[2024-01-24 13:41:18,498] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:41:18,501] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:41:18,502] [INFO] DQC Reference Directory: /var/lib/cwl/stgd24fa4fa-6972-4515-b405-1ef8b8f88e80/dqc_reference
[2024-01-24 13:41:19,785] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:41:19,786] [INFO] Task started: Prodigal
[2024-01-24 13:41:19,786] [INFO] Running command: gunzip -c /var/lib/cwl/stg49c56193-5e81-467f-a535-eb29c650cffe/GCF_002954665.1_ASM295466v1_genomic.fna.gz | prodigal -d GCF_002954665.1_ASM295466v1_genomic.fna/cds.fna -a GCF_002954665.1_ASM295466v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:41:32,323] [INFO] Task succeeded: Prodigal
[2024-01-24 13:41:32,323] [INFO] Task started: HMMsearch
[2024-01-24 13:41:32,324] [INFO] Running command: hmmsearch --tblout GCF_002954665.1_ASM295466v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd24fa4fa-6972-4515-b405-1ef8b8f88e80/dqc_reference/reference_markers.hmm GCF_002954665.1_ASM295466v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:41:32,614] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:41:32,615] [INFO] Found 6/6 markers.
[2024-01-24 13:41:32,660] [INFO] Query marker FASTA was written to GCF_002954665.1_ASM295466v1_genomic.fna/markers.fasta
[2024-01-24 13:41:32,661] [INFO] Task started: Blastn
[2024-01-24 13:41:32,661] [INFO] Running command: blastn -query GCF_002954665.1_ASM295466v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd24fa4fa-6972-4515-b405-1ef8b8f88e80/dqc_reference/reference_markers.fasta -out GCF_002954665.1_ASM295466v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:33,336] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:33,339] [INFO] Selected 17 target genomes.
[2024-01-24 13:41:33,340] [INFO] Target genome list was writen to GCF_002954665.1_ASM295466v1_genomic.fna/target_genomes.txt
[2024-01-24 13:41:33,350] [INFO] Task started: fastANI
[2024-01-24 13:41:33,350] [INFO] Running command: fastANI --query /var/lib/cwl/stg49c56193-5e81-467f-a535-eb29c650cffe/GCF_002954665.1_ASM295466v1_genomic.fna.gz --refList GCF_002954665.1_ASM295466v1_genomic.fna/target_genomes.txt --output GCF_002954665.1_ASM295466v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:47,568] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:47,569] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd24fa4fa-6972-4515-b405-1ef8b8f88e80/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:47,569] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd24fa4fa-6972-4515-b405-1ef8b8f88e80/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:47,584] [INFO] Found 17 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:41:47,584] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:41:47,584] [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 glomeratus	strain=ATCC 43844	GCA_002954665.1	102	102	type	True	99.9991	1342	1352	95	conclusive
Polaribacter glomeratus	strain=ACAM 171	GCA_007997115.1	102	102	type	True	99.9827	1316	1352	95	conclusive
Polaribacter filamentus	strain=ATCC 700397	GCA_002943715.1	53483	53483	type	True	87.6256	862	1352	95	below_threshold
Polaribacter vadi	strain=LPB0003	GCA_001680885.1	1774273	1774273	type	True	80.895	718	1352	95	below_threshold
Polaribacter vadi	strain=LPB0003	GCA_001761365.1	1774273	1774273	type	True	80.8933	721	1352	95	below_threshold
Polaribacter butkevichii	strain=KCTC 12100	GCA_002954605.1	218490	218490	type	True	80.6065	679	1352	95	below_threshold
Polaribacter pectinis	strain=L12M9	GCA_014352875.1	2738844	2738844	type	True	80.586	669	1352	95	below_threshold
Polaribacter undariae	strain=KCTC 42175	GCA_024918935.1	1574269	1574269	type	True	80.5541	636	1352	95	below_threshold
Polaribacter atrinae	strain=KACC 17473	GCA_001640115.1	1333662	1333662	type	True	80.4747	630	1352	95	below_threshold
Polaribacter sejongensis	strain=KCTC 23670	GCA_002814075.1	985043	985043	type	True	80.3785	635	1352	95	below_threshold
Polaribacter haliotis	strain=KCTC 52418	GCA_014784055.1	1888915	1888915	type	True	80.2328	642	1352	95	below_threshold
Polaribacter haliotis	strain=RA4-7	GCA_002201315.1	1888915	1888915	type	True	80.1779	640	1352	95	below_threshold
Polaribacter litorisediminis	strain=OITF-11	GCA_019968605.1	1908341	1908341	type	True	80.0878	704	1352	95	below_threshold
Polaribacter dokdonensis	strain=KCTC 12392	GCA_024362345.1	326329	326329	type	True	79.6671	571	1352	95	below_threshold
Polaribacter cellanae	strain=SM13	GCA_017569185.1	2818493	2818493	type	True	79.6403	602	1352	95	below_threshold
