[2024-01-24 11:58:20,465] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:58:20,466] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:58:20,466] [INFO] DQC Reference Directory: /var/lib/cwl/stg2614f3f7-a97d-4f45-a214-f8f272d7b5f9/dqc_reference
[2024-01-24 11:58:21,671] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:58:21,672] [INFO] Task started: Prodigal
[2024-01-24 11:58:21,672] [INFO] Running command: gunzip -c /var/lib/cwl/stg09618655-8315-41a0-8b4d-0cae5f64cf88/GCF_023700005.1_ASM2370000v1_genomic.fna.gz | prodigal -d GCF_023700005.1_ASM2370000v1_genomic.fna/cds.fna -a GCF_023700005.1_ASM2370000v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:58:31,553] [INFO] Task succeeded: Prodigal
[2024-01-24 11:58:31,554] [INFO] Task started: HMMsearch
[2024-01-24 11:58:31,554] [INFO] Running command: hmmsearch --tblout GCF_023700005.1_ASM2370000v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2614f3f7-a97d-4f45-a214-f8f272d7b5f9/dqc_reference/reference_markers.hmm GCF_023700005.1_ASM2370000v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:58:31,806] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:58:31,807] [INFO] Found 6/6 markers.
[2024-01-24 11:58:31,840] [INFO] Query marker FASTA was written to GCF_023700005.1_ASM2370000v1_genomic.fna/markers.fasta
[2024-01-24 11:58:31,840] [INFO] Task started: Blastn
[2024-01-24 11:58:31,841] [INFO] Running command: blastn -query GCF_023700005.1_ASM2370000v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2614f3f7-a97d-4f45-a214-f8f272d7b5f9/dqc_reference/reference_markers.fasta -out GCF_023700005.1_ASM2370000v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:58:32,621] [INFO] Task succeeded: Blastn
[2024-01-24 11:58:32,625] [INFO] Selected 26 target genomes.
[2024-01-24 11:58:32,625] [INFO] Target genome list was writen to GCF_023700005.1_ASM2370000v1_genomic.fna/target_genomes.txt
[2024-01-24 11:58:32,687] [INFO] Task started: fastANI
[2024-01-24 11:58:32,687] [INFO] Running command: fastANI --query /var/lib/cwl/stg09618655-8315-41a0-8b4d-0cae5f64cf88/GCF_023700005.1_ASM2370000v1_genomic.fna.gz --refList GCF_023700005.1_ASM2370000v1_genomic.fna/target_genomes.txt --output GCF_023700005.1_ASM2370000v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:58:48,005] [INFO] Task succeeded: fastANI
[2024-01-24 11:58:48,006] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2614f3f7-a97d-4f45-a214-f8f272d7b5f9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:58:48,006] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2614f3f7-a97d-4f45-a214-f8f272d7b5f9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:58:48,025] [INFO] Found 22 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:58:48,025] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:58:48,025] [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	78.681	369	1094	95	below_threshold
Larsenimonas suaedae	strain=DSM 22428	GCA_023712105.1	1851019	1851019	type	True	78.5923	395	1094	95	below_threshold
Kushneria phyllosphaerae	strain=EAod3	GCA_900312995.1	2100822	2100822	type	True	78.0527	247	1094	95	below_threshold
Kushneria konosiri	strain=X49	GCA_002155145.1	698828	698828	type	True	78.0222	209	1094	95	below_threshold
Kushneria indalinina	strain=DSM 14324	GCA_003385845.1	184067	184067	type	True	78.0	241	1094	95	below_threshold
Kushneria pakistanensis	strain=KCTC 42082	GCA_014652795.1	1508770	1508770	type	True	77.9225	223	1094	95	below_threshold
Halomonas ilicicola	strain=DSM 19980	GCA_900128925.1	480814	480814	type	True	77.4183	140	1094	95	below_threshold
Halomonas urumqiensis	strain=BZ-SZ-XJ27	GCA_002879635.1	1684789	1684789	type	True	77.4137	118	1094	95	below_threshold
Halomonas pacifica	strain=NBRC 102220	GCA_007989625.1	77098	77098	type	True	77.3688	128	1094	95	below_threshold
Halomonas stenophila	strain=CECT 7744	GCA_014192275.1	795312	795312	type	True	77.3069	147	1094	95	below_threshold
Halomonas pantelleriensis	strain=AAP	GCA_900102875.1	48727	48727	type	True	77.2249	133	1094	95	below_threshold
Halomonas urumqiensis	strain=BZ-SZ-XJ27	GCA_003028575.1	1684789	1684789	type	True	77.1894	122	1094	95	below_threshold
Halomonas zhangzhouensis	strain=MCCC 1A11036	GCA_021404465.1	2733481	2733481	type	True	77.1797	118	1094	95	below_threshold
Cobetia marina	strain=JCM 21022	GCA_001720485.1	28258	28258	type	True	77.1692	182	1094	95	below_threshold
Halomonas elongata	strain=type strain: DSM 2581	GCA_000196875.2	2746	2746	type	True	77.1606	146	1094	95	below_threshold
Halomonas xinjiangensis	strain=TRM 0175	GCA_000759345.1	1166948	1166948	type	True	77.0681	130	1094	95	below_threshold
Kushneria sinocarnis	strain=DSM 23229	GCA_003633775.1	595502	595502	type	True	77.0638	193	1094	95	below_threshold
Halomonas qijiaojingensis	strain=KCTC 22228	GCA_014651875.1	980347	980347	type	True	76.9109	133	1094	95	below_threshold
Carnimonas nigrificans	strain=ATCC BAA-78	GCA_000526695.1	64323	64323	type	True	76.9008	81	1094	95	below_threshold
Pseudomonas nitrititolerans	strain=GL14	GCA_003696285.1	2482751	2482751	type	True	76.2844	62	1094	95	below_threshold
Pseudomonas insulae	strain=UL073	GCA_016901015.1	2809017	2809017	type	True	76.0779	71	1094	95	below_threshold
Pseudomonas viciae	strain=11K1	GCA_004786035.1	2505979	2505979	type	True	76.0599	50	1094	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:58:48,028] [INFO] DFAST Taxonomy check result was written to GCF_023700005.1_ASM2370000v1_genomic.fna/tc_result.tsv
[2024-01-24 11:58:48,029] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:58:48,029] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:58:48,029] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2614f3f7-a97d-4f45-a214-f8f272d7b5f9/dqc_reference/checkm_data
[2024-01-24 11:58:48,030] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:58:48,067] [INFO] Task started: CheckM
