[2024-01-25 17:41:20,525] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:41:20,527] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:41:20,528] [INFO] DQC Reference Directory: /var/lib/cwl/stg25dad38e-648a-4a6a-adb6-f2056f07b3b1/dqc_reference
[2024-01-25 17:41:21,751] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:41:21,752] [INFO] Task started: Prodigal
[2024-01-25 17:41:21,752] [INFO] Running command: gunzip -c /var/lib/cwl/stg669861bc-6d06-47ac-872f-0204cb24c8f4/GCF_014191985.1_ASM1419198v1_genomic.fna.gz | prodigal -d GCF_014191985.1_ASM1419198v1_genomic.fna/cds.fna -a GCF_014191985.1_ASM1419198v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:41:33,067] [INFO] Task succeeded: Prodigal
[2024-01-25 17:41:33,068] [INFO] Task started: HMMsearch
[2024-01-25 17:41:33,068] [INFO] Running command: hmmsearch --tblout GCF_014191985.1_ASM1419198v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg25dad38e-648a-4a6a-adb6-f2056f07b3b1/dqc_reference/reference_markers.hmm GCF_014191985.1_ASM1419198v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:41:33,310] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:41:33,311] [INFO] Found 6/6 markers.
[2024-01-25 17:41:33,345] [INFO] Query marker FASTA was written to GCF_014191985.1_ASM1419198v1_genomic.fna/markers.fasta
[2024-01-25 17:41:33,345] [INFO] Task started: Blastn
[2024-01-25 17:41:33,345] [INFO] Running command: blastn -query GCF_014191985.1_ASM1419198v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg25dad38e-648a-4a6a-adb6-f2056f07b3b1/dqc_reference/reference_markers.fasta -out GCF_014191985.1_ASM1419198v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:41:34,147] [INFO] Task succeeded: Blastn
[2024-01-25 17:41:34,150] [INFO] Selected 29 target genomes.
[2024-01-25 17:41:34,150] [INFO] Target genome list was writen to GCF_014191985.1_ASM1419198v1_genomic.fna/target_genomes.txt
[2024-01-25 17:41:34,225] [INFO] Task started: fastANI
[2024-01-25 17:41:34,225] [INFO] Running command: fastANI --query /var/lib/cwl/stg669861bc-6d06-47ac-872f-0204cb24c8f4/GCF_014191985.1_ASM1419198v1_genomic.fna.gz --refList GCF_014191985.1_ASM1419198v1_genomic.fna/target_genomes.txt --output GCF_014191985.1_ASM1419198v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:41:58,109] [INFO] Task succeeded: fastANI
[2024-01-25 17:41:58,109] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg25dad38e-648a-4a6a-adb6-f2056f07b3b1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:41:58,109] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg25dad38e-648a-4a6a-adb6-f2056f07b3b1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:41:58,125] [INFO] Found 29 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 17:41:58,125] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 17:41:58,125] [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
Azotobacter chroococcum	strain=ATCC 9043	GCA_004327905.1	353	353	type	True	79.2067	415	1327	95	below_threshold
Azotobacter chroococcum subsp. isscasi	strain=P205	GCA_004327895.1	2528971	353	type	True	79.2057	422	1327	95	below_threshold
Pseudomonas indica	strain=JCM 21544	GCA_900100285.1	137658	137658	type	True	78.7734	349	1327	95	below_threshold
Pseudomonas indica	strain=NBRC 103045	GCA_002091635.1	137658	137658	type	True	78.7589	345	1327	95	below_threshold
[Pseudomonas] nosocomialis	strain=A31/70	GCA_005876855.1	1056496	1056496	type	True	78.6151	369	1327	95	below_threshold
Pseudomonas aromaticivorans	strain=MAP12	GCA_019097855.1	2849492	2849492	type	True	78.6073	325	1327	95	below_threshold
Stutzerimonas degradans	strain=DSM 50238	GCA_024448505.1	2968968	2968968	type	True	78.5734	373	1327	95	below_threshold
Stutzerimonas degradans	strain=FDAARGOS_876	GCA_016028635.1	2968968	2968968	suspected-type	True	78.5577	381	1327	95	below_threshold
Stutzerimonas degradans	strain=DSM 50238	GCA_002891015.1	2968968	2968968	type	True	78.5481	380	1327	95	below_threshold
