[2024-01-24 13:18:33,554] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:18:33,557] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:18:33,558] [INFO] DQC Reference Directory: /var/lib/cwl/stgb2893651-d927-45ea-8042-219130ce61b4/dqc_reference
[2024-01-24 13:18:34,893] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:18:34,894] [INFO] Task started: Prodigal
[2024-01-24 13:18:34,894] [INFO] Running command: gunzip -c /var/lib/cwl/stgc3737632-b831-4015-ab55-47b6352b11f7/GCF_000423345.1_ASM42334v1_genomic.fna.gz | prodigal -d GCF_000423345.1_ASM42334v1_genomic.fna/cds.fna -a GCF_000423345.1_ASM42334v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:18:49,013] [INFO] Task succeeded: Prodigal
[2024-01-24 13:18:49,014] [INFO] Task started: HMMsearch
[2024-01-24 13:18:49,014] [INFO] Running command: hmmsearch --tblout GCF_000423345.1_ASM42334v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb2893651-d927-45ea-8042-219130ce61b4/dqc_reference/reference_markers.hmm GCF_000423345.1_ASM42334v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:18:49,386] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:18:49,388] [INFO] Found 6/6 markers.
[2024-01-24 13:18:49,445] [INFO] Query marker FASTA was written to GCF_000423345.1_ASM42334v1_genomic.fna/markers.fasta
[2024-01-24 13:18:49,445] [INFO] Task started: Blastn
[2024-01-24 13:18:49,446] [INFO] Running command: blastn -query GCF_000423345.1_ASM42334v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb2893651-d927-45ea-8042-219130ce61b4/dqc_reference/reference_markers.fasta -out GCF_000423345.1_ASM42334v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:18:50,344] [INFO] Task succeeded: Blastn
[2024-01-24 13:18:50,347] [INFO] Selected 24 target genomes.
[2024-01-24 13:18:50,348] [INFO] Target genome list was writen to GCF_000423345.1_ASM42334v1_genomic.fna/target_genomes.txt
[2024-01-24 13:18:50,361] [INFO] Task started: fastANI
[2024-01-24 13:18:50,361] [INFO] Running command: fastANI --query /var/lib/cwl/stgc3737632-b831-4015-ab55-47b6352b11f7/GCF_000423345.1_ASM42334v1_genomic.fna.gz --refList GCF_000423345.1_ASM42334v1_genomic.fna/target_genomes.txt --output GCF_000423345.1_ASM42334v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:19:07,612] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:07,612] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb2893651-d927-45ea-8042-219130ce61b4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:19:07,612] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb2893651-d927-45ea-8042-219130ce61b4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:19:07,629] [INFO] Found 22 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:19:07,629] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:19:07,629] [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
Marinimicrobium agarilyticum	strain=DSM 16975	GCA_000423345.1	306546	306546	type	True	100.0	1482	1485	95	conclusive
Marinimicrobium koreense	strain=DSM 16974	GCA_003762925.1	306545	306545	type	True	80.2078	667	1485	95	below_threshold
Marinimicrobium alkaliphilum	strain=SW121	GCA_003259155.1	2202654	2202654	type	True	77.8318	260	1485	95	below_threshold
Microbulbifer hydrolyticus	strain=IRE-31	GCA_009931115.1	48074	48074	type	True	77.5791	121	1485	95	below_threshold
Spongiibacter taiwanensis	strain=SPT1	GCA_023702635.1	1748242	1748242	type	True	77.3037	76	1485	95	below_threshold
Cellvibrio polysaccharolyticus	strain=Ka43	GCA_015182315.1	2082724	2082724	type	True	76.9763	114	1485	95	below_threshold
Simiduia agarivorans	strain=SA1 = DSM 21679	GCA_000305785.2	447471	447471	type	True	76.9299	97	1485	95	below_threshold
Microbulbifer flavimaris	strain=WRN-8	GCA_001641755.2	1781068	1781068	type	True	76.924	110	1485	95	below_threshold
Microbulbifer taiwanensis	strain=LMG 26125	GCA_014904815.1	986746	986746	type	True	76.8953	138	1485	95	below_threshold
Microbulbifer hainanensis	strain=NBU-8HK146	GCA_014904735.1	2735675	2735675	type	True	76.8499	120	1485	95	below_threshold
Microbulbifer hydrolyticus	strain=DSM 11525	GCA_014202835.1	48074	48074	type	True	76.8384	113	1485	95	below_threshold
Microbulbifer rhizosphaerae	strain=CECT 8799	GCA_014191725.1	1562603	1562603	type	True	76.8145	148	1485	95	below_threshold
Microbulbifer marinus	strain=CGMCC 1.10657	GCA_900107725.1	658218	658218	type	True	76.6663	124	1485	95	below_threshold
Marinobacter mangrovi	strain=CHFG3-1-5	GCA_016798325.1	2803918	2803918	type	True	76.6166	73	1485	95	below_threshold
Simiduia agarivorans	strain=DSM 21679	GCA_000420285.1	447471	447471	type	True	76.5307	100	1485	95	below_threshold
Pseudomaricurvus alcaniphilus	strain=MEBiC06469	GCA_011440395.1	1166482	1166482	type	True	76.5066	116	1485	95	below_threshold
Exilibacterium tricleocarpae	strain=R142	GCA_007004655.1	2591008	2591008	type	True	76.3589	117	1485	95	below_threshold
Halopseudomonas aestusnigri	strain=CECT 8317	GCA_900108005.1	857252	857252	type	True	76.319	88	1485	95	below_threshold
Halopseudomonas aestusnigri	strain=VGXO14	GCA_002197985.1	857252	857252	type	True	76.2572	87	1485	95	below_threshold
Marinobacterium nitratireducens	strain=CGMCC 1.7286	GCA_014645375.1	518897	518897	type	True	76.1805	82	1485	95	below_threshold
Pseudomonas lurida	strain=LMG 21995	GCA_002563895.1	244566	244566	type	True	76.177	79	1485	95	below_threshold
Alcanivorax limicola	strain=JB21	GCA_019931215.1	2874102	2874102	type	True	75.9867	67	1485	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:19:07,633] [INFO] DFAST Taxonomy check result was written to GCF_000423345.1_ASM42334v1_genomic.fna/tc_result.tsv
[2024-01-24 13:19:07,633] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:19:07,634] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:19:07,634] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb2893651-d927-45ea-8042-219130ce61b4/dqc_reference/checkm_data
