[2024-01-24 12:16:08,752] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:16:08,754] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:16:08,754] [INFO] DQC Reference Directory: /var/lib/cwl/stg1f8f68bd-6554-4a36-ae54-9197499f2851/dqc_reference
[2024-01-24 12:16:10,038] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:16:10,039] [INFO] Task started: Prodigal
[2024-01-24 12:16:10,040] [INFO] Running command: gunzip -c /var/lib/cwl/stg3a416ed3-188b-4c02-be49-a7fe61625e80/GCF_023736155.1_ASM2373615v1_genomic.fna.gz | prodigal -d GCF_023736155.1_ASM2373615v1_genomic.fna/cds.fna -a GCF_023736155.1_ASM2373615v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:16:19,607] [INFO] Task succeeded: Prodigal
[2024-01-24 12:16:19,608] [INFO] Task started: HMMsearch
[2024-01-24 12:16:19,608] [INFO] Running command: hmmsearch --tblout GCF_023736155.1_ASM2373615v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1f8f68bd-6554-4a36-ae54-9197499f2851/dqc_reference/reference_markers.hmm GCF_023736155.1_ASM2373615v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:16:19,880] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:16:19,881] [INFO] Found 6/6 markers.
[2024-01-24 12:16:19,911] [INFO] Query marker FASTA was written to GCF_023736155.1_ASM2373615v1_genomic.fna/markers.fasta
[2024-01-24 12:16:19,911] [INFO] Task started: Blastn
[2024-01-24 12:16:19,911] [INFO] Running command: blastn -query GCF_023736155.1_ASM2373615v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1f8f68bd-6554-4a36-ae54-9197499f2851/dqc_reference/reference_markers.fasta -out GCF_023736155.1_ASM2373615v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:16:20,748] [INFO] Task succeeded: Blastn
[2024-01-24 12:16:20,751] [INFO] Selected 22 target genomes.
[2024-01-24 12:16:20,752] [INFO] Target genome list was writen to GCF_023736155.1_ASM2373615v1_genomic.fna/target_genomes.txt
[2024-01-24 12:16:20,763] [INFO] Task started: fastANI
[2024-01-24 12:16:20,764] [INFO] Running command: fastANI --query /var/lib/cwl/stg3a416ed3-188b-4c02-be49-a7fe61625e80/GCF_023736155.1_ASM2373615v1_genomic.fna.gz --refList GCF_023736155.1_ASM2373615v1_genomic.fna/target_genomes.txt --output GCF_023736155.1_ASM2373615v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:16:35,595] [INFO] Task succeeded: fastANI
[2024-01-24 12:16:35,596] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1f8f68bd-6554-4a36-ae54-9197499f2851/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:16:35,596] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1f8f68bd-6554-4a36-ae54-9197499f2851/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:16:35,618] [INFO] Found 22 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:16:35,618] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 12:16:35,618] [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
Larsenimonas salina	strain=CCM 8464	GCA_023736155.1	1295565	1295565	type	True	100.0	1051	1053	95	inconclusive
Larsenimonas suaedae	strain=DSM 22428	GCA_023712105.1	1851019	1851019	type	True	95.422	959	1053	95	inconclusive
Kushneria konosiri	strain=X49	GCA_002155145.1	698828	698828	type	True	77.8989	240	1053	95	below_threshold
Kushneria indalinina	strain=DSM 14324	GCA_003385845.1	184067	184067	type	True	77.8381	254	1053	95	below_threshold
Kushneria avicenniae	strain=DSM 23439	GCA_900112585.1	402385	402385	type	True	77.7121	250	1053	95	below_threshold
Kushneria marisflavi	strain=DSM 15357	GCA_003610515.1	157779	157779	type	True	77.6917	247	1053	95	below_threshold