Pseudomonas cavernae	strain=K2W31S-8	GCA_003595175.1	2320867	2320867	type	True	78.442	340	1327	95	below_threshold
Stutzerimonas stutzeri	strain=CGMCC 1.1803	GCA_000219605.1	316	316	type	True	78.4226	386	1327	95	below_threshold
Stutzerimonas stutzeri	strain=FDAARGOS_875	GCA_016028655.1	316	316	type	True	78.4215	386	1327	95	below_threshold
Pseudomonas mangiferae	strain=DMKU BBB3-04	GCA_007109405.1	2593654	2593654	type	True	78.4069	321	1327	95	below_threshold
Stutzerimonas frequens	strain=DNSP21	GCA_002890935.1	2968969	2968969	type	True	78.3879	366	1327	95	below_threshold
Pseudomonas alcaligenes	strain=NCTC10367	GCA_900455475.1	43263	43263	type	True	78.3859	333	1327	95	below_threshold
Pseudomonas fluvialis	strain=CCM 8778	GCA_014635625.1	1793966	1793966	suspected-type	True	78.363	266	1327	95	below_threshold
Pseudomonas alcaligenes	strain=NBRC 14159	GCA_000467105.1	43263	43263	type	True	78.3466	330	1327	95	below_threshold
Pseudomonas fluvialis	strain=ASS-1	GCA_002234375.1	1793966	1793966	suspected-type	True	78.342	262	1327	95	below_threshold
Stutzerimonas kunmingensis	strain=DSM 25974	GCA_900114065.1	1211807	1211807	type	True	78.3358	342	1327	95	below_threshold
Stutzerimonas kunmingensis	strain=DSM 25974	GCA_024397575.1	1211807	1211807	type	True	78.269	346	1327	95	below_threshold
Serpens gallinarum	strain=Sa2CUA2	GCA_014836765.1	2763075	2763075	type	True	77.9941	252	1327	95	below_threshold
Pseudomonas taeanensis	strain=MS-3	GCA_000498575.2	574962	574962	type	True	77.8307	287	1327	95	below_threshold
Pseudomonas peli	strain=DSM 17833	GCA_012986145.1	592361	592361	type	True	77.8015	258	1327	95	below_threshold
Pseudomonas peli	strain=DSM 17833	GCA_900099645.1	592361	592361	type	True	77.7591	264	1327	95	below_threshold
Pseudomonas ceruminis	strain=BML-PP028	GCA_013373895.1	2740516	2740516	type	True	77.7429	281	1327	95	below_threshold
Pseudomonas ceruminis	strain=BML-PP028	GCA_021602025.1	2740516	2740516	type	True	77.6316	286	1327	95	below_threshold
Pseudomonas baltica	strain=MBT-2	GCA_014235765.1	2762576	2762576	type	True	77.4899	273	1327	95	below_threshold
Pseudomonas pergaminensis	strain=1008	GCA_024112395.1	2853159	2853159	type	True	77.2719	272	1327	95	below_threshold
Marinobacter gudaonensis	strain=CGMCC 1.6294	GCA_900115175.1	375760	375760	type	True	76.0903	59	1327	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:41:58,127] [INFO] DFAST Taxonomy check result was written to GCF_014191985.1_ASM1419198v1_genomic.fna/tc_result.tsv
[2024-01-25 17:41:58,127] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:41:58,128] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:41:58,128] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg25dad38e-648a-4a6a-adb6-f2056f07b3b1/dqc_reference/checkm_data
[2024-01-25 17:41:58,128] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:41:58,169] [INFO] Task started: CheckM
[2024-01-25 17:41:58,169] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014191985.1_ASM1419198v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014191985.1_ASM1419198v1_genomic.fna/checkm_input GCF_014191985.1_ASM1419198v1_genomic.fna/checkm_result
[2024-01-25 17:42:33,088] [INFO] Task succeeded: CheckM
[2024-01-25 17:42:33,089] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:42:33,104] [INFO] ===== Completeness check finished =====
[2024-01-25 17:42:33,104] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:42:33,105] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014191985.1_ASM1419198v1_genomic.fna/markers.fasta)
[2024-01-25 17:42:33,105] [INFO] Task started: Blastn
[2024-01-25 17:42:33,105] [INFO] Running command: blastn -query GCF_014191985.1_ASM1419198v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg25dad38e-648a-4a6a-adb6-f2056f07b3b1/dqc_reference/reference_markers_gtdb.fasta -out GCF_014191985.1_ASM1419198v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:42:34,581] [INFO] Task succeeded: Blastn
[2024-01-25 17:42:34,585] [INFO] Selected 27 target genomes.
