[2024-01-24 11:06:04,657] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:06:04,659] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:06:04,660] [INFO] DQC Reference Directory: /var/lib/cwl/stg03b5a292-dfe8-41c9-9348-54efaebf7229/dqc_reference
[2024-01-24 11:06:07,009] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:06:07,011] [INFO] Task started: Prodigal
[2024-01-24 11:06:07,011] [INFO] Running command: gunzip -c /var/lib/cwl/stgd9ac85da-2c03-4ec6-afc7-10f6268fde54/GCF_013179735.1_ASM1317973v1_genomic.fna.gz | prodigal -d GCF_013179735.1_ASM1317973v1_genomic.fna/cds.fna -a GCF_013179735.1_ASM1317973v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:06:21,670] [INFO] Task succeeded: Prodigal
[2024-01-24 11:06:21,670] [INFO] Task started: HMMsearch
[2024-01-24 11:06:21,671] [INFO] Running command: hmmsearch --tblout GCF_013179735.1_ASM1317973v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg03b5a292-dfe8-41c9-9348-54efaebf7229/dqc_reference/reference_markers.hmm GCF_013179735.1_ASM1317973v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:06:21,924] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:06:21,925] [INFO] Found 6/6 markers.
[2024-01-24 11:06:21,961] [INFO] Query marker FASTA was written to GCF_013179735.1_ASM1317973v1_genomic.fna/markers.fasta
[2024-01-24 11:06:21,961] [INFO] Task started: Blastn
[2024-01-24 11:06:21,961] [INFO] Running command: blastn -query GCF_013179735.1_ASM1317973v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg03b5a292-dfe8-41c9-9348-54efaebf7229/dqc_reference/reference_markers.fasta -out GCF_013179735.1_ASM1317973v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:06:22,793] [INFO] Task succeeded: Blastn
[2024-01-24 11:06:22,798] [INFO] Selected 30 target genomes.
[2024-01-24 11:06:22,798] [INFO] Target genome list was writen to GCF_013179735.1_ASM1317973v1_genomic.fna/target_genomes.txt
[2024-01-24 11:06:22,811] [INFO] Task started: fastANI
[2024-01-24 11:06:22,811] [INFO] Running command: fastANI --query /var/lib/cwl/stgd9ac85da-2c03-4ec6-afc7-10f6268fde54/GCF_013179735.1_ASM1317973v1_genomic.fna.gz --refList GCF_013179735.1_ASM1317973v1_genomic.fna/target_genomes.txt --output GCF_013179735.1_ASM1317973v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:06:43,228] [INFO] Task succeeded: fastANI
[2024-01-24 11:06:43,229] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg03b5a292-dfe8-41c9-9348-54efaebf7229/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:06:43,229] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg03b5a292-dfe8-41c9-9348-54efaebf7229/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:06:43,251] [INFO] Found 24 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:06:43,251] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:06:43,252] [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
Permianibacter fluminis	strain=IMCC34836	GCA_013179735.1	2738515	2738515	type	True	100.0	1450	1451	95	conclusive
Permianibacter aggregans	strain=DSM 103792	GCA_004363125.1	1510150	1510150	type	True	77.6196	334	1451	95	below_threshold
Permianibacter aggregans	strain=HW001	GCA_009756665.1	1510150	1510150	type	True	77.5593	347	1451	95	below_threshold
Pseudomonas carbonaria	strain=CIP 111764	GCA_904061905.1	2762745	2762745	type	True	76.3419	101	1451	95	below_threshold
Pseudomonas oryzae	strain=KCTC 32247	GCA_900104805.1	1392877	1392877	type	True	76.2026	114	1451	95	below_threshold
Pseudomonas alcaliphila	strain=NBRC 102411	GCA_002091495.1	101564	101564	type	True	76.1247	103	1451	95	below_threshold
Pseudomonas sagittaria	strain=JCM 18195	GCA_900115715.1	1135990	1135990	type	True	76.1137	123	1451	95	below_threshold