Polaribacter dokdonensis	strain=DSW-5	GCA_900106865.1	326329	326329	type	True	79.6297	572	1352	95	below_threshold
Tenacibaculum todarodis	strain=LPB0136	GCA_001889045.1	1850252	1850252	type	True	79.0521	488	1352	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:47,586] [INFO] DFAST Taxonomy check result was written to GCF_002954665.1_ASM295466v1_genomic.fna/tc_result.tsv
[2024-01-24 13:41:47,587] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:47,587] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:47,587] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd24fa4fa-6972-4515-b405-1ef8b8f88e80/dqc_reference/checkm_data
[2024-01-24 13:41:47,589] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:47,640] [INFO] Task started: CheckM
[2024-01-24 13:41:47,640] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002954665.1_ASM295466v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002954665.1_ASM295466v1_genomic.fna/checkm_input GCF_002954665.1_ASM295466v1_genomic.fna/checkm_result
[2024-01-24 13:42:25,315] [INFO] Task succeeded: CheckM
[2024-01-24 13:42:25,316] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:42:25,336] [INFO] ===== Completeness check finished =====
[2024-01-24 13:42:25,336] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:42:25,337] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002954665.1_ASM295466v1_genomic.fna/markers.fasta)
[2024-01-24 13:42:25,337] [INFO] Task started: Blastn
[2024-01-24 13:42:25,337] [INFO] Running command: blastn -query GCF_002954665.1_ASM295466v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd24fa4fa-6972-4515-b405-1ef8b8f88e80/dqc_reference/reference_markers_gtdb.fasta -out GCF_002954665.1_ASM295466v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:42:26,255] [INFO] Task succeeded: Blastn
[2024-01-24 13:42:26,258] [INFO] Selected 13 target genomes.
[2024-01-24 13:42:26,258] [INFO] Target genome list was writen to GCF_002954665.1_ASM295466v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:42:26,267] [INFO] Task started: fastANI
[2024-01-24 13:42:26,267] [INFO] Running command: fastANI --query /var/lib/cwl/stg49c56193-5e81-467f-a535-eb29c650cffe/GCF_002954665.1_ASM295466v1_genomic.fna.gz --refList GCF_002954665.1_ASM295466v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002954665.1_ASM295466v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:42:37,155] [INFO] Task succeeded: fastANI
[2024-01-24 13:42:37,172] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:42:37,173] [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_002954665.1	s__Polaribacter glomeratus	99.9991	1342	1352	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	99.98	99.98	1.00	1.00	2	conclusive
GCF_002943715.1	s__Polaribacter filamentus	87.6235	862	1352	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	84.0223	832	1352	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000981625.1	s__Polaribacter sp000981625	81.2771	566	1352	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	80.9345	716	1352	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	80.7311	665	1352	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905480405.1	s__Polaribacter sp905480405	80.7265	633	1352	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018861005.1	s__Polaribacter vadi_A	80.6723	685	1352	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900106075.1	s__Polaribacter sp900106075	80.6253	666	1352	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	98.66	98.45	0.96	0.92	5	-
GCF_002954605.1	s__Polaribacter butkevichii	80.6023	678	1352	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002163675.1	s__Polaribacter sp002163675	80.5686	698	1352	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002163835.1	s__Polaribacter sp002163835	80.5178	657	1352	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002005425.1	s__Polaribacter sp002005425	79.7187	616	1352	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	96.81	96.81	0.92	0.92	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:42:37,175] [INFO] GTDB search result was written to GCF_002954665.1_ASM295466v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:42:37,175] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:42:37,181] [INFO] DFAST_QC result json was written to GCF_002954665.1_ASM295466v1_genomic.fna/dqc_result.json
[2024-01-24 13:42:37,182] [INFO] DFAST_QC completed!
[2024-01-24 13:42:37,182] [INFO] Total running time: 0h1m19s