[2024-01-24 11:58:48,067] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_023700005.1_ASM2370000v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_023700005.1_ASM2370000v1_genomic.fna/checkm_input GCF_023700005.1_ASM2370000v1_genomic.fna/checkm_result
[2024-01-24 11:59:21,900] [INFO] Task succeeded: CheckM
[2024-01-24 11:59:21,901] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:59:21,920] [INFO] ===== Completeness check finished =====
[2024-01-24 11:59:21,920] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:59:21,921] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_023700005.1_ASM2370000v1_genomic.fna/markers.fasta)
[2024-01-24 11:59:21,921] [INFO] Task started: Blastn
[2024-01-24 11:59:21,921] [INFO] Running command: blastn -query GCF_023700005.1_ASM2370000v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2614f3f7-a97d-4f45-a214-f8f272d7b5f9/dqc_reference/reference_markers_gtdb.fasta -out GCF_023700005.1_ASM2370000v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:59:23,209] [INFO] Task succeeded: Blastn
[2024-01-24 11:59:23,213] [INFO] Selected 27 target genomes.
[2024-01-24 11:59:23,213] [INFO] Target genome list was writen to GCF_023700005.1_ASM2370000v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:59:23,250] [INFO] Task started: fastANI
[2024-01-24 11:59:23,251] [INFO] Running command: fastANI --query /var/lib/cwl/stg09618655-8315-41a0-8b4d-0cae5f64cf88/GCF_023700005.1_ASM2370000v1_genomic.fna.gz --refList GCF_023700005.1_ASM2370000v1_genomic.fna/target_genomes_gtdb.txt --output GCF_023700005.1_ASM2370000v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:59:38,956] [INFO] Task succeeded: fastANI
[2024-01-24 11:59:38,979] [INFO] Found 26 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 11:59:38,979] [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_900312995.1	s__Kushneria phyllosphaerae	78.0378	248	1094	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	78.015	240	1094	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Kushneria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002155145.1	s__Kushneria konosiri	78.0023	209	1094	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	77.9122	228	1094	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Kushneria	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014652795.1	s__Kushneria pakistanensis	77.8929	225	1094	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Kushneria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001545155.1	s__Halomonas chromatireducens	77.6387	117	1094	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900128925.1	s__Halomonas_C ilicicola	77.4306	138	1094	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_900113605.1	s__Halomonas_C xianhensis	77.4006	156	1094	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_003336675.1	s__Halomonas montanilacus	77.3977	133	1094	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001648175.1	s__Halotalea alkalilenta_A	77.3219	112	1094	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halotalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102875.1	s__Halomonas_B pantelleriensis	77.2427	132	1094	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013009075.1	s__Halomonas_B sp013009075	77.2188	127	1094	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas_B	95.0	99.96	99.96	1.00	0.99	3	-
GCF_008247605.1	s__Kushneria phosphatilytica	77.2121	164	1094	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Kushneria	95.0	99.98	99.98	1.00	1.00	2	-
GCF_001720485.1	s__Cobetia marina	77.1983	178	1094	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Cobetia	95.0	98.51	98.31	0.95	0.93	9	-
GCF_008274785.1	s__Halomonas eurihalina	77.1901	135	1094	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000196875.2	s__Halomonas elongata	77.1606	146	1094	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	98.75	98.56	0.95	0.92	4	-
GCF_000754225.1	s__Cobetia amphilecti	77.0858	164	1094	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Cobetia	95.0	96.77	95.09	0.91	0.86	19	-
GCF_000759345.1	s__Halomonas_A xinjiangensis	77.0851	129	1094	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_003633775.1	s__Kushneria sinocarnis	77.0638	193	1094	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Kushneria	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007129225.1	s__Halomonas sp007129225	76.9058	84	1094	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015645095.1	s__Halomonas_F sp015645095	76.903	143	1094	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas_F	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000526695.1	s__Carnimonas nigrificans	76.9008	81	1094	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Carnimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014651875.1	s__Halomonas_A qijiaojingensis	76.8955	132	1094	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_006540005.1	s__Halomonas halmophila	76.83	127	1094	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001507855.1	s__Halomonas sp001507855	76.7287	66	1094	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	99.98	99.98	0.98	0.98	2	-
GCF_003696285.1	s__Pseudomonas_A nitrititolerans	76.2844	62	1094	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	97.45	96.83	0.90	0.83	53	-
--------------------------------------------------------------------------------
[2024-01-24 11:59:38,981] [INFO] GTDB search result was written to GCF_023700005.1_ASM2370000v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:59:38,981] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:59:38,986] [INFO] DFAST_QC result json was written to GCF_023700005.1_ASM2370000v1_genomic.fna/dqc_result.json
[2024-01-24 11:59:38,987] [INFO] DFAST_QC completed!
[2024-01-24 11:59:38,987] [INFO] Total running time: 0h1m19s