Pseudomonas alcaliphila	strain=JCM 10630	GCA_900101755.1	101564	101564	type	True	76.113	102	1451	95	below_threshold
Pseudomonas tensinigenes	strain=ZA 5.3	GCA_014268445.2	2745511	2745511	type	True	76.1063	89	1451	95	below_threshold
Pseudomonas khorasanensis	strain=SWRI153	GCA_014268505.2	2745508	2745508	type	True	76.0571	87	1451	95	below_threshold
Stutzerimonas azotifigens	strain=DSM 17556	GCA_000425625.1	291995	291995	type	True	76.0504	101	1451	95	below_threshold
Luteimonas gilva	strain=H23	GCA_005239095.1	2572684	2572684	type	True	76.0078	80	1451	95	below_threshold
Dyella amyloliquefaciens	strain=DHC06	GCA_004296575.1	1770545	1770545	type	True	76.0034	92	1451	95	below_threshold
Pseudomonas nicosulfuronedens	strain=LAM1902	GCA_005877905.1	2571105	2571105	type	True	75.9791	108	1451	95	below_threshold
Dyella kyungheensis	strain=THG-B117	GCA_016905005.1	1242174	1242174	type	True	75.9544	80	1451	95	below_threshold
Pseudomonas parafulva	strain=DSM 17004	GCA_000425765.1	157782	157782	suspected-type	True	75.9489	68	1451	95	below_threshold
Pseudomonas fakonensis	strain=COW40	GCA_019139895.1	2842355	2842355	type	True	75.9469	120	1451	95	below_threshold
Pseudomonas aeruginosa	strain=DSM 50071	GCA_012987025.1	287	287	type	True	75.9273	109	1451	95	below_threshold
Luteimonas lumbrici	strain=1.1416	GCA_006476065.1	2559601	2559601	type	True	75.8376	70	1451	95	below_threshold
Luteimonas aquatica	strain=RIB1-20	GCA_022662575.1	450364	450364	type	True	75.8202	90	1451	95	below_threshold
Pseudomonas aeruginosa	strain=DSM 50071	GCA_900167195.1	287	287	type	True	75.8113	111	1451	95	below_threshold
Pseudomonas psychrotolerans	strain=DSM 15758	GCA_900102665.1	237610	237610	suspected-type	True	75.6432	102	1451	95	below_threshold
Frateuria terrea	strain=DSM 26515	GCA_900109025.1	529704	529704	type	True	75.4851	69	1451	95	below_threshold
Frateuria terrea	strain=CGMCC 1.7053	GCA_900115705.1	529704	529704	type	True	75.2851	68	1451	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:06:43,253] [INFO] DFAST Taxonomy check result was written to GCF_013179735.1_ASM1317973v1_genomic.fna/tc_result.tsv
[2024-01-24 11:06:43,254] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:06:43,254] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:06:43,254] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg03b5a292-dfe8-41c9-9348-54efaebf7229/dqc_reference/checkm_data
[2024-01-24 11:06:43,255] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:06:43,295] [INFO] Task started: CheckM
[2024-01-24 11:06:43,295] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013179735.1_ASM1317973v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013179735.1_ASM1317973v1_genomic.fna/checkm_input GCF_013179735.1_ASM1317973v1_genomic.fna/checkm_result
[2024-01-24 11:07:28,896] [INFO] Task succeeded: CheckM
[2024-01-24 11:07:28,897] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:07:28,912] [INFO] ===== Completeness check finished =====
[2024-01-24 11:07:28,913] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:07:28,913] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013179735.1_ASM1317973v1_genomic.fna/markers.fasta)
[2024-01-24 11:07:28,913] [INFO] Task started: Blastn
[2024-01-24 11:07:28,914] [INFO] Running command: blastn -query GCF_013179735.1_ASM1317973v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg03b5a292-dfe8-41c9-9348-54efaebf7229/dqc_reference/reference_markers_gtdb.fasta -out GCF_013179735.1_ASM1317973v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:07:30,352] [INFO] Task succeeded: Blastn
[2024-01-24 11:07:30,356] [INFO] Selected 28 target genomes.
