[2024-01-24 13:22:01,657] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:22:01,659] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:22:01,659] [INFO] DQC Reference Directory: /var/lib/cwl/stgaf7568a4-12c0-468b-923f-091a5e7c1d1d/dqc_reference
[2024-01-24 13:22:03,001] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:22:03,002] [INFO] Task started: Prodigal
[2024-01-24 13:22:03,002] [INFO] Running command: gunzip -c /var/lib/cwl/stgd6c17710-8ca9-423b-8c0d-f177384d4aa4/GCF_007004655.1_ASM700465v1_genomic.fna.gz | prodigal -d GCF_007004655.1_ASM700465v1_genomic.fna/cds.fna -a GCF_007004655.1_ASM700465v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:22:24,717] [INFO] Task succeeded: Prodigal
[2024-01-24 13:22:24,717] [INFO] Task started: HMMsearch
[2024-01-24 13:22:24,718] [INFO] Running command: hmmsearch --tblout GCF_007004655.1_ASM700465v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgaf7568a4-12c0-468b-923f-091a5e7c1d1d/dqc_reference/reference_markers.hmm GCF_007004655.1_ASM700465v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:22:25,160] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:22:25,161] [INFO] Found 6/6 markers.
[2024-01-24 13:22:25,217] [INFO] Query marker FASTA was written to GCF_007004655.1_ASM700465v1_genomic.fna/markers.fasta
[2024-01-24 13:22:25,217] [INFO] Task started: Blastn
[2024-01-24 13:22:25,217] [INFO] Running command: blastn -query GCF_007004655.1_ASM700465v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaf7568a4-12c0-468b-923f-091a5e7c1d1d/dqc_reference/reference_markers.fasta -out GCF_007004655.1_ASM700465v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:22:26,004] [INFO] Task succeeded: Blastn
[2024-01-24 13:22:26,008] [INFO] Selected 30 target genomes.
[2024-01-24 13:22:26,008] [INFO] Target genome list was writen to GCF_007004655.1_ASM700465v1_genomic.fna/target_genomes.txt
[2024-01-24 13:22:26,040] [INFO] Task started: fastANI
[2024-01-24 13:22:26,041] [INFO] Running command: fastANI --query /var/lib/cwl/stgd6c17710-8ca9-423b-8c0d-f177384d4aa4/GCF_007004655.1_ASM700465v1_genomic.fna.gz --refList GCF_007004655.1_ASM700465v1_genomic.fna/target_genomes.txt --output GCF_007004655.1_ASM700465v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:22:49,453] [INFO] Task succeeded: fastANI
[2024-01-24 13:22:49,453] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgaf7568a4-12c0-468b-923f-091a5e7c1d1d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:22:49,454] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgaf7568a4-12c0-468b-923f-091a5e7c1d1d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:22:49,476] [INFO] Found 30 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:22:49,476] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:22:49,477] [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
Exilibacterium tricleocarpae	strain=R142	GCA_007004655.1	2591008	2591008	type	True	100.0	2356	2359	95	conclusive
Microbulbifer flavimaris	strain=WRN-8	GCA_001641755.2	1781068	1781068	type	True	76.8508	114	2359	95	below_threshold
Microbulbifer rhizosphaerae	strain=CECT 8799	GCA_014191725.1	1562603	1562603	type	True	76.7433	193	2359	95	below_threshold
Gilvimarinus chinensis	strain=DSM 19667	GCA_000377745.1	396005	396005	type	True	76.6002	70	2359	95	below_threshold
Microbulbifer hydrolyticus	strain=IRE-31	GCA_009931115.1	48074	48074	type	True	76.5358	103	2359	95	below_threshold
Pseudomaricurvus alcaniphilus	strain=MEBiC06469	GCA_011440395.1	1166482	1166482	type	True	76.484	199	2359	95	below_threshold
Microbulbifer hydrolyticus	strain=DSM 11525	GCA_014202835.1	48074	48074	type	True	76.4818	103	2359	95	below_threshold
Marinimicrobium koreense	strain=DSM 16974	GCA_003762925.1	306545	306545	type	True	76.4531	124	2359	95	below_threshold
Microbulbifer thermotolerans	strain=DSM 19189	GCA_900112305.1	252514	252514	type	True	76.4381	108	2359	95	below_threshold
Seongchinamella unica	strain=GH4-78	GCA_004354085.1	2547392	2547392	type	True	76.3586	79	2359	95	below_threshold
