[2023-06-27 03:24:58,201] [INFO] DFAST_QC pipeline started.
[2023-06-27 03:24:58,209] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 03:24:58,209] [INFO] DQC Reference Directory: /var/lib/cwl/stg4dfc723d-7580-487c-8283-9f546df80f4a/dqc_reference
[2023-06-27 03:24:59,476] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 03:24:59,477] [INFO] Task started: Prodigal
[2023-06-27 03:24:59,477] [INFO] Running command: gunzip -c /var/lib/cwl/stge75a9d6f-e79d-4c7c-8529-35fb4e7bc5fe/GCA_002416505.1_ASM241650v1_genomic.fna.gz | prodigal -d GCA_002416505.1_ASM241650v1_genomic.fna/cds.fna -a GCA_002416505.1_ASM241650v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 03:25:09,640] [INFO] Task succeeded: Prodigal
[2023-06-27 03:25:09,640] [INFO] Task started: HMMsearch
[2023-06-27 03:25:09,640] [INFO] Running command: hmmsearch --tblout GCA_002416505.1_ASM241650v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4dfc723d-7580-487c-8283-9f546df80f4a/dqc_reference/reference_markers.hmm GCA_002416505.1_ASM241650v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 03:25:09,922] [INFO] Task succeeded: HMMsearch
[2023-06-27 03:25:09,924] [INFO] Found 6/6 markers.
[2023-06-27 03:25:09,956] [INFO] Query marker FASTA was written to GCA_002416505.1_ASM241650v1_genomic.fna/markers.fasta
[2023-06-27 03:25:09,957] [INFO] Task started: Blastn
[2023-06-27 03:25:09,957] [INFO] Running command: blastn -query GCA_002416505.1_ASM241650v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4dfc723d-7580-487c-8283-9f546df80f4a/dqc_reference/reference_markers.fasta -out GCA_002416505.1_ASM241650v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 03:25:10,694] [INFO] Task succeeded: Blastn
[2023-06-27 03:25:10,699] [INFO] Selected 35 target genomes.
[2023-06-27 03:25:10,699] [INFO] Target genome list was writen to GCA_002416505.1_ASM241650v1_genomic.fna/target_genomes.txt
[2023-06-27 03:25:10,716] [INFO] Task started: fastANI
[2023-06-27 03:25:10,717] [INFO] Running command: fastANI --query /var/lib/cwl/stge75a9d6f-e79d-4c7c-8529-35fb4e7bc5fe/GCA_002416505.1_ASM241650v1_genomic.fna.gz --refList GCA_002416505.1_ASM241650v1_genomic.fna/target_genomes.txt --output GCA_002416505.1_ASM241650v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 03:25:32,724] [INFO] Task succeeded: fastANI
[2023-06-27 03:25:32,724] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4dfc723d-7580-487c-8283-9f546df80f4a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 03:25:32,724] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4dfc723d-7580-487c-8283-9f546df80f4a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 03:25:32,734] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 03:25:32,734] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-27 03:25:32,734] [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 cuatrocienegasensis	strain=CIP 109853	GCA_900110925.1	543360	543360	type	True	77.8587	62	1213	95	below_threshold
Pseudomonas alcaliphila	strain=NBRC 102411	GCA_002091495.1	101564	101564	type	True	77.6151	70	1213	95	below_threshold
Pseudomonas alcaliphila	strain=JCM 10630	GCA_900101755.1	101564	101564	type	True	77.5848	71	1213	95	below_threshold
Pseudomonas yangonensis	strain=MY50	GCA_009932725.1	2579922	2579922	type	True	77.4422	64	1213	95	below_threshold
Pseudomonas sediminis	strain=PI11	GCA_002741105.1	1691904	1691904	type	True	77.4121	64	1213	95	below_threshold
[Pseudomonas] nosocomialis	strain=A31/70	GCA_005876855.1	1056496	1056496	type	True	77.0893	58	1213	95	below_threshold
Pseudomonas panipatensis	strain=CCM 7469	GCA_900099785.1	428992	428992	type	True	77.0584	63	1213	95	below_threshold
Pseudomonas songnenensis	strain=DSM 27560T	GCA_024448495.1	1176259	1176259	type	True	76.8424	57	1213	95	below_threshold
Pseudomonas songnenensis	strain=NEAU-ST5-5	GCA_003696315.1	1176259	1176259	type	True	76.7695	57	1213	95	below_threshold
