[2024-01-24 13:57:41,529] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:57:41,531] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:57:41,531] [INFO] DQC Reference Directory: /var/lib/cwl/stgf40f0cf6-0f2c-4098-8619-5131bc057ced/dqc_reference
[2024-01-24 13:57:42,871] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:57:42,873] [INFO] Task started: Prodigal
[2024-01-24 13:57:42,873] [INFO] Running command: gunzip -c /var/lib/cwl/stgabe13ee7-292f-460b-8598-d19a58db7be2/GCF_013374995.1_ASM1337499v1_genomic.fna.gz | prodigal -d GCF_013374995.1_ASM1337499v1_genomic.fna/cds.fna -a GCF_013374995.1_ASM1337499v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:58:09,102] [INFO] Task succeeded: Prodigal
[2024-01-24 13:58:09,102] [INFO] Task started: HMMsearch
[2024-01-24 13:58:09,102] [INFO] Running command: hmmsearch --tblout GCF_013374995.1_ASM1337499v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf40f0cf6-0f2c-4098-8619-5131bc057ced/dqc_reference/reference_markers.hmm GCF_013374995.1_ASM1337499v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:58:09,507] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:58:09,509] [INFO] Found 6/6 markers.
[2024-01-24 13:58:09,577] [INFO] Query marker FASTA was written to GCF_013374995.1_ASM1337499v1_genomic.fna/markers.fasta
[2024-01-24 13:58:09,578] [INFO] Task started: Blastn
[2024-01-24 13:58:09,578] [INFO] Running command: blastn -query GCF_013374995.1_ASM1337499v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf40f0cf6-0f2c-4098-8619-5131bc057ced/dqc_reference/reference_markers.fasta -out GCF_013374995.1_ASM1337499v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:10,748] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:10,752] [INFO] Selected 23 target genomes.
[2024-01-24 13:58:10,752] [INFO] Target genome list was writen to GCF_013374995.1_ASM1337499v1_genomic.fna/target_genomes.txt
[2024-01-24 13:58:10,773] [INFO] Task started: fastANI
[2024-01-24 13:58:10,773] [INFO] Running command: fastANI --query /var/lib/cwl/stgabe13ee7-292f-460b-8598-d19a58db7be2/GCF_013374995.1_ASM1337499v1_genomic.fna.gz --refList GCF_013374995.1_ASM1337499v1_genomic.fna/target_genomes.txt --output GCF_013374995.1_ASM1337499v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:58:42,516] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:42,517] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf40f0cf6-0f2c-4098-8619-5131bc057ced/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:58:42,517] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf40f0cf6-0f2c-4098-8619-5131bc057ced/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:58:42,534] [INFO] Found 23 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:58:42,535] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:58:42,535] [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
Pseudomonas eucalypticola	strain=NP-1	GCA_013374995.1	2599595	2599595	type	True	100.0	2133	2133	95	conclusive
Pseudomonas brassicae	strain=MAFF 212427	GCA_010671725.1	2708063	2708063	type	True	82.7797	843	2133	95	below_threshold
Pseudomonas ekonensis	strain=COR58	GCA_019145435.1	2842353	2842353	type	True	82.6952	1096	2133	95	below_threshold
Pseudomonas faucium	strain=BML-PP048	GCA_021602585.1	2740518	2740518	type	True	82.5411	1001	2133	95	below_threshold
Pseudomonas faucium	strain=BML-PP048	GCA_013373935.1	2740518	2740518	type	True	82.4779	976	2133	95	below_threshold
Pseudomonas japonica	strain=NBRC 103040	GCA_000730585.1	256466	256466	type	True	82.4397	1007	2133	95	below_threshold
Pseudomonas japonica	strain=DSM 22348	GCA_900188455.1	256466	256466	type	True	82.3706	998	2133	95	below_threshold
Pseudomonas chlororaphis subsp. aurantiaca	strain=DSM 19603	GCA_003851835.1	86192	587753	type	True	82.3678	1159	2133	95	below_threshold
Pseudomonas rhizosphaerae	strain=DSM 16299	GCA_000761155.1	216142	216142	type	True	82.3322	909	2133	95	below_threshold
Pseudomonas batumici	strain=UCM B-321	GCA_000820515.1	226910	226910	type	True	82.3115	984	2133	95	below_threshold
Pseudomonas coleopterorum	strain=LMG 28558	GCA_900105555.1	1605838	1605838	type	True	82.2985	926	2133	95	below_threshold
Pseudomonas alkylphenolica	strain=KL28	GCA_000746525.1	237609	237609	type	True	82.2734	927	2133	95	below_threshold
Pseudomonas baltica	strain=MBT-2	GCA_014235765.1	2762576	2762576	type	True	82.0328	906	2133	95	below_threshold
Pseudomonas kilonensis	strain=DSM 13647	GCA_001269885.1	132476	132476	type	True	81.9821	970	2133	95	below_threshold
Pseudomonas zanjanensis	strain=SWRI12	GCA_014268745.2	2745496	2745496	type	True	81.9205	956	2133	95	below_threshold
Pseudomonas urethralis	strain=BML-PP042	GCA_021602465.1	2740517	2740517	suspected-type	True	81.8926	989	2133	95	below_threshold
Pseudomonas sessilinigenes	strain=CMR12a	GCA_019139855.1	658629	658629	type	True	81.8488	1030	2133	95	below_threshold
Pseudomonas thivervalensis	strain=DSM 13194	GCA_001269655.1	86265	86265	type	True	81.8472	983	2133	95	below_threshold
Pseudomonas urethralis	strain=BML-PP042	GCA_013373915.1	2740517	2740517	suspected-type	True	81.7947	968	2133	95	below_threshold
Pseudomonas brassicacearum	strain=JCM 11938	GCA_012034345.1	930166	930166	suspected-type	True	81.7933	984	2133	95	below_threshold
