[2024-01-24 12:46:57,834] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:46:57,836] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:46:57,836] [INFO] DQC Reference Directory: /var/lib/cwl/stg554cc300-f993-49c5-90f8-d3068d45cb95/dqc_reference
[2024-01-24 12:46:59,271] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:46:59,272] [INFO] Task started: Prodigal
[2024-01-24 12:46:59,272] [INFO] Running command: gunzip -c /var/lib/cwl/stgf2961ed1-b5dd-4e1d-ae9c-e0db29a64d3f/GCF_009674825.1_ASM967482v1_genomic.fna.gz | prodigal -d GCF_009674825.1_ASM967482v1_genomic.fna/cds.fna -a GCF_009674825.1_ASM967482v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:47:20,842] [INFO] Task succeeded: Prodigal
[2024-01-24 12:47:20,843] [INFO] Task started: HMMsearch
[2024-01-24 12:47:20,843] [INFO] Running command: hmmsearch --tblout GCF_009674825.1_ASM967482v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg554cc300-f993-49c5-90f8-d3068d45cb95/dqc_reference/reference_markers.hmm GCF_009674825.1_ASM967482v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:47:21,147] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:47:21,148] [INFO] Found 6/6 markers.
[2024-01-24 12:47:21,187] [INFO] Query marker FASTA was written to GCF_009674825.1_ASM967482v1_genomic.fna/markers.fasta
[2024-01-24 12:47:21,187] [INFO] Task started: Blastn
[2024-01-24 12:47:21,188] [INFO] Running command: blastn -query GCF_009674825.1_ASM967482v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg554cc300-f993-49c5-90f8-d3068d45cb95/dqc_reference/reference_markers.fasta -out GCF_009674825.1_ASM967482v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:47:21,850] [INFO] Task succeeded: Blastn
[2024-01-24 12:47:21,853] [INFO] Selected 18 target genomes.
[2024-01-24 12:47:21,853] [INFO] Target genome list was writen to GCF_009674825.1_ASM967482v1_genomic.fna/target_genomes.txt
[2024-01-24 12:47:21,860] [INFO] Task started: fastANI
[2024-01-24 12:47:21,860] [INFO] Running command: fastANI --query /var/lib/cwl/stgf2961ed1-b5dd-4e1d-ae9c-e0db29a64d3f/GCF_009674825.1_ASM967482v1_genomic.fna.gz --refList GCF_009674825.1_ASM967482v1_genomic.fna/target_genomes.txt --output GCF_009674825.1_ASM967482v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:47:36,025] [INFO] Task succeeded: fastANI
[2024-01-24 12:47:36,026] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg554cc300-f993-49c5-90f8-d3068d45cb95/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:47:36,026] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg554cc300-f993-49c5-90f8-d3068d45cb95/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:47:36,047] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:47:36,047] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:47:36,047] [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
Maribacter luteus	strain=RZ05	GCA_009674825.1	2594478	2594478	type	True	100.0	1534	1535	95	conclusive
Maribacter polysiphoniae	strain=DSM 23514	GCA_003148665.1	429344	429344	type	True	82.6095	922	1535	95	below_threshold
Maribacter polysiphoniae	strain=KCTC 22021	GCA_014673435.1	429344	429344	type	True	82.5748	933	1535	95	below_threshold
Maribacter arenosus	strain=CAU 1321	GCA_014610845.1	1854708	1854708	type	True	78.828	504	1535	95	below_threshold
Maribacter thermophilus	strain=HT7-2	GCA_001020565.1	1197874	1197874	type	True	78.0499	209	1535	95	below_threshold
Maribacter hydrothermalis	strain=T28	GCA_001913155.1	1836467	1836467	type	True	77.166	171	1535	95	below_threshold
Zobellia laminariae	strain=KMM 3676	GCA_009725995.1	248906	248906	type	True	76.9725	165	1535	95	below_threshold
Arenibacter arenosicollis	strain=BSSL-BM3	GCA_014397245.1	2762274	2762274	type	True	76.9225	184	1535	95	below_threshold
Muricauda oceanensis	strain=40DY170	GCA_003992595.1	2499163	2499163	type	True	76.8232	128	1535	95	below_threshold
Maribacter orientalis	strain=DSM 16471	GCA_900109345.1	228957	228957	type	True	76.7578	167	1535	95	below_threshold
Muricauda lutimaris	strain=KCTC 22173	GCA_003581615.1	475082	475082	type	True	76.7281	137	1535	95	below_threshold
Muricauda alvinocaridis	strain=SCR12	GCA_004916895.1	2530200	2530200	type	True	76.6934	124	1535	95	below_threshold
Muricauda hymeniacidonis	strain=176CP4-71	GCA_004296335.1	2517819	2517819	type	True	76.5651	91	1535	95	below_threshold
Pelagihabitans pacificus	strain=TP-CH-4	GCA_009371985.2	2696054	2696054	type	True	76.4996	128	1535	95	below_threshold
Euzebyella saccharophila	strain=7SM30	GCA_014855495.1	679664	679664	type	True	76.4341	155	1535	95	below_threshold
Poritiphilus flavus	strain=R33	GCA_009901585.1	2697053	2697053	type	True	76.2716	87	1535	95	below_threshold
Aggregatimonas sangjinii	strain=F202Z8	GCA_005943945.1	2583587	2583587	type	True	76.2612	149	1535	95	below_threshold