Marinimicrobium agarilyticum	strain=DSM 16975	GCA_000423345.1	306546	306546	type	True	76.3407	120	2359	95	below_threshold
Simiduia agarivorans	strain=SA1 = DSM 21679	GCA_000305785.2	447471	447471	type	True	76.3341	119	2359	95	below_threshold
Aestuariicella albida	strain=HHU G3-2	GCA_018863235.1	2842452	2842452	type	True	76.2754	85	2359	95	below_threshold
Pseudoteredinibacter isoporae	strain=DSM 22368	GCA_014207695.1	570281	570281	type	True	76.2337	57	2359	95	below_threshold
Marinimicrobium alkaliphilum	strain=SW121	GCA_003259155.1	2202654	2202654	type	True	76.1734	125	2359	95	below_threshold
Pseudoteredinibacter isoporae	strain=DSM 22368	GCA_011683895.1	570281	570281	type	True	76.1687	57	2359	95	below_threshold
Simiduia agarivorans	strain=DSM 21679	GCA_000420285.1	447471	447471	type	True	76.1054	119	2359	95	below_threshold
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	76.045	134	2359	95	below_threshold
Pseudoteredinibacter isoporae	strain=LMG 25246	GCA_011602085.1	570281	570281	type	True	76.017	56	2359	95	below_threshold
Halomonas nitroreducens	strain=11S	GCA_003966155.1	447425	447425	type	True	75.9821	104	2359	95	below_threshold
Halomonas denitrificans	strain=DSM 18045	GCA_003056305.1	370769	370769	type	True	75.9723	124	2359	95	below_threshold
Pseudomonas benzenivorans	strain=DSM 8628	GCA_900100495.1	556533	556533	type	True	75.9157	130	2359	95	below_threshold
Stutzerimonas degradans	strain=DSM 50238	GCA_024448505.1	2968968	2968968	type	True	75.8226	84	2359	95	below_threshold
Stutzerimonas degradans	strain=FDAARGOS_876	GCA_016028635.1	2968968	2968968	suspected-type	True	75.7977	88	2359	95	below_threshold
Stutzerimonas degradans	strain=DSM 50238	GCA_002891015.1	2968968	2968968	type	True	75.7591	88	2359	95	below_threshold
Pseudomonas guguanensis	strain=JCM 18416	GCA_900104265.1	1198456	1198456	type	True	75.7569	117	2359	95	below_threshold
Pseudomonas hydrolytica	strain=DSWY01	GCA_021495345.2	2493633	2493633	type	True	75.706	130	2359	95	below_threshold
Sulfurivermis fontis	strain=JG42	GCA_004001245.1	1972068	1972068	type	True	75.6929	81	2359	95	below_threshold
Kushneria aurantia	strain=DSM 21353	GCA_000382245.1	504092	504092	type	True	75.68	71	2359	95	below_threshold
Marinobacterium lutimaris	strain=DSM 22012	GCA_900108065.1	568106	568106	type	True	75.5722	64	2359	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:22:49,479] [INFO] DFAST Taxonomy check result was written to GCF_007004655.1_ASM700465v1_genomic.fna/tc_result.tsv
[2024-01-24 13:22:49,479] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:22:49,479] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:22:49,479] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgaf7568a4-12c0-468b-923f-091a5e7c1d1d/dqc_reference/checkm_data
[2024-01-24 13:22:49,480] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:22:49,550] [INFO] Task started: CheckM
[2024-01-24 13:22:49,550] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007004655.1_ASM700465v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007004655.1_ASM700465v1_genomic.fna/checkm_input GCF_007004655.1_ASM700465v1_genomic.fna/checkm_result
[2024-01-24 13:23:48,817] [INFO] Task succeeded: CheckM
[2024-01-24 13:23:48,819] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:23:48,841] [INFO] ===== Completeness check finished =====
[2024-01-24 13:23:48,842] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:23:48,842] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007004655.1_ASM700465v1_genomic.fna/markers.fasta)
[2024-01-24 13:23:48,843] [INFO] Task started: Blastn
[2024-01-24 13:23:48,843] [INFO] Running command: blastn -query GCF_007004655.1_ASM700465v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaf7568a4-12c0-468b-923f-091a5e7c1d1d/dqc_reference/reference_markers_gtdb.fasta -out GCF_007004655.1_ASM700465v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:23:50,101] [INFO] Task succeeded: Blastn
[2024-01-24 13:23:50,111] [INFO] Selected 26 target genomes.