Pseudomonas brassicacearum subsp. brassicacearum	strain=CCUG 51508	GCA_008801605.1	86264	930166	type	True	81.7876	993	2133	95	below_threshold
Pseudomonas capeferrum	strain=WCS358	GCA_022548835.1	1495066	1495066	type	True	81.7736	944	2133	95	below_threshold
Pseudomonas laurentiana	strain=JCM 32154	GCA_014648275.1	2364649	2364649	type	True	81.1314	820	2133	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:58:42,539] [INFO] DFAST Taxonomy check result was written to GCF_013374995.1_ASM1337499v1_genomic.fna/tc_result.tsv
[2024-01-24 13:58:42,540] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:58:42,540] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:58:42,541] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf40f0cf6-0f2c-4098-8619-5131bc057ced/dqc_reference/checkm_data
[2024-01-24 13:58:42,543] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:58:42,604] [INFO] Task started: CheckM
[2024-01-24 13:58:42,604] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013374995.1_ASM1337499v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013374995.1_ASM1337499v1_genomic.fna/checkm_input GCF_013374995.1_ASM1337499v1_genomic.fna/checkm_result
[2024-01-24 13:59:57,142] [INFO] Task succeeded: CheckM
[2024-01-24 13:59:57,143] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:59:57,165] [INFO] ===== Completeness check finished =====
[2024-01-24 13:59:57,166] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:59:57,166] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013374995.1_ASM1337499v1_genomic.fna/markers.fasta)
[2024-01-24 13:59:57,166] [INFO] Task started: Blastn
[2024-01-24 13:59:57,167] [INFO] Running command: blastn -query GCF_013374995.1_ASM1337499v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf40f0cf6-0f2c-4098-8619-5131bc057ced/dqc_reference/reference_markers_gtdb.fasta -out GCF_013374995.1_ASM1337499v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:59:59,138] [INFO] Task succeeded: Blastn
[2024-01-24 13:59:59,142] [INFO] Selected 15 target genomes.
[2024-01-24 13:59:59,142] [INFO] Target genome list was writen to GCF_013374995.1_ASM1337499v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:59:59,156] [INFO] Task started: fastANI
[2024-01-24 13:59:59,156] [INFO] Running command: fastANI --query /var/lib/cwl/stgabe13ee7-292f-460b-8598-d19a58db7be2/GCF_013374995.1_ASM1337499v1_genomic.fna.gz --refList GCF_013374995.1_ASM1337499v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013374995.1_ASM1337499v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:00:20,527] [INFO] Task succeeded: fastANI
[2024-01-24 14:00:20,552] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:00:20,553] [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_013374995.1	s__Pseudomonas_E eucalypticola	100.0	2133	2133	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.03	99.03	0.96	0.96	2	conclusive
GCA_000497835.1	s__Pseudomonas_E sp000497835	86.9108	1614	2133	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_000263855.1	s__Pseudomonas_E sp000263855	86.6473	1503	2133	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_900497695.1	s__Pseudomonas_E wadenswilerensis	82.6452	1020	2133	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.26	99.26	0.95	0.95	2	-
GCF_000259195.1	s__Pseudomonas_E donghuensis	82.603	992	2133	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.33	99.30	0.94	0.92	5	-
GCF_000800615.1	s__Pseudomonas_E putida_F	82.5787	1019	2133	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.83	99.76	0.97	0.96	3	-
GCF_003105155.1	s__Pseudomonas_E sp003105155	82.4466	915	2133	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_000761155.1	s__Pseudomonas_E rhizosphaerae	82.3577	905	2133	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.13	98.13	0.92	0.92	2	-
GCF_011355085.1	s__Pseudomonas_E sp011355085	82.2852	921	2133	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_900105555.1	s__Pseudomonas_E coleopterorum	82.2594	928	2133	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.66	96.53	0.90	0.88	9	-
GCF_000746525.1	s__Pseudomonas_E alkylphenolica	82.2532	924	2133	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.61	96.52	0.84	0.83	3	-
GCF_900187455.1	s__Pseudomonas_E sp900187455	82.1998	1050	2133	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_001269885.1	s__Pseudomonas_E kilonensis	81.9666	972	2133	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.12	95.91	0.90	0.87	15	-
GCA_002379585.1	s__Pseudomonas_E sp002379585	81.9111	919	2133	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_001269655.1	s__Pseudomonas_E thivervalensis	81.8752	976	2133	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.35	98.81	0.96	0.93	6	-
--------------------------------------------------------------------------------
[2024-01-24 14:00:20,555] [INFO] GTDB search result was written to GCF_013374995.1_ASM1337499v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:00:20,555] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:00:20,560] [INFO] DFAST_QC result json was written to GCF_013374995.1_ASM1337499v1_genomic.fna/dqc_result.json
[2024-01-24 14:00:20,560] [INFO] DFAST_QC completed!
[2024-01-24 14:00:20,561] [INFO] Total running time: 0h2m39s