[2024-01-25 19:50:06,000] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:50:06,006] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:50:06,006] [INFO] DQC Reference Directory: /var/lib/cwl/stg9c55935f-6dd0-44a3-a0e7-575228ab1306/dqc_reference
[2024-01-25 19:50:07,181] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:50:07,182] [INFO] Task started: Prodigal
[2024-01-25 19:50:07,182] [INFO] Running command: gunzip -c /var/lib/cwl/stg74c0591f-578a-4803-aaa3-c012bd96647f/GCF_002895435.1_ASM289543v1_genomic.fna.gz | prodigal -d GCF_002895435.1_ASM289543v1_genomic.fna/cds.fna -a GCF_002895435.1_ASM289543v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:50:22,773] [INFO] Task succeeded: Prodigal
[2024-01-25 19:50:22,773] [INFO] Task started: HMMsearch
[2024-01-25 19:50:22,773] [INFO] Running command: hmmsearch --tblout GCF_002895435.1_ASM289543v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9c55935f-6dd0-44a3-a0e7-575228ab1306/dqc_reference/reference_markers.hmm GCF_002895435.1_ASM289543v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:50:23,056] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:50:23,057] [INFO] Found 6/6 markers.
[2024-01-25 19:50:23,103] [INFO] Query marker FASTA was written to GCF_002895435.1_ASM289543v1_genomic.fna/markers.fasta
[2024-01-25 19:50:23,103] [INFO] Task started: Blastn
[2024-01-25 19:50:23,103] [INFO] Running command: blastn -query GCF_002895435.1_ASM289543v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9c55935f-6dd0-44a3-a0e7-575228ab1306/dqc_reference/reference_markers.fasta -out GCF_002895435.1_ASM289543v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:50:23,711] [INFO] Task succeeded: Blastn
[2024-01-25 19:50:23,716] [INFO] Selected 16 target genomes.
[2024-01-25 19:50:23,716] [INFO] Target genome list was writen to GCF_002895435.1_ASM289543v1_genomic.fna/target_genomes.txt
[2024-01-25 19:50:23,726] [INFO] Task started: fastANI
[2024-01-25 19:50:23,726] [INFO] Running command: fastANI --query /var/lib/cwl/stg74c0591f-578a-4803-aaa3-c012bd96647f/GCF_002895435.1_ASM289543v1_genomic.fna.gz --refList GCF_002895435.1_ASM289543v1_genomic.fna/target_genomes.txt --output GCF_002895435.1_ASM289543v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:50:38,511] [INFO] Task succeeded: fastANI
[2024-01-25 19:50:38,512] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9c55935f-6dd0-44a3-a0e7-575228ab1306/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:50:38,512] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9c55935f-6dd0-44a3-a0e7-575228ab1306/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:50:38,522] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:50:38,522] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:50:38,522] [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 sediminis	strain=w01	GCA_002895435.1	2070536	2070536	type	True	100.0	1925	1926	95	conclusive
Aquimarina macrocephali	strain=JAMB N27	GCA_000520995.1	666563	666563	type	True	80.2203	935	1926	95	below_threshold
Aquimarina atlantica	strain=22II-S11-z7	GCA_000626715.1	1317122	1317122	type	True	80.1957	937	1926	95	below_threshold
Aquimarina megaterium	strain=XH134	GCA_000520975.1	1443666	1443666	type	True	80.1505	960	1926	95	below_threshold
Aquimarina longa	strain=SW024	GCA_001401755.1	1080221	1080221	type	True	79.5938	749	1926	95	below_threshold
Aquimarina muelleri	strain=KCTC 12285	GCA_014651355.1	279356	279356	type	True	79.4333	738	1926	95	below_threshold
Aquimarina muelleri	strain=DSM 19832	GCA_000430665.1	279356	279356	type	True	79.4246	728	1926	95	below_threshold
Aquimarina mytili	strain=KCTC 23302	GCA_016735115.1	874423	874423	type	True	78.7101	585	1926	95	below_threshold
Aquimarina aggregata	strain=RZW4-3-2	GCA_001632745.1	1642818	1642818	type	True	78.4488	568	1926	95	below_threshold
Salegentibacter lacus	strain=LM13S	GCA_020164555.1	2873599	2873599	type	True	76.211	84	1926	95	below_threshold
Tenacibaculum holothuriorum	strain=S2-2	GCA_002120225.1	1635173	1635173	type	True	75.9289	97	1926	95	below_threshold
Flavobacterium muglaense	strain=F-60	GCA_014305155.1	2764716	2764716	type	True	75.9216	66	1926	95	below_threshold
Flavobacterium piscinae	strain=ICH-30	GCA_004122145.1	2506424	2506424	type	True	75.8807	63	1926	95	below_threshold
Flavobacterium tyrosinilyticum	strain=KCTC 42726	GCA_023656565.1	1658740	1658740	type	True	75.7502	96	1926	95	below_threshold
