[2023-06-30 03:13:29,563] [INFO] DFAST_QC pipeline started.
[2023-06-30 03:13:29,571] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 03:13:29,571] [INFO] DQC Reference Directory: /var/lib/cwl/stgce8adb26-4891-4f19-9519-60842d6653f5/dqc_reference
[2023-06-30 03:13:30,781] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 03:13:30,782] [INFO] Task started: Prodigal
[2023-06-30 03:13:30,782] [INFO] Running command: gunzip -c /var/lib/cwl/stgb5e3c46a-509a-40b9-980d-0644d0d88666/GCA_903886005.1_freshwater_MAG_---_LJ_bin-3854_genomic.fna.gz | prodigal -d GCA_903886005.1_freshwater_MAG_---_LJ_bin-3854_genomic.fna/cds.fna -a GCA_903886005.1_freshwater_MAG_---_LJ_bin-3854_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 03:13:34,262] [INFO] Task succeeded: Prodigal
[2023-06-30 03:13:34,263] [INFO] Task started: HMMsearch
[2023-06-30 03:13:34,263] [INFO] Running command: hmmsearch --tblout GCA_903886005.1_freshwater_MAG_---_LJ_bin-3854_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgce8adb26-4891-4f19-9519-60842d6653f5/dqc_reference/reference_markers.hmm GCA_903886005.1_freshwater_MAG_---_LJ_bin-3854_genomic.fna/protein.faa > /dev/null
[2023-06-30 03:13:34,495] [INFO] Task succeeded: HMMsearch
[2023-06-30 03:13:34,498] [INFO] Found 6/6 markers.
[2023-06-30 03:13:34,519] [INFO] Query marker FASTA was written to GCA_903886005.1_freshwater_MAG_---_LJ_bin-3854_genomic.fna/markers.fasta
[2023-06-30 03:13:34,519] [INFO] Task started: Blastn
[2023-06-30 03:13:34,519] [INFO] Running command: blastn -query GCA_903886005.1_freshwater_MAG_---_LJ_bin-3854_genomic.fna/markers.fasta -db /var/lib/cwl/stgce8adb26-4891-4f19-9519-60842d6653f5/dqc_reference/reference_markers.fasta -out GCA_903886005.1_freshwater_MAG_---_LJ_bin-3854_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 03:13:35,141] [INFO] Task succeeded: Blastn
[2023-06-30 03:13:35,146] [INFO] Selected 16 target genomes.
[2023-06-30 03:13:35,146] [INFO] Target genome list was writen to GCA_903886005.1_freshwater_MAG_---_LJ_bin-3854_genomic.fna/target_genomes.txt
[2023-06-30 03:13:35,148] [INFO] Task started: fastANI
[2023-06-30 03:13:35,148] [INFO] Running command: fastANI --query /var/lib/cwl/stgb5e3c46a-509a-40b9-980d-0644d0d88666/GCA_903886005.1_freshwater_MAG_---_LJ_bin-3854_genomic.fna.gz --refList GCA_903886005.1_freshwater_MAG_---_LJ_bin-3854_genomic.fna/target_genomes.txt --output GCA_903886005.1_freshwater_MAG_---_LJ_bin-3854_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 03:13:41,578] [INFO] Task succeeded: fastANI
[2023-06-30 03:13:41,579] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgce8adb26-4891-4f19-9519-60842d6653f5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 03:13:41,580] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgce8adb26-4891-4f19-9519-60842d6653f5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 03:13:41,595] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 03:13:41,595] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 03:13:41,595] [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 alcilacus	strain=UK-Pondora-W15	GCA_018881545.1	1819739	1819739	type	True	86.8565	318	378	95	below_threshold
Polynucleobacter hirudinilacicola	strain=MWH-EgelM1-30-B4	GCA_002192535.1	1743166	1743166	type	True	81.4339	263	378	95	below_threshold
Polynucleobacter parvulilacunae	strain=Ross1-W9	GCA_018881715.1	1855631	1855631	type	True	81.2752	241	378	95	below_threshold
Polynucleobacter nymphae	strain=AP-Mumm-500A-B3	GCA_018882155.1	2081043	2081043	type	True	81.2096	261	378	95	below_threshold
Polynucleobacter yangtzensis	strain=MWH-JaK3	GCA_001595965.1	1743159	1743159	type	True	81.2013	231	378	95	below_threshold
Polynucleobacter ibericus	strain=es-MAR-2	GCA_018687955.1	1819725	1819725	type	True	81.054	225	378	95	below_threshold
Polynucleobacter wuianus	strain=QLW-P1FAT50C-4	GCA_001659725.1	1743168	1743168	type	True	81.0238	219	378	95	below_threshold
Polynucleobacter campilacus	strain=MWH-Feld-100	GCA_002206625.1	1743163	1743163	type	True	80.7545	258	378	95	below_threshold
Polynucleobacter asymbioticus	strain=QLW-P1DMWA-1	GCA_000016345.1	576611	576611	type	True	80.6238	218	378	95	below_threshold
Polynucleobacter finlandensis	strain=MWH-Mekk-B1	GCA_018881755.1	1855894	1855894	type	True	80.195	209	378	95	below_threshold
Polynucleobacter tropicus	strain=MWH-UH21B	GCA_013307225.1	1743174	1743174	type	True	80.085	204	378	95	below_threshold
Polynucleobacter arcticus	strain=UK-Long2-W17	GCA_013307205.1	1743165	1743165	type	True	79.5603	167	378	95	below_threshold
Polynucleobacter bastaniensis	strain=AP-Basta-1000A-D1	GCA_018882205.1	2081039	2081039	type	True	79.5448	187	378	95	below_threshold
Polynucleobacter corsicus	strain=AP-Melu-1000-A1	GCA_018688255.1	2081042	2081042	type	True	79.5137	209	378	95	below_threshold
Polynucleobacter meluiroseus	strain=AP-Melu-1000-B4	GCA_900205755.1	1938814	1938814	type	True	78.7496	123	378	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 03:13:41,597] [INFO] DFAST Taxonomy check result was written to GCA_903886005.1_freshwater_MAG_---_LJ_bin-3854_genomic.fna/tc_result.tsv
