[2024-01-24 13:19:12,783] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:19:12,784] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:19:12,785] [INFO] DQC Reference Directory: /var/lib/cwl/stg51102155-5a75-4557-9fd2-a2249d719fc3/dqc_reference
[2024-01-24 13:19:14,002] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:19:14,003] [INFO] Task started: Prodigal
[2024-01-24 13:19:14,003] [INFO] Running command: gunzip -c /var/lib/cwl/stg774af9c8-b9bf-44fa-9484-435548ead85b/GCF_000430645.1_ASM43064v1_genomic.fna.gz | prodigal -d GCF_000430645.1_ASM43064v1_genomic.fna/cds.fna -a GCF_000430645.1_ASM43064v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:19:32,377] [INFO] Task succeeded: Prodigal
[2024-01-24 13:19:32,378] [INFO] Task started: HMMsearch
[2024-01-24 13:19:32,378] [INFO] Running command: hmmsearch --tblout GCF_000430645.1_ASM43064v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg51102155-5a75-4557-9fd2-a2249d719fc3/dqc_reference/reference_markers.hmm GCF_000430645.1_ASM43064v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:19:32,704] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:19:32,706] [INFO] Found 6/6 markers.
[2024-01-24 13:19:32,760] [INFO] Query marker FASTA was written to GCF_000430645.1_ASM43064v1_genomic.fna/markers.fasta
[2024-01-24 13:19:32,760] [INFO] Task started: Blastn
[2024-01-24 13:19:32,760] [INFO] Running command: blastn -query GCF_000430645.1_ASM43064v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg51102155-5a75-4557-9fd2-a2249d719fc3/dqc_reference/reference_markers.fasta -out GCF_000430645.1_ASM43064v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:33,445] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:33,450] [INFO] Selected 17 target genomes.
[2024-01-24 13:19:33,451] [INFO] Target genome list was writen to GCF_000430645.1_ASM43064v1_genomic.fna/target_genomes.txt
[2024-01-24 13:19:33,465] [INFO] Task started: fastANI
[2024-01-24 13:19:33,466] [INFO] Running command: fastANI --query /var/lib/cwl/stg774af9c8-b9bf-44fa-9484-435548ead85b/GCF_000430645.1_ASM43064v1_genomic.fna.gz --refList GCF_000430645.1_ASM43064v1_genomic.fna/target_genomes.txt --output GCF_000430645.1_ASM43064v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:19:48,957] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:48,958] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg51102155-5a75-4557-9fd2-a2249d719fc3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:19:48,959] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg51102155-5a75-4557-9fd2-a2249d719fc3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:19:48,978] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:19:48,978] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:19:48,979] [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
Aquimarina latercula	strain=DSM 2041	GCA_000430645.1	987	987	type	True	100.0	2060	2064	95	conclusive
Aquimarina amphilecti	strain=DSM 25232	GCA_900109375.1	1038014	1038014	type	True	88.2242	1527	2064	95	below_threshold
Aquimarina mytili	strain=KCTC 23302	GCA_016735115.1	874423	874423	type	True	78.3131	492	2064	95	below_threshold
Aquimarina longa	strain=SW024	GCA_001401755.1	1080221	1080221	type	True	78.2431	493	2064	95	below_threshold
Aquimarina megaterium	strain=XH134	GCA_000520975.1	1443666	1443666	type	True	78.1867	544	2064	95	below_threshold
Aquimarina macrocephali	strain=JAMB N27	GCA_000520995.1	666563	666563	type	True	78.1669	552	2064	95	below_threshold
Aquimarina atlantica	strain=22II-S11-z7	GCA_000626715.1	1317122	1317122	type	True	78.1025	492	2064	95	below_threshold
Aquimarina muelleri	strain=KCTC 12285	GCA_014651355.1	279356	279356	type	True	78.0946	481	2064	95	below_threshold
Aquimarina muelleri	strain=DSM 19832	GCA_000430665.1	279356	279356	type	True	78.0442	480	2064	95	below_threshold
Aquimarina aggregata	strain=RZW4-3-2	GCA_001632745.1	1642818	1642818	type	True	77.995	569	2064	95	below_threshold
Aquimarina sediminis	strain=w01	GCA_002895435.1	2070536	2070536	type	True	77.8247	487	2064	95	below_threshold
Psychroserpens luteolus	strain=XSD401	GCA_021032705.1	2855840	2855840	type	True	76.4755	141	2064	95	below_threshold
Tenacibaculum lutimaris	strain=DSM 16505	GCA_003610735.1	285258	285258	type	True	76.4492	122	2064	95	below_threshold
Tenacibaculum haliotis	strain=KCTC 52419	GCA_025215075.1	1888914	1888914	type	True	76.3674	127	2064	95	below_threshold
Tenacibaculum todarodis	strain=LPB0136	GCA_001889045.1	1850252	1850252	type	True	76.2307	131	2064	95	below_threshold
Polaribacter undariae	strain=KCTC 42175	GCA_024918935.1	1574269	1574269	type	True	75.9732	143	2064	95	below_threshold