[2024-01-24 11:07:30,357] [INFO] Target genome list was writen to GCF_013179735.1_ASM1317973v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:07:30,404] [INFO] Task started: fastANI
[2024-01-24 11:07:30,405] [INFO] Running command: fastANI --query /var/lib/cwl/stgd9ac85da-2c03-4ec6-afc7-10f6268fde54/GCF_013179735.1_ASM1317973v1_genomic.fna.gz --refList GCF_013179735.1_ASM1317973v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013179735.1_ASM1317973v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:07:50,150] [INFO] Task succeeded: fastANI
[2024-01-24 11:07:50,172] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:07:50,172] [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_013179735.1	s__Permianibacter fluminis	100.0	1450	1451	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__DSM-103792;g__Permianibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_009756665.1	s__Permianibacter aggregans	77.5593	347	1451	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__DSM-103792;g__Permianibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCA_016182845.1	s__JACPFT01 sp016182845	76.2831	117	1451	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__DSM-103792;g__JACPFT01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902506495.1	s__Pseudomonas_E sp902506495	76.2469	97	1451	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.72	95.94	0.90	0.87	3	-
GCF_900104805.1	s__Pseudomonas_K oryzae	76.2308	112	1451	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_015680705.1	s__Pseudomonas_E fulva_C	76.1814	78	1451	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_004011755.1	s__Pseudomonas_E sp004011755	76.1813	98	1451	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.20	98.13	0.94	0.93	4	-
GCF_017491605.1	s__Pseudomonas sp017491605	76.1187	101	1451	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004801855.1	s__Pseudomonas_K sp004801855	76.1059	118	1451	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_K	95.0	98.38	98.38	0.89	0.89	2	-
GCF_000017205.1	s__Pseudomonas aeruginosa_A	76.0768	105	1451	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.0	99.07	98.78	0.93	0.80	42	-
GCF_000955805.1	s__Pseudomonas sp000955805	76.0114	108	1451	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.0	99.94	99.94	0.99	0.99	2	-
GCF_004296575.1	s__Dyella sp004296575	76.0034	92	1451	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000420045.1	s__Perlucidibaca piscinae	75.9818	75	1451	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Perlucidibaca	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000632805.1	s__Dyella jiangningensis	75.9717	80	1451	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002452115.1	s__Pseudomonas nitroreducens_B	75.9561	86	1451	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000313755.1	s__Pseudomonas nitroreducens_A	75.9362	114	1451	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.0	96.60	96.60	0.86	0.86	2	-
GCA_014654535.1	s__Pseudomonas_S boreopolis	75.8786	92	1451	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudomonas_S	95.0	98.68	98.68	0.91	0.91	2	-
GCF_013523125.1	s__Pseudomonas_E entomophila_B	75.8549	84	1451	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_001457615.1	s__Pseudomonas aeruginosa	75.8417	111	1451	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.0	99.12	97.38	0.94	0.84	5623	-
GCF_016586165.1	s__Dyella sp016586165	75.8292	89	1451	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900115705.1	s__Frateuria_A terrea	75.2851	68	1451	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Frateuria_A	95.0	100.00	100.00	1.00	1.00	2	-
GCA_002376325.1	s__Sulfurivermis sp002376325	75.1441	54	1451	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiohalomonadales;f__Thiohalomonadaceae;g__Sulfurivermis	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:07:50,174] [INFO] GTDB search result was written to GCF_013179735.1_ASM1317973v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:07:50,175] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:07:50,181] [INFO] DFAST_QC result json was written to GCF_013179735.1_ASM1317973v1_genomic.fna/dqc_result.json
[2024-01-24 11:07:50,181] [INFO] DFAST_QC completed!
[2024-01-24 11:07:50,182] [INFO] Total running time: 0h1m46s