Kushneria marisflavi	strain=SW32	GCA_002157205.1	157779	157779	type	True	77.6888	239	1053	95	below_threshold
Cobetia marina	strain=JCM 21022	GCA_001720485.1	28258	28258	type	True	77.6589	197	1053	95	below_threshold
Kushneria phyllosphaerae	strain=EAod3	GCA_900312995.1	2100822	2100822	type	True	77.6568	249	1053	95	below_threshold
Salinicola endophyticus	strain=CPA92	GCA_003206575.1	1949083	1949083	type	True	77.6414	256	1053	95	below_threshold
Halomonas sulfidoxydans	strain=MCCC 1A11059	GCA_017868775.1	2733484	2733484	type	True	77.4141	199	1053	95	below_threshold
Halomonas lutea	strain=KCTC 12847	GCA_014651575.1	453962	453962	type	True	77.3926	157	1053	95	below_threshold
Halomonas lutea	strain=DSM 23508	GCA_000378505.1	453962	453962	type	True	77.3807	156	1053	95	below_threshold
Halomonas tianxiuensis	strain=BC-M4-5	GCA_009834345.1	2497861	2497861	type	True	77.3718	191	1053	95	below_threshold
Halomonas rituensis	strain=TQ8S	GCA_003336665.1	2282306	2282306	type	True	77.3696	119	1053	95	below_threshold
Halomonas kenyensis	strain=DSM 17331	GCA_022341445.1	321266	321266	type	True	77.3251	194	1053	95	below_threshold
Kushneria phosphatilytica	strain=YCWA18	GCA_008247605.1	657387	657387	type	True	77.2511	146	1053	95	below_threshold
Halomonas aestuarii	strain=Hb3	GCA_001886615.1	1897729	1897729	type	True	77.2373	180	1053	95	below_threshold
Kushneria phosphatilytica	strain=YCWA18	GCA_001854625.1	657387	657387	type	True	77.0806	144	1053	95	below_threshold
Halomonas xinjiangensis	strain=TRM 0175	GCA_000759345.1	1166948	1166948	type	True	77.0163	151	1053	95	below_threshold
Pseudomonas salmasensis	strain=SWRI126	GCA_014268375.2	2745514	2745514	type	True	76.3524	87	1053	95	below_threshold
Pseudomonas fuscovaginae	strain=LMG 2158	GCA_900108595.1	50340	50340	suspected-type	True	76.2174	94	1053	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:16:35,620] [INFO] DFAST Taxonomy check result was written to GCF_023736155.1_ASM2373615v1_genomic.fna/tc_result.tsv
[2024-01-24 12:16:35,621] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:16:35,621] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:16:35,621] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1f8f68bd-6554-4a36-ae54-9197499f2851/dqc_reference/checkm_data
[2024-01-24 12:16:35,622] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:16:35,661] [INFO] Task started: CheckM
[2024-01-24 12:16:35,662] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_023736155.1_ASM2373615v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_023736155.1_ASM2373615v1_genomic.fna/checkm_input GCF_023736155.1_ASM2373615v1_genomic.fna/checkm_result
[2024-01-24 12:17:07,987] [INFO] Task succeeded: CheckM
[2024-01-24 12:17:07,989] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:17:08,014] [INFO] ===== Completeness check finished =====
[2024-01-24 12:17:08,015] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:17:08,015] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_023736155.1_ASM2373615v1_genomic.fna/markers.fasta)
[2024-01-24 12:17:08,016] [INFO] Task started: Blastn
[2024-01-24 12:17:08,016] [INFO] Running command: blastn -query GCF_023736155.1_ASM2373615v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1f8f68bd-6554-4a36-ae54-9197499f2851/dqc_reference/reference_markers_gtdb.fasta -out GCF_023736155.1_ASM2373615v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:17:09,375] [INFO] Task succeeded: Blastn
[2024-01-24 12:17:09,379] [INFO] Selected 34 target genomes.
