[2024-01-24 14:02:51,782] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:02:51,784] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:02:51,784] [INFO] DQC Reference Directory: /var/lib/cwl/stg845d161a-2628-43b9-9e48-1c7fc55f5e32/dqc_reference
[2024-01-24 14:02:53,192] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:02:53,193] [INFO] Task started: Prodigal
[2024-01-24 14:02:53,194] [INFO] Running command: gunzip -c /var/lib/cwl/stgfe61faa3-243f-478a-af4d-db36fc69cece/GCF_014596945.1_ASM1459694v1_genomic.fna.gz | prodigal -d GCF_014596945.1_ASM1459694v1_genomic.fna/cds.fna -a GCF_014596945.1_ASM1459694v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:03:06,605] [INFO] Task succeeded: Prodigal
[2024-01-24 14:03:06,605] [INFO] Task started: HMMsearch
[2024-01-24 14:03:06,605] [INFO] Running command: hmmsearch --tblout GCF_014596945.1_ASM1459694v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg845d161a-2628-43b9-9e48-1c7fc55f5e32/dqc_reference/reference_markers.hmm GCF_014596945.1_ASM1459694v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:03:06,891] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:03:06,892] [INFO] Found 6/6 markers.
[2024-01-24 14:03:06,928] [INFO] Query marker FASTA was written to GCF_014596945.1_ASM1459694v1_genomic.fna/markers.fasta
[2024-01-24 14:03:06,929] [INFO] Task started: Blastn
[2024-01-24 14:03:06,929] [INFO] Running command: blastn -query GCF_014596945.1_ASM1459694v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg845d161a-2628-43b9-9e48-1c7fc55f5e32/dqc_reference/reference_markers.fasta -out GCF_014596945.1_ASM1459694v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:03:07,643] [INFO] Task succeeded: Blastn
[2024-01-24 14:03:07,646] [INFO] Selected 17 target genomes.
[2024-01-24 14:03:07,647] [INFO] Target genome list was writen to GCF_014596945.1_ASM1459694v1_genomic.fna/target_genomes.txt
[2024-01-24 14:03:07,652] [INFO] Task started: fastANI
[2024-01-24 14:03:07,652] [INFO] Running command: fastANI --query /var/lib/cwl/stgfe61faa3-243f-478a-af4d-db36fc69cece/GCF_014596945.1_ASM1459694v1_genomic.fna.gz --refList GCF_014596945.1_ASM1459694v1_genomic.fna/target_genomes.txt --output GCF_014596945.1_ASM1459694v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:03:19,808] [INFO] Task succeeded: fastANI
[2024-01-24 14:03:19,808] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg845d161a-2628-43b9-9e48-1c7fc55f5e32/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:03:19,808] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg845d161a-2628-43b9-9e48-1c7fc55f5e32/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:03:19,823] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:03:19,823] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:03:19,823] [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
Aestuariibaculum sediminum	strain=TT11	GCA_014596945.1	2770637	2770637	type	True	100.0	1335	1337	95	conclusive
Aestuariibaculum marinum	strain=IP7	GCA_014596975.1	2683592	2683592	type	True	81.2775	681	1337	95	below_threshold
Aestuariibaculum suncheonense	strain=SC17	GCA_014596935.1	1028745	1028745	type	True	80.9334	694	1337	95	below_threshold
Mariniflexile fucanivorans	strain=DSM 18792	GCA_004341235.1	264023	264023	type	True	78.3533	377	1337	95	below_threshold
Mariniflexile gromovii	strain=KCTC 12570	GCA_017814435.1	362523	362523	type	True	78.3163	365	1337	95	below_threshold
Tamlana agarivorans	strain=JW-26	GCA_001642835.1	481183	481183	type	True	78.0785	302	1337	95	below_threshold
Algibacter pacificus	strain=H164	GCA_008033385.1	2599389	2599389	type	True	77.8549	294	1337	95	below_threshold
Arenitalea lutea	strain=P7-3-5	GCA_000283015.1	1178825	1178825	type	True	77.8331	301	1337	95	below_threshold
Arenitalea lutea	strain=CGMCC 1.12213	GCA_900141715.1	1178825	1178825	type	True	77.8176	306	1337	95	below_threshold
Flavivirga rizhaonensis	strain=RZ03	GCA_004791695.1	2559571	2559571	type	True	77.5926	316	1337	95	below_threshold
Seonamhaeicola maritimus	strain=1505	GCA_008056315.1	2591822	2591822	type	True	77.5888	272	1337	95	below_threshold
Hanstruepera marina	strain=NBU2968	GCA_019880635.1	2873265	2873265	type	True	77.5594	200	1337	95	below_threshold
Hyunsoonleella flava	strain=T58	GCA_004310325.1	2527939	2527939	type	True	77.5225	217	1337	95	below_threshold
Hanstruepera flava	strain=NBU2984	GCA_023634025.1	2930218	2930218	type	True	77.5164	185	1337	95	below_threshold
Confluentibacter lentus	strain=HJM-3	GCA_002806995.1	1699412	1699412	type	True	77.3945	265	1337	95	below_threshold
Hyunsoonleella ulvae	strain=HU1-3	GCA_016827605.1	2799948	2799948	type	True	77.2331	223	1337	95	below_threshold
Hyunsoonleella aquatilis	strain=SJ7	GCA_014270105.1	2762758	2762758	type	True	76.9595	156	1337	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:03:19,825] [INFO] DFAST Taxonomy check result was written to GCF_014596945.1_ASM1459694v1_genomic.fna/tc_result.tsv