[2023-06-30 03:13:41,598] [INFO] ===== Taxonomy check completed =====
[2023-06-30 03:13:41,598] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 03:13:41,598] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgce8adb26-4891-4f19-9519-60842d6653f5/dqc_reference/checkm_data
[2023-06-30 03:13:41,599] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 03:13:41,639] [INFO] Task started: CheckM
[2023-06-30 03:13:41,639] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903886005.1_freshwater_MAG_---_LJ_bin-3854_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903886005.1_freshwater_MAG_---_LJ_bin-3854_genomic.fna/checkm_input GCA_903886005.1_freshwater_MAG_---_LJ_bin-3854_genomic.fna/checkm_result
[2023-06-30 03:13:59,877] [INFO] Task succeeded: CheckM
[2023-06-30 03:13:59,878] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 93.75%
Contamintation: 0.46%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 03:13:59,903] [INFO] ===== Completeness check finished =====
[2023-06-30 03:13:59,903] [INFO] ===== Start GTDB Search =====
[2023-06-30 03:13:59,904] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903886005.1_freshwater_MAG_---_LJ_bin-3854_genomic.fna/markers.fasta)
[2023-06-30 03:13:59,904] [INFO] Task started: Blastn
[2023-06-30 03:13:59,904] [INFO] Running command: blastn -query GCA_903886005.1_freshwater_MAG_---_LJ_bin-3854_genomic.fna/markers.fasta -db /var/lib/cwl/stgce8adb26-4891-4f19-9519-60842d6653f5/dqc_reference/reference_markers_gtdb.fasta -out GCA_903886005.1_freshwater_MAG_---_LJ_bin-3854_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 03:14:00,779] [INFO] Task succeeded: Blastn
[2023-06-30 03:14:00,783] [INFO] Selected 22 target genomes.
[2023-06-30 03:14:00,783] [INFO] Target genome list was writen to GCA_903886005.1_freshwater_MAG_---_LJ_bin-3854_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 03:14:00,786] [INFO] Task started: fastANI
[2023-06-30 03:14:00,786] [INFO] Running command: fastANI --query /var/lib/cwl/stgb5e3c46a-509a-40b9-980d-0644d0d88666/GCA_903886005.1_freshwater_MAG_---_LJ_bin-3854_genomic.fna.gz --refList GCA_903886005.1_freshwater_MAG_---_LJ_bin-3854_genomic.fna/target_genomes_gtdb.txt --output GCA_903886005.1_freshwater_MAG_---_LJ_bin-3854_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 03:14:09,460] [INFO] Task succeeded: fastANI
[2023-06-30 03:14:09,480] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 03:14:09,480] [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_903843315.1	s__Polynucleobacter sp903843315	99.4024	338	378	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	99.21	99.08	0.85	0.77	17	conclusive
GCF_018881545.1	s__Polynucleobacter sp018881545	86.8565	318	378	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	81.7143	253	378	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	81.5809	229	378	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018882465.1	s__Polynucleobacter sp018882465	81.4929	257	378	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	81.4339	263	378	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	81.2202	252	378	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	98.63	98.63	0.93	0.93	2	-
GCF_018882155.1	s__Polynucleobacter sp018882155	81.2096	261	378	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	81.1397	208	378	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	96.21	96.15	0.92	0.92	3	-
GCA_903995005.1	s__Polynucleobacter sp903995005	81.1254	171	378	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	81.0902	226	378	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018687955.1	s__Polynucleobacter sp018687955	81.054	225	378	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	81.0348	232	378	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	81.0031	253	378	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018882185.1	s__Polynucleobacter sp018882185	80.9616	216	378	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	80.9062	236	378	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	80.7545	258	378	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018881975.1	s__Polynucleobacter sp018881975	80.716	231	378	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	80.508	239	378	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018687095.1	s__Polynucleobacter sp018687095	79.9856	199	378	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903909925.1	s__Polynucleobacter sp903909925	79.9836	190	378	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900205755.1	s__Polynucleobacter meluiroseus	78.7496	123	378	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 03:14:09,484] [INFO] GTDB search result was written to GCA_903886005.1_freshwater_MAG_---_LJ_bin-3854_genomic.fna/result_gtdb.tsv
[2023-06-30 03:14:09,484] [INFO] ===== GTDB Search completed =====
[2023-06-30 03:14:09,490] [INFO] DFAST_QC result json was written to GCA_903886005.1_freshwater_MAG_---_LJ_bin-3854_genomic.fna/dqc_result.json
[2023-06-30 03:14:09,490] [INFO] DFAST_QC completed!
[2023-06-30 03:14:09,490] [INFO] Total running time: 0h0m40s