[2023-06-30 19:16:21,530] [INFO] DFAST_QC pipeline started.
[2023-06-30 19:16:21,552] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 19:16:21,552] [INFO] DQC Reference Directory: /var/lib/cwl/stg322321d8-ba73-41e6-88ca-19c9159ce6d6/dqc_reference
[2023-06-30 19:16:23,088] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 19:16:23,089] [INFO] Task started: Prodigal
[2023-06-30 19:16:23,089] [INFO] Running command: gunzip -c /var/lib/cwl/stgc82cab2b-c636-4eb8-9675-81c9a99e9281/GCA_903866865.1_freshwater_MAG_---_C5coas_bin-0931_genomic.fna.gz | prodigal -d GCA_903866865.1_freshwater_MAG_---_C5coas_bin-0931_genomic.fna/cds.fna -a GCA_903866865.1_freshwater_MAG_---_C5coas_bin-0931_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 19:16:26,629] [INFO] Task succeeded: Prodigal
[2023-06-30 19:16:26,629] [INFO] Task started: HMMsearch
[2023-06-30 19:16:26,629] [INFO] Running command: hmmsearch --tblout GCA_903866865.1_freshwater_MAG_---_C5coas_bin-0931_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg322321d8-ba73-41e6-88ca-19c9159ce6d6/dqc_reference/reference_markers.hmm GCA_903866865.1_freshwater_MAG_---_C5coas_bin-0931_genomic.fna/protein.faa > /dev/null
[2023-06-30 19:16:26,864] [INFO] Task succeeded: HMMsearch
[2023-06-30 19:16:26,865] [INFO] Found 6/6 markers.
[2023-06-30 19:16:26,893] [INFO] Query marker FASTA was written to GCA_903866865.1_freshwater_MAG_---_C5coas_bin-0931_genomic.fna/markers.fasta
[2023-06-30 19:16:26,893] [INFO] Task started: Blastn
[2023-06-30 19:16:26,893] [INFO] Running command: blastn -query GCA_903866865.1_freshwater_MAG_---_C5coas_bin-0931_genomic.fna/markers.fasta -db /var/lib/cwl/stg322321d8-ba73-41e6-88ca-19c9159ce6d6/dqc_reference/reference_markers.fasta -out GCA_903866865.1_freshwater_MAG_---_C5coas_bin-0931_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 19:16:27,498] [INFO] Task succeeded: Blastn
[2023-06-30 19:16:27,502] [INFO] Selected 16 target genomes.
[2023-06-30 19:16:27,502] [INFO] Target genome list was writen to GCA_903866865.1_freshwater_MAG_---_C5coas_bin-0931_genomic.fna/target_genomes.txt
[2023-06-30 19:16:27,504] [INFO] Task started: fastANI
[2023-06-30 19:16:27,505] [INFO] Running command: fastANI --query /var/lib/cwl/stgc82cab2b-c636-4eb8-9675-81c9a99e9281/GCA_903866865.1_freshwater_MAG_---_C5coas_bin-0931_genomic.fna.gz --refList GCA_903866865.1_freshwater_MAG_---_C5coas_bin-0931_genomic.fna/target_genomes.txt --output GCA_903866865.1_freshwater_MAG_---_C5coas_bin-0931_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 19:16:32,980] [INFO] Task succeeded: fastANI
[2023-06-30 19:16:32,980] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg322321d8-ba73-41e6-88ca-19c9159ce6d6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 19:16:32,981] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg322321d8-ba73-41e6-88ca-19c9159ce6d6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 19:16:32,994] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2023-06-30 19:16:32,994] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-30 19:16:32,994] [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 sphagniphilus	strain=MWH-Weng1-1	GCA_001953355.1	1743169	1743169	type	True	96.373	291	340	95	conclusive
Polynucleobacter corsicus	strain=AP-Melu-1000-A1	GCA_018688255.1	2081042	2081042	type	True	79.5375	115	340	95	below_threshold
Polynucleobacter asymbioticus	strain=QLW-P1DMWA-1	GCA_000016345.1	576611	576611	type	True	79.522	116	340	95	below_threshold
Polynucleobacter ibericus	strain=es-MAR-2	GCA_018687955.1	1819725	1819725	type	True	79.4861	119	340	95	below_threshold
Polynucleobacter hirudinilacicola	strain=MWH-EgelM1-30-B4	GCA_002192535.1	1743166	1743166	type	True	79.4749	116	340	95	below_threshold
Polynucleobacter finlandensis	strain=MWH-Mekk-B1	GCA_018881755.1	1855894	1855894	type	True	79.4456	130	340	95	below_threshold
Polynucleobacter bastaniensis	strain=AP-Basta-1000A-D1	GCA_018882205.1	2081039	2081039	type	True	79.3232	118	340	95	below_threshold
Polynucleobacter sinensis	strain=MWH-HuW1	GCA_001595985.1	1743157	1743157	type	True	79.2654	118	340	95	below_threshold
Polynucleobacter wuianus	strain=QLW-P1FAT50C-4	GCA_001659725.1	1743168	1743168	type	True	79.2549	125	340	95	below_threshold
Polynucleobacter hallstattensis	strain=MWH-Hall10	GCA_018881835.1	1855586	1855586	type	True	79.1982	121	340	95	below_threshold
Polynucleobacter nymphae	strain=AP-Mumm-500A-B3	GCA_018882155.1	2081043	2081043	type	True	79.004	113	340	95	below_threshold
Polynucleobacter alcilacus	strain=UK-Pondora-W15	GCA_018881545.1	1819739	1819739	type	True	78.9828	115	340	95	below_threshold
Polynucleobacter tropicus	strain=MWH-UH21B	GCA_013307225.1	1743174	1743174	type	True	78.9203	117	340	95	below_threshold
Polynucleobacter aenigmaticus	strain=MWH-K35W1	GCA_002206635.1	1743164	1743164	type	True	78.8219	116	340	95	below_threshold
Polynucleobacter paludilacus	strain=MWH-Mekk-C3	GCA_018687595.1	1855895	1855895	type	True	78.5526	103	340	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 19:16:32,997] [INFO] DFAST Taxonomy check result was written to GCA_903866865.1_freshwater_MAG_---_C5coas_bin-0931_genomic.fna/tc_result.tsv
[2023-06-30 19:16:32,997] [INFO] ===== Taxonomy check completed =====
[2023-06-30 19:16:32,998] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 19:16:32,998] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg322321d8-ba73-41e6-88ca-19c9159ce6d6/dqc_reference/checkm_data