Flavobacterium panacis	strain=DCY106	GCA_024649945.1	2962567	2962567	type	True	75.6716	92	1926	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:50:38,524] [INFO] DFAST Taxonomy check result was written to GCF_002895435.1_ASM289543v1_genomic.fna/tc_result.tsv
[2024-01-25 19:50:38,524] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:50:38,524] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:50:38,525] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9c55935f-6dd0-44a3-a0e7-575228ab1306/dqc_reference/checkm_data
[2024-01-25 19:50:38,525] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:50:38,582] [INFO] Task started: CheckM
[2024-01-25 19:50:38,582] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002895435.1_ASM289543v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002895435.1_ASM289543v1_genomic.fna/checkm_input GCF_002895435.1_ASM289543v1_genomic.fna/checkm_result
[2024-01-25 19:51:24,703] [INFO] Task succeeded: CheckM
[2024-01-25 19:51:24,704] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:51:24,739] [INFO] ===== Completeness check finished =====
[2024-01-25 19:51:24,739] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:51:24,740] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002895435.1_ASM289543v1_genomic.fna/markers.fasta)
[2024-01-25 19:51:24,740] [INFO] Task started: Blastn
[2024-01-25 19:51:24,740] [INFO] Running command: blastn -query GCF_002895435.1_ASM289543v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9c55935f-6dd0-44a3-a0e7-575228ab1306/dqc_reference/reference_markers_gtdb.fasta -out GCF_002895435.1_ASM289543v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:51:25,665] [INFO] Task succeeded: Blastn
[2024-01-25 19:51:25,668] [INFO] Selected 12 target genomes.
[2024-01-25 19:51:25,669] [INFO] Target genome list was writen to GCF_002895435.1_ASM289543v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:51:25,684] [INFO] Task started: fastANI
[2024-01-25 19:51:25,684] [INFO] Running command: fastANI --query /var/lib/cwl/stg74c0591f-578a-4803-aaa3-c012bd96647f/GCF_002895435.1_ASM289543v1_genomic.fna.gz --refList GCF_002895435.1_ASM289543v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002895435.1_ASM289543v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:51:38,205] [INFO] Task succeeded: fastANI
[2024-01-25 19:51:38,213] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:51:38,213] [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_002895435.1	s__Aquimarina sediminis	100.0	1925	1926	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_900299525.1	s__Aquimarina sp900299525	80.2443	946	1926	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquimarina	95.0	99.99	99.99	0.99	0.99	2	-
GCF_000520995.1	s__Aquimarina macrocephali	80.2077	938	1926	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	80.1938	937	1926	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquimarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002846555.1	s__Aquimarina sp002846555	80.1677	926	1926	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquimarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000520975.1	s__Aquimarina megaterium	80.1521	959	1926	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquimarina	95.0	98.79	98.77	0.92	0.92	4	-
GCF_900312745.1	s__Aquimarina sp900312745	80.1011	964	1926	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquimarina	95.0	95.61	95.54	0.91	0.91	4	-
GCF_001401755.1	s__Aquimarina longa	79.5941	749	1926	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	79.416	729	1926	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	79.3843	721	1926	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquimarina	95.0	95.11	95.11	0.81	0.81	2	-
GCF_002120225.1	s__Tenacibaculum holothuriorum	75.9193	99	1926	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004122145.1	s__Flavobacterium piscinae	75.8573	64	1926	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.76	99.76	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-25 19:51:38,217] [INFO] GTDB search result was written to GCF_002895435.1_ASM289543v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:51:38,218] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:51:38,221] [INFO] DFAST_QC result json was written to GCF_002895435.1_ASM289543v1_genomic.fna/dqc_result.json
[2024-01-25 19:51:38,221] [INFO] DFAST_QC completed!
[2024-01-25 19:51:38,221] [INFO] Total running time: 0h1m32s