b91b52/GCA_903845455.1_freshwater_MAG_---_Ki2-D4_bin-0267_genomic.fna.gz --refList GCA_903845455.1_freshwater_MAG_---_Ki2-D4_bin-0267_genomic.fna/target_genomes.txt --output GCA_903845455.1_freshwater_MAG_---_Ki2-D4_bin-0267_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 21:28:27,473] [INFO] Task succeeded: fastANI
[2023-06-29 21:28:27,473] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg77acad0b-5908-436f-bb21-cc1e8eee6f76/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 21:28:27,473] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg77acad0b-5908-436f-bb21-cc1e8eee6f76/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 21:28:27,485] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 21:28:27,485] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 21:28:27,485] [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	83.821	411	630	95	below_threshold
Polynucleobacter aenigmaticus	strain=MWH-K35W1	GCA_002206635.1	1743164	1743164	type	True	79.5414	216	630	95	below_threshold
Polynucleobacter parvulilacunae	strain=Ross1-W9	GCA_018881715.1	1855631	1855631	type	True	79.4229	231	630	95	below_threshold
Polynucleobacter yangtzensis	strain=MWH-JaK3	GCA_001595965.1	1743159	1743159	type	True	79.3096	221	630	95	below_threshold
Polynucleobacter corsicus	strain=AP-Melu-1000-A1	GCA_018688255.1	2081042	2081042	type	True	79.2547	233	630	95	below_threshold
Polynucleobacter ibericus	strain=es-MAR-2	GCA_018687955.1	1819725	1819725	type	True	79.1638	217	630	95	below_threshold
Polynucleobacter asymbioticus	strain=QLW-P1DMWA-1	GCA_000016345.1	576611	576611	type	True	79.1587	214	630	95	below_threshold
Polynucleobacter hirudinilacicola	strain=MWH-EgelM1-30-B4	GCA_002192535.1	1743166	1743166	type	True	79.0825	235	630	95	below_threshold
Polynucleobacter alcilacus	strain=UK-Pondora-W15	GCA_018881545.1	1819739	1819739	type	True	79.0471	229	630	95	below_threshold
Polynucleobacter nymphae	strain=AP-Mumm-500A-B3	GCA_018882155.1	2081043	2081043	type	True	78.9984	236	630	95	below_threshold
Polynucleobacter campilacus	strain=MWH-Feld-100	GCA_002206625.1	1743163	1743163	type	True	78.8934	220	630	95	below_threshold
Polynucleobacter brandtiae	strain=UB-Domo-W1	GCA_002797575.1	1938816	1938816	type	True	78.0838	171	630	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 21:28:27,488] [INFO] DFAST Taxonomy check result was written to GCA_903845455.1_freshwater_MAG_---_Ki2-D4_bin-0267_genomic.fna/tc_result.tsv
[2023-06-29 21:28:27,488] [INFO] ===== Taxonomy check completed =====
[2023-06-29 21:28:27,489] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 21:28:27,489] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg77acad0b-5908-436f-bb21-cc1e8eee6f76/dqc_reference/checkm_data
[2023-06-29 21:28:27,491] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 21:28:27,521] [INFO] Task started: CheckM
[2023-06-29 21:28:27,521] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903845455.1_freshwater_MAG_---_Ki2-D4_bin-0267_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903845455.1_freshwater_MAG_---_Ki2-D4_bin-0267_genomic.fna/checkm_input GCA_903845455.1_freshwater_MAG_---_Ki2-D4_bin-0267_genomic.fna/checkm_result
[2023-06-29 21:28:50,051] [INFO] Task succeeded: CheckM
[2023-06-29 21:28:50,052] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 50.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 21:28:50,073] [INFO] ===== Completeness check finished =====
[2023-06-29 21:28:50,074] [INFO] ===== Start GTDB Search =====
[2023-06-29 21:28:50,074] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903845455.1_freshwater_MAG_---_Ki2-D4_bin-0267_genomic.fna/markers.fasta)
[2023-06-29 21:28:50,075] [INFO] Task started: Blastn
[2023-06-29 21:28:50,075] [INFO] Running command: blastn -query GCA_903845455.1_freshwater_MAG_---_Ki2-D4_bin-0267_genomic.fna/markers.fasta -db /var/lib/cwl/stg77acad0b-5908-436f-bb21-cc1e8eee6f76/dqc_reference/reference_markers_gtdb.fasta -out GCA_903845455.1_freshwater_MAG_---_Ki2-D4_bin-0267_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 21:28:50,566] [INFO] Task succeeded: Blastn
[2023-06-29 21:28:50,571] [INFO] Selected 16 target genomes.
[2023-06-29 21:28:50,572] [INFO] Target genome list was writen to GCA_903845455.1_freshwater_MAG_---_Ki2-D4_bin-0267_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 21:28:50,576] [INFO] Task started: fastANI
[2023-06-29 21:28:50,576] [INFO] Running command: fastANI --query /var/lib/cwl/stgca4cc78b-697f-4a81-b6de-2c1592b91b52/GCA_903845455.1_freshwater_MAG_---_Ki2-D4_bin-0267_genomic.fna.gz --refList GCA_903845455.1_freshwater_MAG_---_Ki2-D4_bin-0267_genomic.fna/target_genomes_gtdb.txt --output GCA_903845455.1_freshwater_MAG_---_Ki2-D4_bin-0267_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 21:28:56,896] [INFO] Task succeeded: fastANI
[2023-06-29 21:28:56,915] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 21:28:56,916] [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_903845455.1	s__Polynucleobacter sp903845455	100.0	621	630	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	98.50	98.25	0.75	0.69	7	conclusive
GCF_018881755.1	s__Polynucleobacter sp903953215	83.8607	409	630	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	98.19	97.38	0.93	0.86	15	-
GCA_903843235.1	s__Polynucleobacter sp903843235	83.117	303	630	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	99.64	99.31	0.88	0.84	5	-
GCF_018881925.1	s__Polynucleobacter sp903880555	81.2478	340	630	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	80.8308	336	630	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018882055.1	s__Polynucleobacter sp018882055	79.5986	223	630	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018881905.1	s__Polynucleobacter sp018881905	79.3988	236	630	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018881855.1	s__Polynucleobacter sp018881855	79.3904	223	630	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018882245.1	s__Polynucleobacter sp018882245	79.383	219	630	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	79.3718	225	630	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001595965.1	s__Polynucleobacter yangtzensis	79.3309	220	630	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018881605.1	s__Polynucleobacter sp018881605	79.3263	222	630	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018881635.1	s__Polynucleobacter sp018881635	79.0245	204	630	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018687455.1	s__Polynucleobacter sp001870365	79.0042	226	630	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	96.21	96.15	0.92	0.92	3	-
GCF_002206625.1	s__Polynucleobacter campilacus	78.9313	217	630	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018881505.1	s__Polynucleobacter sp018881505	78.8458	224	630	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 21:28:56,918] [INFO] GTDB search result was written to GCA_903845455.1_freshwater_MAG_---_Ki2-D4_bin-0267_genomic.fna/result_gtdb.tsv
[2023-06-29 21:28:56,919] [INFO] ===== GTDB Search completed =====
[2023-06-29 21:28:56,927] [INFO] DFAST_QC result json was written to GCA_903845455.1_freshwater_MAG_---_Ki2-D4_bin-0267_genomic.fna/dqc_result.json
[2023-06-29 21:28:56,928] [INFO] DFAST_QC completed!
[2023-06-29 21:28:56,928] [INFO] Total running time: 0h0m43s