[2023-06-30 19:16:32,999] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 19:16:33,020] [INFO] Task started: CheckM
[2023-06-30 19:16:33,020] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903866865.1_freshwater_MAG_---_C5coas_bin-0931_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903866865.1_freshwater_MAG_---_C5coas_bin-0931_genomic.fna/checkm_input GCA_903866865.1_freshwater_MAG_---_C5coas_bin-0931_genomic.fna/checkm_result
[2023-06-30 19:16:52,102] [INFO] Task succeeded: CheckM
[2023-06-30 19:16:52,104] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 54.17%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 19:16:52,131] [INFO] ===== Completeness check finished =====
[2023-06-30 19:16:52,131] [INFO] ===== Start GTDB Search =====
[2023-06-30 19:16:52,132] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903866865.1_freshwater_MAG_---_C5coas_bin-0931_genomic.fna/markers.fasta)
[2023-06-30 19:16:52,132] [INFO] Task started: Blastn
[2023-06-30 19:16:52,132] [INFO] Running command: blastn -query GCA_903866865.1_freshwater_MAG_---_C5coas_bin-0931_genomic.fna/markers.fasta -db /var/lib/cwl/stg322321d8-ba73-41e6-88ca-19c9159ce6d6/dqc_reference/reference_markers_gtdb.fasta -out GCA_903866865.1_freshwater_MAG_---_C5coas_bin-0931_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 19:16:52,975] [INFO] Task succeeded: Blastn
[2023-06-30 19:16:52,981] [INFO] Selected 25 target genomes.
[2023-06-30 19:16:52,981] [INFO] Target genome list was writen to GCA_903866865.1_freshwater_MAG_---_C5coas_bin-0931_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 19:16:52,987] [INFO] Task started: fastANI
[2023-06-30 19:16:52,987] [INFO] Running command: fastANI --query /var/lib/cwl/stgc82cab2b-c636-4eb8-9675-81c9a99e9281/GCA_903866865.1_freshwater_MAG_---_C5coas_bin-0931_genomic.fna.gz --refList GCA_903866865.1_freshwater_MAG_---_C5coas_bin-0931_genomic.fna/target_genomes_gtdb.txt --output GCA_903866865.1_freshwater_MAG_---_C5coas_bin-0931_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 19:17:01,423] [INFO] Task succeeded: fastANI
[2023-06-30 19:17:01,445] [INFO] Found 25 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 19:17:01,445] [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_001953355.1	s__Polynucleobacter sphagniphilus	96.373	291	340	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	98.85	96.86	0.95	0.92	8	conclusive
GCA_903930665.1	s__Polynucleobacter sp903930665	80.4552	94	340	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018882405.1	s__Polynucleobacter sp018882405	79.7839	125	340	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	79.7795	120	340	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	79.6526	124	340	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	79.617	128	340	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	96.71	95.84	0.78	0.66	4	-
GCF_018687815.1	s__Polynucleobacter sp018687815	79.5809	126	340	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018882365.1	s__Polynucleobacter sp018882365	79.5604	124	340	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	79.5441	107	340	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018688255.1	s__Polynucleobacter sp018688255	79.5375	115	340	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000016345.1	s__Polynucleobacter asymbioticus	79.522	116	340	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	98.87	97.92	0.92	0.85	11	-
GCF_018688335.1	s__Polynucleobacter sp018688335	79.4792	120	340	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	95.20	95.20	0.89	0.89	2	-
GCF_002192535.1	s__Polynucleobacter hirudinilacicola	79.4749	116	340	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	79.4718	130	340	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	79.4463	123	340	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	79.4394	131	340	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	79.4358	129	340	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018687695.1	s__Polynucleobacter sp018687695	79.381	112	340	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	79.3456	121	340	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018687895.1	s__Polynucleobacter sp018687895	79.3358	126	340	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	79.2607	124	340	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001659725.1	s__Polynucleobacter wuianus	79.2549	125	340	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	98.91	97.82	0.95	0.89	3	-
GCF_018881975.1	s__Polynucleobacter sp018881975	79.0523	126	340	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903835865.1	s__Polynucleobacter sp903835865	78.7454	71	340	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000019745.1	s__Polynucleobacter necessarius_D	78.6662	111	340	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 19:17:01,464] [INFO] GTDB search result was written to GCA_903866865.1_freshwater_MAG_---_C5coas_bin-0931_genomic.fna/result_gtdb.tsv
[2023-06-30 19:17:01,465] [INFO] ===== GTDB Search completed =====
[2023-06-30 19:17:01,471] [INFO] DFAST_QC result json was written to GCA_903866865.1_freshwater_MAG_---_C5coas_bin-0931_genomic.fna/dqc_result.json
[2023-06-30 19:17:01,471] [INFO] DFAST_QC completed!
[2023-06-30 19:17:01,471] [INFO] Total running time: 0h0m40s