[2024-01-24 12:23:03,469] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:23:03,474] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:23:03,475] [INFO] DQC Reference Directory: /var/lib/cwl/stg81e229f6-29fd-4ba1-adfb-31b441b67321/dqc_reference
[2024-01-24 12:23:04,589] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:23:04,589] [INFO] Task started: Prodigal
[2024-01-24 12:23:04,590] [INFO] Running command: gunzip -c /var/lib/cwl/stgf30c7a58-9d28-49b7-aa55-bf3ba05b87ca/GCF_016735115.1_ASM1673511v1_genomic.fna.gz | prodigal -d GCF_016735115.1_ASM1673511v1_genomic.fna/cds.fna -a GCF_016735115.1_ASM1673511v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:23:18,414] [INFO] Task succeeded: Prodigal
[2024-01-24 12:23:18,414] [INFO] Task started: HMMsearch
[2024-01-24 12:23:18,414] [INFO] Running command: hmmsearch --tblout GCF_016735115.1_ASM1673511v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg81e229f6-29fd-4ba1-adfb-31b441b67321/dqc_reference/reference_markers.hmm GCF_016735115.1_ASM1673511v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:23:18,665] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:23:18,665] [INFO] Found 6/6 markers.
[2024-01-24 12:23:18,705] [INFO] Query marker FASTA was written to GCF_016735115.1_ASM1673511v1_genomic.fna/markers.fasta
[2024-01-24 12:23:18,705] [INFO] Task started: Blastn
[2024-01-24 12:23:18,705] [INFO] Running command: blastn -query GCF_016735115.1_ASM1673511v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg81e229f6-29fd-4ba1-adfb-31b441b67321/dqc_reference/reference_markers.fasta -out GCF_016735115.1_ASM1673511v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:23:19,325] [INFO] Task succeeded: Blastn
[2024-01-24 12:23:19,328] [INFO] Selected 16 target genomes.
[2024-01-24 12:23:19,328] [INFO] Target genome list was writen to GCF_016735115.1_ASM1673511v1_genomic.fna/target_genomes.txt
[2024-01-24 12:23:19,333] [INFO] Task started: fastANI
[2024-01-24 12:23:19,333] [INFO] Running command: fastANI --query /var/lib/cwl/stgf30c7a58-9d28-49b7-aa55-bf3ba05b87ca/GCF_016735115.1_ASM1673511v1_genomic.fna.gz --refList GCF_016735115.1_ASM1673511v1_genomic.fna/target_genomes.txt --output GCF_016735115.1_ASM1673511v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:23:34,134] [INFO] Task succeeded: fastANI
[2024-01-24 12:23:34,135] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg81e229f6-29fd-4ba1-adfb-31b441b67321/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:23:34,135] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg81e229f6-29fd-4ba1-adfb-31b441b67321/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:23:34,145] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:23:34,145] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:23:34,145] [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 mytili	strain=KCTC 23302	GCA_016735115.1	874423	874423	type	True	100.0	1648	1650	95	conclusive
Aquimarina macrocephali	strain=JAMB N27	GCA_000520995.1	666563	666563	type	True	79.2486	611	1650	95	below_threshold
Aquimarina atlantica	strain=22II-S11-z7	GCA_000626715.1	1317122	1317122	type	True	79.197	618	1650	95	below_threshold
Aquimarina megaterium	strain=XH134	GCA_000520975.1	1443666	1443666	type	True	79.1966	605	1650	95	below_threshold
Aquimarina aggregata	strain=RZW4-3-2	GCA_001632745.1	1642818	1642818	type	True	78.8686	608	1650	95	below_threshold
Aquimarina sediminis	strain=w01	GCA_002895435.1	2070536	2070536	type	True	78.816	562	1650	95	below_threshold
Aquimarina longa	strain=SW024	GCA_001401755.1	1080221	1080221	type	True	78.6468	533	1650	95	below_threshold
Aquimarina spongiae	strain=DSM 22623	GCA_900141785.1	570521	570521	type	True	78.5942	522	1650	95	below_threshold
Aquimarina amphilecti	strain=DSM 25232	GCA_900109375.1	1038014	1038014	type	True	78.1725	470	1650	95	below_threshold
Hanstruepera marina	strain=NBU2968	GCA_019880635.1	2873265	2873265	type	True	77.3106	98	1650	95	below_threshold
Hyunsoonleella ulvae	strain=HU1-3	GCA_016827605.1	2799948	2799948	type	True	76.9004	93	1650	95	below_threshold
Winogradskyella jejuensis	strain=DSM 25330	GCA_900129745.1	1089305	1089305	type	True	76.8019	93	1650	95	below_threshold
Saonia flava	strain=DSM 29762	GCA_011927795.1	523696	523696	type	True	76.2233	73	1650	95	below_threshold
Zobellia barbeyronii	strain=KMM 6746	GCA_018603515.1	2748009	2748009	type	True	75.98	76	1650	95	below_threshold
Flavobacterium panacis	strain=DCY106	GCA_024649945.1	2962567	2962567	type	True	75.7068	73	1650	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:23:34,147] [INFO] DFAST Taxonomy check result was written to GCF_016735115.1_ASM1673511v1_genomic.fna/tc_result.tsv