[2024-01-25 17:42:34,585] [INFO] Target genome list was writen to GCF_014191985.1_ASM1419198v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:42:34,608] [INFO] Task started: fastANI
[2024-01-25 17:42:34,608] [INFO] Running command: fastANI --query /var/lib/cwl/stg669861bc-6d06-47ac-872f-0204cb24c8f4/GCF_014191985.1_ASM1419198v1_genomic.fna.gz --refList GCF_014191985.1_ASM1419198v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014191985.1_ASM1419198v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:42:58,294] [INFO] Task succeeded: fastANI
[2024-01-25 17:42:58,309] [INFO] Found 27 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:42:58,309] [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_014191985.1	s__Azomonas macrocytogenes	100.0	1324	1327	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Azomonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_004339665.1	s__Azotobacter chroococcum	79.1988	418	1327	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Azotobacter	95.0	97.27	96.18	0.89	0.83	10	-
GCF_015070855.1	s__Pseudomonas_A lopnurensis	78.8616	417	1327	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	98.76	98.41	0.83	0.83	4	-
GCF_904061905.1	s__Pseudomonas_E carbonaria	78.7608	379	1327	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_000307775.2	s__Pseudomonas_A stutzeri_B	78.7583	390	1327	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	98.65	98.65	0.90	0.90	2	-
GCF_002091635.1	s__Pseudomonas_M indica	78.7535	346	1327	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_M	95.0	99.16	98.73	0.94	0.91	4	-
GCF_005844005.1	s__Pseudomonas_A sp000765155	78.7327	372	1327	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	98.19	98.01	0.92	0.89	5	-
GCF_002890915.1	s__Pseudomonas_A stutzeri_AF	78.6996	427	1327	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	98.35	98.08	0.91	0.89	3	-
GCF_004327335.1	s__Pseudomonas_Q kirkiae	78.6869	348	1327	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_Q	95.0	99.65	99.41	0.96	0.94	4	-
GCF_005876855.1	s__Pseudomonas_R nosocomialis	78.6265	368	1327	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_R	95.0	98.98	98.95	0.91	0.90	3	-
GCF_002286785.1	s__Pseudomonas_M sp002286785	78.6059	334	1327	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_M	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019097855.1	s__Pseudomonas_K sp019097855	78.5998	325	1327	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_K	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007109405.1	s__VJOY01 sp007109405	78.4193	320	1327	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__VJOY01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003205495.1	s__Pseudomonas_E alcaligenes_B	78.4139	343	1327	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_000219605.1	s__Pseudomonas_A stutzeri	78.403	388	1327	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	97.69	96.98	0.90	0.83	156	-
GCF_000467105.1	s__Pseudomonas_E alcaligenes	78.3813	327	1327	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.23	96.43	0.89	0.81	8	-
GCF_000364625.1	s__Pseudomonas_E thermotolerans	78.3604	302	1327	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.25	99.24	0.93	0.93	3	-
GCF_002234375.1	s__Pseudomonas_E fluvialis	78.342	262	1327	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.26	98.53	0.96	0.92	3	-
GCF_001592875.1	s__Pseudomonas_E sp001592875	78.2418	315	1327	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_007993865.1	s__Pseudomonas_E sp007993865	78.1834	292	1327	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_014207935.1	s__Pseudomonas_E fluvialis_A	78.1829	299	1327	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002418465.1	s__Pseudomonas_O sp002418465	78.1599	292	1327	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_O	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009789555.1	s__Pseudomonas_A stutzeri_R	78.0706	317	1327	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	99.81	99.81	0.96	0.96	2	-
GCA_019056435.1	s__Pseudomonas_A stutzeri_AM	78.0542	306	1327	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002339675.1	s__Pseudomonas_A stutzeri_O	78.0442	348	1327	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015163715.1	s__Pseudomonas_E cyclaminis	77.3253	240	1327	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.88	95.83	0.83	0.80	14	-
GCF_013778505.1	s__Pseudomonas_E sivasensis	77.2518	242	1327	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.92	98.83	0.93	0.91	13	-
--------------------------------------------------------------------------------
[2024-01-25 17:42:58,311] [INFO] GTDB search result was written to GCF_014191985.1_ASM1419198v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:42:58,312] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:42:58,316] [INFO] DFAST_QC result json was written to GCF_014191985.1_ASM1419198v1_genomic.fna/dqc_result.json
[2024-01-25 17:42:58,316] [INFO] DFAST_QC completed!
[2024-01-25 17:42:58,316] [INFO] Total running time: 0h1m38s