[2024-01-24 14:03:19,826] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:03:19,826] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:03:19,826] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg845d161a-2628-43b9-9e48-1c7fc55f5e32/dqc_reference/checkm_data
[2024-01-24 14:03:19,828] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:03:19,869] [INFO] Task started: CheckM
[2024-01-24 14:03:19,869] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014596945.1_ASM1459694v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014596945.1_ASM1459694v1_genomic.fna/checkm_input GCF_014596945.1_ASM1459694v1_genomic.fna/checkm_result
[2024-01-24 14:03:59,523] [INFO] Task succeeded: CheckM
[2024-01-24 14:03:59,525] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:03:59,548] [INFO] ===== Completeness check finished =====
[2024-01-24 14:03:59,548] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:03:59,549] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014596945.1_ASM1459694v1_genomic.fna/markers.fasta)
[2024-01-24 14:03:59,549] [INFO] Task started: Blastn
[2024-01-24 14:03:59,550] [INFO] Running command: blastn -query GCF_014596945.1_ASM1459694v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg845d161a-2628-43b9-9e48-1c7fc55f5e32/dqc_reference/reference_markers_gtdb.fasta -out GCF_014596945.1_ASM1459694v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:04:00,561] [INFO] Task succeeded: Blastn
[2024-01-24 14:04:00,579] [INFO] Selected 14 target genomes.
[2024-01-24 14:04:00,579] [INFO] Target genome list was writen to GCF_014596945.1_ASM1459694v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:04:00,591] [INFO] Task started: fastANI
[2024-01-24 14:04:00,591] [INFO] Running command: fastANI --query /var/lib/cwl/stgfe61faa3-243f-478a-af4d-db36fc69cece/GCF_014596945.1_ASM1459694v1_genomic.fna.gz --refList GCF_014596945.1_ASM1459694v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014596945.1_ASM1459694v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:04:10,393] [INFO] Task succeeded: fastANI
[2024-01-24 14:04:10,412] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:04:10,412] [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_014596945.1	s__Aestuariibaculum sediminum	100.0	1335	1337	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aestuariibaculum	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014596975.1	s__Aestuariibaculum marinum	81.2609	683	1337	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aestuariibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014596935.1	s__Aestuariibaculum suncheonense	80.9423	693	1337	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aestuariibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000941055.1	s__Siansivirga zeaxanthinifaciens	78.6028	389	1337	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Siansivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000425645.1	s__Gaetbulibacter saemankumensis	78.595	384	1337	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gaetbulibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004341235.1	s__Mariniflexile fucanivorans	78.3533	377	1337	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mariniflexile	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017814435.1	s__Mariniflexile gromovii	78.2999	368	1337	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mariniflexile	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018860245.1	s__Tamlana_A agarivorans_A	78.074	281	1337	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tamlana_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001642835.1	s__Tamlana_A agarivorans	78.0721	304	1337	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tamlana_A	95.0	95.46	95.44	0.83	0.81	3	-
GCF_003143755.1	s__Algibacter_B sp003143755	78.0376	307	1337	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900141715.1	s__Arenitalea lutea	77.8287	305	1337	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Arenitalea	95.0	100.00	100.00	1.00	1.00	2	-
GCF_009796825.1	s__Algibacter sp009796825	77.7653	327	1337	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008056315.1	s__Seonamhaeicola maritimus	77.5986	272	1337	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Seonamhaeicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004791695.1	s__Flavivirga rizhaonensis	77.5747	317	1337	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavivirga	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:04:10,414] [INFO] GTDB search result was written to GCF_014596945.1_ASM1459694v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:04:10,415] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:04:10,419] [INFO] DFAST_QC result json was written to GCF_014596945.1_ASM1459694v1_genomic.fna/dqc_result.json
[2024-01-24 14:04:10,420] [INFO] DFAST_QC completed!
[2024-01-24 14:04:10,420] [INFO] Total running time: 0h1m19s