[2024-01-24 13:23:50,111] [INFO] Target genome list was writen to GCF_007004655.1_ASM700465v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:23:50,167] [INFO] Task started: fastANI
[2024-01-24 13:23:50,167] [INFO] Running command: fastANI --query /var/lib/cwl/stgd6c17710-8ca9-423b-8c0d-f177384d4aa4/GCF_007004655.1_ASM700465v1_genomic.fna.gz --refList GCF_007004655.1_ASM700465v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007004655.1_ASM700465v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:24:09,634] [INFO] Task succeeded: fastANI
[2024-01-24 13:24:09,656] [INFO] Found 25 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:24:09,657] [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_007004655.1	s__Exilibacterium tricleocarpae	100.0	2356	2359	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Exilibacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001641755.2	s__Microbulbifer flavimaris	76.8701	113	2359	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Microbulbifer	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014191725.1	s__Microbulbifer rhizosphaerae	76.7658	191	2359	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Microbulbifer	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000377745.1	s__Gilvimarinus chinensis	76.6293	69	2359	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Gilvimarinus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004361885.1	s__Halomonas ventosae_C	76.5125	67	2359	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011440395.1	s__Pseudomaricurvus alcaniphilus	76.4936	198	2359	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Pseudomaricurvus	95.0	98.35	98.35	0.88	0.88	2	-
GCF_009857815.1	s__Pseudomaricurvus sp009857815	76.4657	131	2359	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Pseudomaricurvus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003762925.1	s__Marinimicrobium koreense	76.4653	126	2359	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Marinimicrobium	95.0	96.56	95.81	0.88	0.87	5	-
GCF_000423345.1	s__Marinimicrobium agarilyticum	76.385	120	2359	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Marinimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000305785.2	s__Simiduia agarivorans	76.3341	119	2359	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Simiduia	95.0	99.99	99.99	1.00	1.00	2	-
GCF_000832015.1	s__Gilvimarinus agarilyticus	76.2822	63	2359	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Gilvimarinus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000961645.1	s__BRH-c0 sp000961645	76.216	95	2359	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__BRH-c0	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017303155.1	s__Microbulbifer salipaludis	76.2153	128	2359	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Microbulbifer	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011683955.1	s__Pseudomaricurvus alkylphenolicus	76.1847	144	2359	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Pseudomaricurvus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011602365.1	s__Pseudomaricurvus hydrocarbonicus	76.1818	80	2359	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Pseudomaricurvus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003259155.1	s__Marinimicrobium_A alkaliphilum	76.158	123	2359	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Marinimicrobium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017255185.1	s__Parahaliea mediterranea_A	76.1041	182	2359	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Parahaliea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018069465.1	s__50-400-T64 sp018069465	76.0625	52	2359	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__50-400-T64	95.0	100.00	100.00	0.99	0.99	2	-
GCF_015182315.1	s__Cellvibrio polysaccharolyticus	76.062	70	2359	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Cellvibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011602085.1	s__Pseudoteredinibacter isoporae	75.9944	57	2359	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Pseudoteredinibacter	95.0	100.00	100.00	1.00	0.99	3	-
GCF_003966155.1	s__Halomonas nitroreducens	75.9679	105	2359	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004001245.1	s__Sulfurivermis fontis	75.6929	81	2359	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiohalomonadales;f__Thiohalomonadaceae;g__Sulfurivermis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900108065.1	s__Marinobacterium lutimaris	75.5556	65	2359	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002432555.1	s__UBA5868 sp002432555	75.5237	50	2359	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__UBA5868	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900115905.1	s__Pseudomonas_D formosensis	75.4646	76	2359	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	98.74	98.74	0.94	0.94	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:24:09,658] [INFO] GTDB search result was written to GCF_007004655.1_ASM700465v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:24:09,659] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:24:09,663] [INFO] DFAST_QC result json was written to GCF_007004655.1_ASM700465v1_genomic.fna/dqc_result.json
[2024-01-24 13:24:09,663] [INFO] DFAST_QC completed!
[2024-01-24 13:24:09,664] [INFO] Total running time: 0h2m8s