Abyssalbus ytuae	strain=MT3330	GCA_022807975.1	2926907	2926907	type	True	75.8456	95	2064	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:19:48,981] [INFO] DFAST Taxonomy check result was written to GCF_000430645.1_ASM43064v1_genomic.fna/tc_result.tsv
[2024-01-24 13:19:48,981] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:19:48,981] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:19:48,982] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg51102155-5a75-4557-9fd2-a2249d719fc3/dqc_reference/checkm_data
[2024-01-24 13:19:48,983] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:19:49,044] [INFO] Task started: CheckM
[2024-01-24 13:19:49,044] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000430645.1_ASM43064v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000430645.1_ASM43064v1_genomic.fna/checkm_input GCF_000430645.1_ASM43064v1_genomic.fna/checkm_result
[2024-01-24 13:20:42,570] [INFO] Task succeeded: CheckM
[2024-01-24 13:20:42,571] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:20:42,588] [INFO] ===== Completeness check finished =====
[2024-01-24 13:20:42,589] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:20:42,589] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000430645.1_ASM43064v1_genomic.fna/markers.fasta)
[2024-01-24 13:20:42,589] [INFO] Task started: Blastn
[2024-01-24 13:20:42,589] [INFO] Running command: blastn -query GCF_000430645.1_ASM43064v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg51102155-5a75-4557-9fd2-a2249d719fc3/dqc_reference/reference_markers_gtdb.fasta -out GCF_000430645.1_ASM43064v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:20:43,487] [INFO] Task succeeded: Blastn
[2024-01-24 13:20:43,494] [INFO] Selected 11 target genomes.
[2024-01-24 13:20:43,494] [INFO] Target genome list was writen to GCF_000430645.1_ASM43064v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:20:43,507] [INFO] Task started: fastANI
[2024-01-24 13:20:43,507] [INFO] Running command: fastANI --query /var/lib/cwl/stg774af9c8-b9bf-44fa-9484-435548ead85b/GCF_000430645.1_ASM43064v1_genomic.fna.gz --refList GCF_000430645.1_ASM43064v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000430645.1_ASM43064v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:20:54,933] [INFO] Task succeeded: fastANI
[2024-01-24 13:20:54,946] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:20:54,947] [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_000430645.1	s__Aquimarina latercula	100.0	2059	2064	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquimarina	95.0	98.44	98.41	0.94	0.92	4	conclusive
GCF_900299505.1	s__Aquimarina sp900299505	94.2185	1558	2064	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquimarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109375.1	s__Aquimarina amphilecti	88.2379	1525	2064	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquimarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003443675.1	s__Aquimarina sp003443675	81.8531	1202	2064	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquimarina	95.0	99.99	99.99	1.00	1.00	2	-
GCF_008370685.1	s__Aquimarina sp008370685	78.6654	666	2064	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquimarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018100805.1	s__Aquimarina sp018100805	78.4885	595	2064	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquimarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900312815.1	s__Aquimarina sp900312815	78.1222	516	2064	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquimarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000430665.1	s__Aquimarina muelleri	78.0368	481	2064	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquimarina	95.0	99.98	99.98	0.99	0.99	2	-
GCF_900299535.1	s__Aquimarina sp900299535	78.005	438	2064	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquimarina	95.0	95.11	95.11	0.81	0.81	2	-
GCF_003610735.1	s__Tenacibaculum lutimaris	76.4486	122	2064	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	97.15	97.15	0.89	0.89	2	-
GCA_013003655.1	s__Winogradskyella sp013003655	76.1504	67	2064	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	98.63	98.32	0.72	0.67	5	-
--------------------------------------------------------------------------------
[2024-01-24 13:20:54,948] [INFO] GTDB search result was written to GCF_000430645.1_ASM43064v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:20:54,949] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:20:54,952] [INFO] DFAST_QC result json was written to GCF_000430645.1_ASM43064v1_genomic.fna/dqc_result.json
[2024-01-24 13:20:54,953] [INFO] DFAST_QC completed!
[2024-01-24 13:20:54,953] [INFO] Total running time: 0h1m42s