Sinomicrobium weinanense	strain=FJxs	GCA_014518365.1	2842200	2842200	type	True	75.9539	51	1535	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:47:36,049] [INFO] DFAST Taxonomy check result was written to GCF_009674825.1_ASM967482v1_genomic.fna/tc_result.tsv
[2024-01-24 12:47:36,049] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:47:36,049] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:47:36,050] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg554cc300-f993-49c5-90f8-d3068d45cb95/dqc_reference/checkm_data
[2024-01-24 12:47:36,051] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:47:36,106] [INFO] Task started: CheckM
[2024-01-24 12:47:36,106] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009674825.1_ASM967482v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009674825.1_ASM967482v1_genomic.fna/checkm_input GCF_009674825.1_ASM967482v1_genomic.fna/checkm_result
[2024-01-24 12:48:36,579] [INFO] Task succeeded: CheckM
[2024-01-24 12:48:36,580] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:48:36,602] [INFO] ===== Completeness check finished =====
[2024-01-24 12:48:36,603] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:48:36,603] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009674825.1_ASM967482v1_genomic.fna/markers.fasta)
[2024-01-24 12:48:36,604] [INFO] Task started: Blastn
[2024-01-24 12:48:36,604] [INFO] Running command: blastn -query GCF_009674825.1_ASM967482v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg554cc300-f993-49c5-90f8-d3068d45cb95/dqc_reference/reference_markers_gtdb.fasta -out GCF_009674825.1_ASM967482v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:48:37,440] [INFO] Task succeeded: Blastn
[2024-01-24 12:48:37,444] [INFO] Selected 14 target genomes.
[2024-01-24 12:48:37,444] [INFO] Target genome list was writen to GCF_009674825.1_ASM967482v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:48:37,454] [INFO] Task started: fastANI
[2024-01-24 12:48:37,454] [INFO] Running command: fastANI --query /var/lib/cwl/stgf2961ed1-b5dd-4e1d-ae9c-e0db29a64d3f/GCF_009674825.1_ASM967482v1_genomic.fna.gz --refList GCF_009674825.1_ASM967482v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009674825.1_ASM967482v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:48:47,513] [INFO] Task succeeded: fastANI
[2024-01-24 12:48:47,530] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:48:47,530] [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_009674825.1	s__Maribacter_A luteus	100.0	1534	1535	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter_A	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003148665.1	s__Maribacter_A polysiphoniae	82.604	923	1535	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter_A	95.0	99.27	98.55	0.95	0.91	3	-
GCF_014596745.1	s__Maribacter_A sp014596745	81.2008	882	1535	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002749285.1	s__Maribacter_A sp002749285	79.1237	366	1535	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014610845.1	s__Maribacter_A arenosus	78.828	504	1535	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000153165.2	s__Maribacter_A sp000153165	77.9642	346	1535	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013001935.1	s__Maribacter_A sp013001935	77.8068	175	1535	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter_A	95.0	96.76	96.72	0.66	0.66	3	-
GCF_003970695.1	s__Maribacter sp002742365	77.6555	176	1535	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	96.61	96.61	0.86	0.86	2	-
GCA_018679695.1	s__Maribacter_A sp018679695	77.611	293	1535	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter_A	95.0	99.00	99.00	0.82	0.82	2	-
GCF_001913155.1	s__Maribacter hydrothermalis	77.1513	172	1535	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_009725995.1	s__Zobellia laminariae	76.9725	165	1535	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Zobellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109345.1	s__Maribacter orientalis	76.7578	167	1535	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129275.1	s__Arenibacter palladensis	76.7565	189	1535	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Arenibacter	95.0	97.38	97.38	0.84	0.84	2	-
GCF_010468565.1	s__Muricauda sp010468565	76.7174	113	1535	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:48:47,532] [INFO] GTDB search result was written to GCF_009674825.1_ASM967482v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:48:47,532] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:48:47,536] [INFO] DFAST_QC result json was written to GCF_009674825.1_ASM967482v1_genomic.fna/dqc_result.json
[2024-01-24 12:48:47,536] [INFO] DFAST_QC completed!
[2024-01-24 12:48:47,536] [INFO] Total running time: 0h1m50s