[2023-06-30 00:25:00,491] [INFO] DFAST_QC pipeline started.
[2023-06-30 00:25:00,493] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 00:25:00,494] [INFO] DQC Reference Directory: /var/lib/cwl/stg4382da79-efe5-47ab-be16-5fb7bf98fc01/dqc_reference
[2023-06-30 00:25:01,813] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 00:25:01,814] [INFO] Task started: Prodigal
[2023-06-30 00:25:01,814] [INFO] Running command: gunzip -c /var/lib/cwl/stg1cc1a25f-b15c-4252-8884-8dfe70c365a0/GCA_903894735.1_freshwater_MAG_---_Kiruna2_bin-3293_genomic.fna.gz | prodigal -d GCA_903894735.1_freshwater_MAG_---_Kiruna2_bin-3293_genomic.fna/cds.fna -a GCA_903894735.1_freshwater_MAG_---_Kiruna2_bin-3293_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 00:25:04,901] [INFO] Task succeeded: Prodigal
[2023-06-30 00:25:04,901] [INFO] Task started: HMMsearch
[2023-06-30 00:25:04,902] [INFO] Running command: hmmsearch --tblout GCA_903894735.1_freshwater_MAG_---_Kiruna2_bin-3293_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4382da79-efe5-47ab-be16-5fb7bf98fc01/dqc_reference/reference_markers.hmm GCA_903894735.1_freshwater_MAG_---_Kiruna2_bin-3293_genomic.fna/protein.faa > /dev/null
[2023-06-30 00:25:05,147] [INFO] Task succeeded: HMMsearch
[2023-06-30 00:25:05,149] [INFO] Found 6/6 markers.
[2023-06-30 00:25:05,204] [INFO] Query marker FASTA was written to GCA_903894735.1_freshwater_MAG_---_Kiruna2_bin-3293_genomic.fna/markers.fasta
[2023-06-30 00:25:05,205] [INFO] Task started: Blastn
[2023-06-30 00:25:05,205] [INFO] Running command: blastn -query GCA_903894735.1_freshwater_MAG_---_Kiruna2_bin-3293_genomic.fna/markers.fasta -db /var/lib/cwl/stg4382da79-efe5-47ab-be16-5fb7bf98fc01/dqc_reference/reference_markers.fasta -out GCA_903894735.1_freshwater_MAG_---_Kiruna2_bin-3293_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 00:25:05,880] [INFO] Task succeeded: Blastn
[2023-06-30 00:25:05,888] [INFO] Selected 15 target genomes.
[2023-06-30 00:25:05,889] [INFO] Target genome list was writen to GCA_903894735.1_freshwater_MAG_---_Kiruna2_bin-3293_genomic.fna/target_genomes.txt
[2023-06-30 00:25:05,891] [INFO] Task started: fastANI
[2023-06-30 00:25:05,892] [INFO] Running command: fastANI --query /var/lib/cwl/stg1cc1a25f-b15c-4252-8884-8dfe70c365a0/GCA_903894735.1_freshwater_MAG_---_Kiruna2_bin-3293_genomic.fna.gz --refList GCA_903894735.1_freshwater_MAG_---_Kiruna2_bin-3293_genomic.fna/target_genomes.txt --output GCA_903894735.1_freshwater_MAG_---_Kiruna2_bin-3293_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 00:25:11,623] [INFO] Task succeeded: fastANI
[2023-06-30 00:25:11,624] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4382da79-efe5-47ab-be16-5fb7bf98fc01/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 00:25:11,625] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4382da79-efe5-47ab-be16-5fb7bf98fc01/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 00:25:11,641] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2023-06-30 00:25:11,642] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-30 00:25:11,642] [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 paneuropaeus	strain=MG-25-Pas1-D2	GCA_003261235.1	2527775	2527775	type	True	99.0597	320	333	95	conclusive
Polynucleobacter paludilacus	strain=MWH-Mekk-C3	GCA_018687595.1	1855895	1855895	type	True	85.8719	300	333	95	below_threshold
Polynucleobacter wuianus	strain=QLW-P1FAT50C-4	GCA_001659725.1	1743168	1743168	type	True	79.4952	160	333	95	below_threshold
Polynucleobacter yangtzensis	strain=MWH-JaK3	GCA_001595965.1	1743159	1743159	type	True	79.1048	152	333	95	below_threshold
Polynucleobacter parvulilacunae	strain=Ross1-W9	GCA_018881715.1	1855631	1855631	type	True	79.0782	156	333	95	below_threshold
Polynucleobacter hirudinilacicola	strain=MWH-EgelM1-30-B4	GCA_002192535.1	1743166	1743166	type	True	79.0143	169	333	95	below_threshold
Polynucleobacter finlandensis	strain=MWH-Mekk-B1	GCA_018881755.1	1855894	1855894	type	True	78.9387	158	333	95	below_threshold
Polynucleobacter alcilacus	strain=UK-Pondora-W15	GCA_018881545.1	1819739	1819739	type	True	78.8791	165	333	95	below_threshold
Polynucleobacter aenigmaticus	strain=MWH-K35W1	GCA_002206635.1	1743164	1743164	type	True	78.7159	154	333	95	below_threshold
Polynucleobacter nymphae	strain=AP-Mumm-500A-B3	GCA_018882155.1	2081043	2081043	type	True	78.6398	169	333	95	below_threshold
Polynucleobacter arcticus	strain=UK-Long2-W17	GCA_013307205.1	1743165	1743165	type	True	78.5587	144	333	95	below_threshold
Polynucleobacter antarcticus	strain=LimPoW16	GCA_013307245.1	1743162	1743162	type	True	78.5377	128	333	95	below_threshold
Polynucleobacter bastaniensis	strain=AP-Basta-1000A-D1	GCA_018882205.1	2081039	2081039	type	True	78.4609	164	333	95	below_threshold
Polynucleobacter tropicus	strain=MWH-UH21B	GCA_013307225.1	1743174	1743174	type	True	78.4309	146	333	95	below_threshold
Polynucleobacter sphagniphilus	strain=MWH-Weng1-1	GCA_001953355.1	1743169	1743169	type	True	78.3678	142	333	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 00:25:11,644] [INFO] DFAST Taxonomy check result was written to GCA_903894735.1_freshwater_MAG_---_Kiruna2_bin-3293_genomic.fna/tc_result.tsv