[2024-01-24 13:19:07,635] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:19:07,681] [INFO] Task started: CheckM
[2024-01-24 13:19:07,681] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000423345.1_ASM42334v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000423345.1_ASM42334v1_genomic.fna/checkm_input GCF_000423345.1_ASM42334v1_genomic.fna/checkm_result
[2024-01-24 13:19:49,564] [INFO] Task succeeded: CheckM
[2024-01-24 13:19:49,565] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:19:49,584] [INFO] ===== Completeness check finished =====
[2024-01-24 13:19:49,584] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:19:49,585] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000423345.1_ASM42334v1_genomic.fna/markers.fasta)
[2024-01-24 13:19:49,585] [INFO] Task started: Blastn
[2024-01-24 13:19:49,585] [INFO] Running command: blastn -query GCF_000423345.1_ASM42334v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb2893651-d927-45ea-8042-219130ce61b4/dqc_reference/reference_markers_gtdb.fasta -out GCF_000423345.1_ASM42334v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:50,955] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:50,958] [INFO] Selected 22 target genomes.
[2024-01-24 13:19:50,958] [INFO] Target genome list was writen to GCF_000423345.1_ASM42334v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:19:50,975] [INFO] Task started: fastANI
[2024-01-24 13:19:50,975] [INFO] Running command: fastANI --query /var/lib/cwl/stgc3737632-b831-4015-ab55-47b6352b11f7/GCF_000423345.1_ASM42334v1_genomic.fna.gz --refList GCF_000423345.1_ASM42334v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000423345.1_ASM42334v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:20:10,782] [INFO] Task succeeded: fastANI
[2024-01-24 13:20:10,809] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:20:10,810] [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_000423345.1	s__Marinimicrobium agarilyticum	100.0	1482	1485	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Marinimicrobium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003762925.1	s__Marinimicrobium koreense	80.2079	667	1485	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Marinimicrobium	95.0	96.56	95.81	0.88	0.87	5	-
GCF_003259155.1	s__Marinimicrobium_A alkaliphilum	77.8267	258	1485	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_002959965.1	s__Microbulbifer pacificus	77.5886	129	1485	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Microbulbifer	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007183175.1	s__Microbulbifer sp007183175	77.547	62	1485	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Microbulbifer	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009931115.1	s__Microbulbifer hydrolyticus	77.5098	119	1485	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Microbulbifer	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000708675.1	s__Microbulbifer sp000708675	77.1999	110	1485	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Microbulbifer	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000305785.2	s__Simiduia agarivorans	76.9299	97	1485	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Simiduia	95.0	99.99	99.99	1.00	1.00	2	-
GCF_015182315.1	s__Cellvibrio polysaccharolyticus	76.9043	111	1485	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Cellvibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014904815.1	s__Microbulbifer taiwanensis	76.8953	138	1485	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Microbulbifer	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002162135.1	s__Cellvibrio sp002162135	76.848	135	1485	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Cellvibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014904735.1	s__Microbulbifer hainanensis	76.8333	119	1485	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Microbulbifer	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014191725.1	s__Microbulbifer rhizosphaerae	76.8003	147	1485	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Microbulbifer	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900107725.1	s__Microbulbifer marinus	76.6663	124	1485	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Microbulbifer	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003402235.1	s__Parahaliea mediterranea	76.6626	131	1485	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Parahaliea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011440395.1	s__Pseudomaricurvus alcaniphilus	76.4905	117	1485	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Pseudomaricurvus	95.0	98.35	98.35	0.88	0.88	2	-
GCF_007004655.1	s__Exilibacterium tricleocarpae	76.3259	116	1485	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Exilibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002197985.1	s__Pseudomonas_D aestusnigri	76.2572	87	1485	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	97.11	96.74	0.91	0.81	25	-
GCF_003789045.1	s__Marinobacter_A sp003789045	76.2261	83	1485	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter_A	95.0	97.70	97.70	0.91	0.91	2	-
GCF_014645375.1	s__Marinobacterium_A nitratireducens	76.1805	82	1485	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011683955.1	s__Pseudomaricurvus alkylphenolicus	75.997	100	1485	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Pseudomaricurvus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004327985.1	s__Marinobacter_A halodurans	75.991	85	1485	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:20:10,814] [INFO] GTDB search result was written to GCF_000423345.1_ASM42334v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:20:10,817] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:20:10,824] [INFO] DFAST_QC result json was written to GCF_000423345.1_ASM42334v1_genomic.fna/dqc_result.json
[2024-01-24 13:20:10,824] [INFO] DFAST_QC completed!
[2024-01-24 13:20:10,824] [INFO] Total running time: 0h1m37s