[2023-06-28 05:54:53,069] [INFO] DFAST_QC pipeline started.
[2023-06-28 05:54:53,072] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 05:54:53,072] [INFO] DQC Reference Directory: /var/lib/cwl/stgb423abec-7ee2-4d05-add3-0a653eeb5bd5/dqc_reference
[2023-06-28 05:54:54,374] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 05:54:54,375] [INFO] Task started: Prodigal
[2023-06-28 05:54:54,376] [INFO] Running command: gunzip -c /var/lib/cwl/stga81121df-acb8-4004-9fb9-95b2686103b2/GCA_913020555.1_SRR5469033_bin.61_MetaBAT_v2.12.1_MAG_genomic.fna.gz | prodigal -d GCA_913020555.1_SRR5469033_bin.61_MetaBAT_v2.12.1_MAG_genomic.fna/cds.fna -a GCA_913020555.1_SRR5469033_bin.61_MetaBAT_v2.12.1_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 05:55:01,544] [INFO] Task succeeded: Prodigal
[2023-06-28 05:55:01,545] [INFO] Task started: HMMsearch
[2023-06-28 05:55:01,545] [INFO] Running command: hmmsearch --tblout GCA_913020555.1_SRR5469033_bin.61_MetaBAT_v2.12.1_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb423abec-7ee2-4d05-add3-0a653eeb5bd5/dqc_reference/reference_markers.hmm GCA_913020555.1_SRR5469033_bin.61_MetaBAT_v2.12.1_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-28 05:55:01,776] [INFO] Task succeeded: HMMsearch
[2023-06-28 05:55:01,777] [WARNING] Found 5/6 markers. [/var/lib/cwl/stga81121df-acb8-4004-9fb9-95b2686103b2/GCA_913020555.1_SRR5469033_bin.61_MetaBAT_v2.12.1_MAG_genomic.fna.gz]
[2023-06-28 05:55:01,806] [INFO] Query marker FASTA was written to GCA_913020555.1_SRR5469033_bin.61_MetaBAT_v2.12.1_MAG_genomic.fna/markers.fasta
[2023-06-28 05:55:01,806] [INFO] Task started: Blastn
[2023-06-28 05:55:01,807] [INFO] Running command: blastn -query GCA_913020555.1_SRR5469033_bin.61_MetaBAT_v2.12.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgb423abec-7ee2-4d05-add3-0a653eeb5bd5/dqc_reference/reference_markers.fasta -out GCA_913020555.1_SRR5469033_bin.61_MetaBAT_v2.12.1_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 05:55:02,428] [INFO] Task succeeded: Blastn
[2023-06-28 05:55:02,433] [INFO] Selected 19 target genomes.
[2023-06-28 05:55:02,433] [INFO] Target genome list was writen to GCA_913020555.1_SRR5469033_bin.61_MetaBAT_v2.12.1_MAG_genomic.fna/target_genomes.txt
[2023-06-28 05:55:02,436] [INFO] Task started: fastANI
[2023-06-28 05:55:02,436] [INFO] Running command: fastANI --query /var/lib/cwl/stga81121df-acb8-4004-9fb9-95b2686103b2/GCA_913020555.1_SRR5469033_bin.61_MetaBAT_v2.12.1_MAG_genomic.fna.gz --refList GCA_913020555.1_SRR5469033_bin.61_MetaBAT_v2.12.1_MAG_genomic.fna/target_genomes.txt --output GCA_913020555.1_SRR5469033_bin.61_MetaBAT_v2.12.1_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 05:55:14,103] [INFO] Task succeeded: fastANI
[2023-06-28 05:55:14,103] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb423abec-7ee2-4d05-add3-0a653eeb5bd5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 05:55:14,104] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb423abec-7ee2-4d05-add3-0a653eeb5bd5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 05:55:14,119] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 05:55:14,119] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 05:55:14,119] [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
Polaribacter reichenbachii	strain=KCTC 23969	GCA_002814055.1	996801	996801	type	True	80.2915	478	797	95	below_threshold
Polaribacter reichenbachii	strain=KCTC 23969	GCA_001680875.1	996801	996801	type	True	80.2778	472	797	95	below_threshold
Polaribacter reichenbachii	strain=6Alg 8T	GCA_001975665.1	996801	996801	type	True	80.2764	476	797	95	below_threshold
Polaribacter reichenbachii	strain=LMG 26443	GCA_020532845.1	996801	996801	type	True	80.2504	475	797	95	below_threshold
Polaribacter porphyrae	strain=LMG 26671	GCA_020532745.1	1137780	1137780	type	True	80.1985	473	797	95	below_threshold
Polaribacter porphyrae	strain=NBRC 108759	GCA_002954685.1	1137780	1137780	type	True	80.1904	473	797	95	below_threshold
Polaribacter vadi	strain=LPB0003	GCA_001680885.1	1774273	1774273	type	True	80.0714	461	797	95	below_threshold
Polaribacter vadi	strain=LPB0003	GCA_001761365.1	1774273	1774273	type	True	80.0544	466	797	95	below_threshold
Polaribacter dokdonensis	strain=DSW-5	GCA_001280865.1	326329	326329	type	True	79.7326	410	797	95	below_threshold
Polaribacter dokdonensis	strain=DSW-5	GCA_900106865.1	326329	326329	type	True	79.7027	416	797	95	below_threshold
Polaribacter aquimarinus	strain=ZY113	GCA_003129485.1	2100726	2100726	type	True	79.5615	393	797	95	below_threshold
Polaribacter septentrionalilitoris	strain=ANORD1	GCA_009832745.1	2494657	2494657	type	True	79.4749	392	797	95	below_threshold
Polaribacter pectinis	strain=L12M9	GCA_014352875.1	2738844	2738844	type	True	79.3923	419	797	95	below_threshold
Polaribacter haliotis	strain=KCTC 52418	GCA_014784055.1	1888915	1888915	type	True	79.3343	393	797	95	below_threshold
Polaribacter haliotis	strain=RA4-7	GCA_002201315.1	1888915	1888915	type	True	79.2309	400	797	95	below_threshold
Polaribacter undariae	strain=KCTC 42175	GCA_024918935.1	1574269	1574269	type	True	78.8157	362	797	95	below_threshold