[2024-01-24 12:17:09,379] [INFO] Target genome list was writen to GCF_023736155.1_ASM2373615v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:17:09,412] [INFO] Task started: fastANI
[2024-01-24 12:17:09,413] [INFO] Running command: fastANI --query /var/lib/cwl/stg3a416ed3-188b-4c02-be49-a7fe61625e80/GCF_023736155.1_ASM2373615v1_genomic.fna.gz --refList GCF_023736155.1_ASM2373615v1_genomic.fna/target_genomes_gtdb.txt --output GCF_023736155.1_ASM2373615v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:17:31,088] [INFO] Task succeeded: fastANI
[2024-01-24 12:17:31,114] [INFO] Found 34 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:17:31,114] [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
GCA_000737985.1	s__Salinicola sp000737985	77.9262	258	1053	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Salinicola	95.0	96.18	96.18	0.88	0.88	2	-
GCF_002155145.1	s__Kushneria konosiri	77.8877	240	1053	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Kushneria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003385845.1	s__Kushneria indalinina	77.8078	255	1053	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Kushneria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002157205.1	s__Kushneria marisflavi	77.7058	238	1053	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Kushneria	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900112585.1	s__Kushneria avicenniae	77.7003	250	1053	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Kushneria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900312995.1	s__Kushneria phyllosphaerae	77.6879	245	1053	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Kushneria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001720485.1	s__Cobetia marina	77.6683	195	1053	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Cobetia	95.0	98.51	98.31	0.95	0.93	9	-
GCF_013349955.1	s__Halomonas_E taeanensis_B	77.6543	207	1053	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012062845.1	s__Halomonas_E sp012062845	77.6431	179	1053	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003206575.1	s__Salinicola endophyticus	77.6312	256	1053	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Salinicola	95.0	99.06	99.06	0.96	0.96	2	-
GCA_001577635.1	s__Halomonas_C sp001577635	77.5701	236	1053	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004117855.1	s__Halomonas_C coralii	77.5389	233	1053	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003006155.1	s__Salinicola tamaricis	77.5201	242	1053	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Salinicola	95.0	99.82	99.82	0.99	0.99	2	-
GCF_003206155.1	s__Salinicola halophilus	77.5097	213	1053	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Salinicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900113605.1	s__Halomonas_C xianhensis	77.4795	184	1053	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas_C	95.0	96.25	96.25	0.87	0.87	2	-
GCF_003206645.1	s__Salinicola aestuarinus	77.4402	194	1053	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Salinicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015992245.1	s__Halomonas sp015992245	77.4306	200	1053	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	99.35	99.35	0.94	0.94	2	-
GCF_010993675.1	s__Halomonas_C sp010993675	77.3975	241	1053	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003336665.1	s__Halomonas sp003336665	77.3744	117	1053	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000378505.1	s__Halomonas_C lutea	77.3477	155	1053	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas_C	95.0	99.99	99.99	0.99	0.99	2	-
GCF_008274785.1	s__Halomonas eurihalina	77.2993	164	1053	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011742165.1	s__Halomonas bachuensis	77.2871	179	1053	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003339685.1	s__Halomonas sp003339685	77.2784	136	1053	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008247605.1	s__Kushneria phosphatilytica	77.2745	144	1053	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Kushneria	95.0	99.98	99.98	1.00	1.00	2	-
GCF_009363755.1	s__Halomonas sp009363755	77.2739	205	1053	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001886615.1	s__Halomonas aestuarii	77.2683	178	1053	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001545155.1	s__Halomonas chromatireducens	77.2348	153	1053	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009902005.1	s__Halomonas alimentaria	77.1319	166	1053	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000759345.1	s__Halomonas_A xinjiangensis	77.0176	150	1053	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109725.1	s__Halomonas daqiaonensis	77.0081	151	1053	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004327355.1	s__Pseudomonas_E dryadis	76.6572	99	1053	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.58	99.16	0.96	0.92	3	-
GCF_002087235.1	s__Pseudomonas_E floridensis	76.3985	72	1053	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002814235.1	s__Pseudomonas_E sp002814235	76.3434	80	1053	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.25	95.56	0.91	0.90	3	-
GCA_002379585.1	s__Pseudomonas_E sp002379585	76.1162	65	1053	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:17:31,116] [INFO] GTDB search result was written to GCF_023736155.1_ASM2373615v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:17:31,117] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:17:31,125] [INFO] DFAST_QC result json was written to GCF_023736155.1_ASM2373615v1_genomic.fna/dqc_result.json
[2024-01-24 12:17:31,125] [INFO] DFAST_QC completed!
[2024-01-24 12:17:31,125] [INFO] Total running time: 0h1m22s