[2023-06-30 00:25:11,645] [INFO] ===== Taxonomy check completed =====
[2023-06-30 00:25:11,645] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 00:25:11,645] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4382da79-efe5-47ab-be16-5fb7bf98fc01/dqc_reference/checkm_data
[2023-06-30 00:25:11,646] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 00:25:11,676] [INFO] Task started: CheckM
[2023-06-30 00:25:11,676] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903894735.1_freshwater_MAG_---_Kiruna2_bin-3293_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903894735.1_freshwater_MAG_---_Kiruna2_bin-3293_genomic.fna/checkm_input GCA_903894735.1_freshwater_MAG_---_Kiruna2_bin-3293_genomic.fna/checkm_result
[2023-06-30 00:25:29,811] [INFO] Task succeeded: CheckM
[2023-06-30 00:25:29,812] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.17%
Contamintation: 6.25%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-06-30 00:25:29,853] [INFO] ===== Completeness check finished =====
[2023-06-30 00:25:29,854] [INFO] ===== Start GTDB Search =====
[2023-06-30 00:25:29,854] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903894735.1_freshwater_MAG_---_Kiruna2_bin-3293_genomic.fna/markers.fasta)
[2023-06-30 00:25:29,854] [INFO] Task started: Blastn
[2023-06-30 00:25:29,855] [INFO] Running command: blastn -query GCA_903894735.1_freshwater_MAG_---_Kiruna2_bin-3293_genomic.fna/markers.fasta -db /var/lib/cwl/stg4382da79-efe5-47ab-be16-5fb7bf98fc01/dqc_reference/reference_markers_gtdb.fasta -out GCA_903894735.1_freshwater_MAG_---_Kiruna2_bin-3293_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 00:25:30,814] [INFO] Task succeeded: Blastn
[2023-06-30 00:25:30,818] [INFO] Selected 17 target genomes.
[2023-06-30 00:25:30,818] [INFO] Target genome list was writen to GCA_903894735.1_freshwater_MAG_---_Kiruna2_bin-3293_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 00:25:30,825] [INFO] Task started: fastANI
[2023-06-30 00:25:30,825] [INFO] Running command: fastANI --query /var/lib/cwl/stg1cc1a25f-b15c-4252-8884-8dfe70c365a0/GCA_903894735.1_freshwater_MAG_---_Kiruna2_bin-3293_genomic.fna.gz --refList GCA_903894735.1_freshwater_MAG_---_Kiruna2_bin-3293_genomic.fna/target_genomes_gtdb.txt --output GCA_903894735.1_freshwater_MAG_---_Kiruna2_bin-3293_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 00:25:37,781] [INFO] Task succeeded: fastANI
[2023-06-30 00:25:37,799] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 00:25:37,799] [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_003261235.1	s__Polynucleobacter paneuropaeus	99.0597	320	333	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	98.74	98.42	0.90	0.83	33	conclusive
GCF_018687595.1	s__Polynucleobacter asymbioticus_B	85.8719	300	333	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018687555.1	s__Polynucleobacter sp018687555	84.3634	305	333	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	97.44	97.44	0.90	0.90	2	-
GCF_018687455.1	s__Polynucleobacter sp001870365	79.1611	158	333	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	96.21	96.15	0.92	0.92	3	-
GCF_018687815.1	s__Polynucleobacter sp018687815	79.1602	150	333	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	79.0508	171	333	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018881965.1	s__Polynucleobacter sp018881965	78.9965	156	333	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	78.9596	150	333	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018882445.1	s__Polynucleobacter sp018882445	78.9513	162	333	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	78.9058	155	333	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018881655.1	s__Polynucleobacter sp001889925	78.7946	150	333	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	96.71	95.84	0.78	0.66	4	-
GCF_018881595.1	s__Polynucleobacter sp018881595	78.7533	173	333	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018882085.1	s__Polynucleobacter sp018882085	78.7472	161	333	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018882155.1	s__Polynucleobacter sp018882155	78.6398	169	333	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	78.6248	167	333	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013205155.1	s__Polynucleobacter sp013205155	78.3886	96	333	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903930665.1	s__Polynucleobacter sp903930665	77.68	99	333	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 00:25:37,802] [INFO] GTDB search result was written to GCA_903894735.1_freshwater_MAG_---_Kiruna2_bin-3293_genomic.fna/result_gtdb.tsv
[2023-06-30 00:25:37,804] [INFO] ===== GTDB Search completed =====
[2023-06-30 00:25:37,837] [INFO] DFAST_QC result json was written to GCA_903894735.1_freshwater_MAG_---_Kiruna2_bin-3293_genomic.fna/dqc_result.json
[2023-06-30 00:25:37,838] [INFO] DFAST_QC completed!
[2023-06-30 00:25:37,838] [INFO] Total running time: 0h0m37s