Polaribacter cellanae	strain=SM13	GCA_017569185.1	2818493	2818493	type	True	78.7338	377	797	95	below_threshold
Polaribacter batillariae	strain=G4M1	GCA_017498485.1	2808900	2808900	type	True	78.6516	374	797	95	below_threshold
Tenacibaculum todarodis	strain=LPB0136	GCA_001889045.1	1850252	1850252	type	True	78.4819	285	797	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 05:55:14,121] [INFO] DFAST Taxonomy check result was written to GCA_913020555.1_SRR5469033_bin.61_MetaBAT_v2.12.1_MAG_genomic.fna/tc_result.tsv
[2023-06-28 05:55:14,122] [INFO] ===== Taxonomy check completed =====
[2023-06-28 05:55:14,122] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 05:55:14,122] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb423abec-7ee2-4d05-add3-0a653eeb5bd5/dqc_reference/checkm_data
[2023-06-28 05:55:14,123] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 05:55:14,156] [INFO] Task started: CheckM
[2023-06-28 05:55:14,156] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_913020555.1_SRR5469033_bin.61_MetaBAT_v2.12.1_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_913020555.1_SRR5469033_bin.61_MetaBAT_v2.12.1_MAG_genomic.fna/checkm_input GCA_913020555.1_SRR5469033_bin.61_MetaBAT_v2.12.1_MAG_genomic.fna/checkm_result
[2023-06-28 05:55:41,043] [INFO] Task succeeded: CheckM
[2023-06-28 05:55:41,044] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 58.33%
Contamintation: 8.33%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 05:55:41,071] [INFO] ===== Completeness check finished =====
[2023-06-28 05:55:41,071] [INFO] ===== Start GTDB Search =====
[2023-06-28 05:55:41,072] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_913020555.1_SRR5469033_bin.61_MetaBAT_v2.12.1_MAG_genomic.fna/markers.fasta)
[2023-06-28 05:55:41,072] [INFO] Task started: Blastn
[2023-06-28 05:55:41,072] [INFO] Running command: blastn -query GCA_913020555.1_SRR5469033_bin.61_MetaBAT_v2.12.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgb423abec-7ee2-4d05-add3-0a653eeb5bd5/dqc_reference/reference_markers_gtdb.fasta -out GCA_913020555.1_SRR5469033_bin.61_MetaBAT_v2.12.1_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 05:55:42,073] [INFO] Task succeeded: Blastn
[2023-06-28 05:55:42,078] [INFO] Selected 15 target genomes.
[2023-06-28 05:55:42,078] [INFO] Target genome list was writen to GCA_913020555.1_SRR5469033_bin.61_MetaBAT_v2.12.1_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 05:55:42,084] [INFO] Task started: fastANI
[2023-06-28 05:55:42,084] [INFO] Running command: fastANI --query /var/lib/cwl/stga81121df-acb8-4004-9fb9-95b2686103b2/GCA_913020555.1_SRR5469033_bin.61_MetaBAT_v2.12.1_MAG_genomic.fna.gz --refList GCA_913020555.1_SRR5469033_bin.61_MetaBAT_v2.12.1_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_913020555.1_SRR5469033_bin.61_MetaBAT_v2.12.1_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 05:55:52,042] [INFO] Task succeeded: fastANI
[2023-06-28 05:55:52,070] [INFO] Found 15 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 05:55:52,071] [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_018861005.1	s__Polaribacter vadi_A	80.621	477	797	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001975665.1	s__Polaribacter reichenbachii	80.2842	475	797	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	99.98	99.97	1.00	1.00	3	-
GCF_002954685.1	s__Polaribacter porphyrae	80.1832	474	797	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001761365.1	s__Polaribacter vadi	80.0431	467	797	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000766795.1	s__Polaribacter sp000766795	79.7574	419	797	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001280865.1	s__Polaribacter dokdonensis	79.6949	413	797	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000152945.2	s__Polaribacter sp000152945	79.6565	404	797	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900105145.1	s__Polaribacter sp900105145	79.6194	438	797	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003129485.1	s__Polaribacter sp003129485	79.5618	393	797	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009832745.1	s__Polaribacter sp009832745	79.4564	393	797	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014352875.1	s__Polaribacter sp014352875	79.3722	418	797	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014784055.1	s__Polaribacter haliotis	79.334	393	797	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002163675.1	s__Polaribacter sp002163675	79.2172	427	797	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002831685.1	s__Polaribacter sp002831685	78.7847	381	797	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017498485.1	s__Polaribacter sp017498485	78.6624	373	797	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 05:55:52,073] [INFO] GTDB search result was written to GCA_913020555.1_SRR5469033_bin.61_MetaBAT_v2.12.1_MAG_genomic.fna/result_gtdb.tsv
[2023-06-28 05:55:52,073] [INFO] ===== GTDB Search completed =====
[2023-06-28 05:55:52,077] [INFO] DFAST_QC result json was written to GCA_913020555.1_SRR5469033_bin.61_MetaBAT_v2.12.1_MAG_genomic.fna/dqc_result.json
[2023-06-28 05:55:52,078] [INFO] DFAST_QC completed!
[2023-06-28 05:55:52,078] [INFO] Total running time: 0h0m59s