[2024-01-24 12:23:34,147] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:23:34,147] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:23:34,147] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg81e229f6-29fd-4ba1-adfb-31b441b67321/dqc_reference/checkm_data
[2024-01-24 12:23:34,148] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:23:34,195] [INFO] Task started: CheckM
[2024-01-24 12:23:34,195] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016735115.1_ASM1673511v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016735115.1_ASM1673511v1_genomic.fna/checkm_input GCF_016735115.1_ASM1673511v1_genomic.fna/checkm_result
[2024-01-24 12:24:14,670] [INFO] Task succeeded: CheckM
[2024-01-24 12:24:14,671] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:24:14,701] [INFO] ===== Completeness check finished =====
[2024-01-24 12:24:14,701] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:24:14,701] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016735115.1_ASM1673511v1_genomic.fna/markers.fasta)
[2024-01-24 12:24:14,702] [INFO] Task started: Blastn
[2024-01-24 12:24:14,702] [INFO] Running command: blastn -query GCF_016735115.1_ASM1673511v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg81e229f6-29fd-4ba1-adfb-31b441b67321/dqc_reference/reference_markers_gtdb.fasta -out GCF_016735115.1_ASM1673511v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:24:15,586] [INFO] Task succeeded: Blastn
[2024-01-24 12:24:15,589] [INFO] Selected 15 target genomes.
[2024-01-24 12:24:15,589] [INFO] Target genome list was writen to GCF_016735115.1_ASM1673511v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:24:15,596] [INFO] Task started: fastANI
[2024-01-24 12:24:15,597] [INFO] Running command: fastANI --query /var/lib/cwl/stgf30c7a58-9d28-49b7-aa55-bf3ba05b87ca/GCF_016735115.1_ASM1673511v1_genomic.fna.gz --refList GCF_016735115.1_ASM1673511v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016735115.1_ASM1673511v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:24:30,937] [INFO] Task succeeded: fastANI
[2024-01-24 12:24:30,946] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:24:30,946] [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_016735115.1	s__Aquimarina mytili	100.0	1648	1650	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquimarina	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000520995.1	s__Aquimarina macrocephali	79.2529	611	1650	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquimarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000626715.1	s__Aquimarina atlantica	79.2053	617	1650	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquimarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900299525.1	s__Aquimarina sp900299525	79.2049	627	1650	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquimarina	95.0	99.99	99.99	0.99	0.99	2	-
GCF_000520975.1	s__Aquimarina megaterium	79.2001	606	1650	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquimarina	95.0	98.79	98.77	0.92	0.92	4	-
GCF_007489275.1	s__Aquimarina algiphila	79.1181	688	1650	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquimarina	95.0	98.78	98.78	0.88	0.88	2	-
GCF_900312815.1	s__Aquimarina sp900312815	79.1173	630	1650	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquimarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900312745.1	s__Aquimarina sp900312745	79.0881	613	1650	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquimarina	95.0	95.61	95.54	0.91	0.91	4	-
GCF_001632745.1	s__Aquimarina aggregata	78.8664	608	1650	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquimarina	95.0	98.64	98.63	0.93	0.92	3	-
GCF_002895435.1	s__Aquimarina sediminis	78.8015	564	1650	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	78.7179	595	1650	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquimarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001401755.1	s__Aquimarina longa	78.6374	535	1650	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquimarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900141785.1	s__Aquimarina spongiae	78.6018	524	1650	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	78.182	470	1650	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquimarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011927795.1	s__Saonia flava	76.1998	74	1650	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Saonia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:24:30,948] [INFO] GTDB search result was written to GCF_016735115.1_ASM1673511v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:24:30,948] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:24:30,951] [INFO] DFAST_QC result json was written to GCF_016735115.1_ASM1673511v1_genomic.fna/dqc_result.json
[2024-01-24 12:24:30,951] [INFO] DFAST_QC completed!
[2024-01-24 12:24:30,951] [INFO] Total running time: 0h1m27s