Stutzerimonas kunmingensis	strain=DSM 25974	GCA_024397575.1	1211807	1211807	type	True	76.6232	57	1213	95	below_threshold
Stutzerimonas chloritidismutans	strain=AW-1	GCA_000495915.1	203192	203192	type	True	76.3625	59	1213	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-27 03:25:32,736] [INFO] DFAST Taxonomy check result was written to GCA_002416505.1_ASM241650v1_genomic.fna/tc_result.tsv
[2023-06-27 03:25:32,737] [INFO] ===== Taxonomy check completed =====
[2023-06-27 03:25:32,737] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 03:25:32,737] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4dfc723d-7580-487c-8283-9f546df80f4a/dqc_reference/checkm_data
[2023-06-27 03:25:32,738] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 03:25:32,778] [INFO] Task started: CheckM
[2023-06-27 03:25:32,778] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_002416505.1_ASM241650v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_002416505.1_ASM241650v1_genomic.fna/checkm_input GCA_002416505.1_ASM241650v1_genomic.fna/checkm_result
[2023-06-27 03:26:06,450] [INFO] Task succeeded: CheckM
[2023-06-27 03:26:06,451] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 03:26:06,473] [INFO] ===== Completeness check finished =====
[2023-06-27 03:26:06,473] [INFO] ===== Start GTDB Search =====
[2023-06-27 03:26:06,473] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_002416505.1_ASM241650v1_genomic.fna/markers.fasta)
[2023-06-27 03:26:06,474] [INFO] Task started: Blastn
[2023-06-27 03:26:06,474] [INFO] Running command: blastn -query GCA_002416505.1_ASM241650v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4dfc723d-7580-487c-8283-9f546df80f4a/dqc_reference/reference_markers_gtdb.fasta -out GCA_002416505.1_ASM241650v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 03:26:07,619] [INFO] Task succeeded: Blastn
[2023-06-27 03:26:07,624] [INFO] Selected 24 target genomes.
[2023-06-27 03:26:07,624] [INFO] Target genome list was writen to GCA_002416505.1_ASM241650v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 03:26:07,649] [INFO] Task started: fastANI
[2023-06-27 03:26:07,649] [INFO] Running command: fastANI --query /var/lib/cwl/stge75a9d6f-e79d-4c7c-8529-35fb4e7bc5fe/GCA_002416505.1_ASM241650v1_genomic.fna.gz --refList GCA_002416505.1_ASM241650v1_genomic.fna/target_genomes_gtdb.txt --output GCA_002416505.1_ASM241650v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 03:26:21,427] [INFO] Task succeeded: fastANI
[2023-06-27 03:26:21,442] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-27 03:26:21,443] [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_002416505.1	s__UBA5078 sp002416505	100.0	1210	1213	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__UBA5078	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_009932725.1	s__Pseudomonas_E sp009932725	77.4422	64	1213	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.40	98.35	0.94	0.88	4	-
GCA_001802565.1	s__UBA5078 sp001802565	77.3824	229	1213	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__UBA5078	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903889815.1	s__UBA5078 sp903889815	77.1364	145	1213	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__UBA5078	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903862645.1	s__UBA5078 sp903862645	77.1082	182	1213	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__UBA5078	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005876855.1	s__Pseudomonas_R nosocomialis	77.09	59	1213	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_R	95.0	98.98	98.95	0.91	0.90	3	-
GCA_903876785.1	s__UBA5078 sp903876785	77.016	161	1213	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__UBA5078	95.0	99.18	99.13	0.80	0.78	4	-
GCF_000327065.1	s__Pseudomonas_A stutzeri_AE	76.6023	54	1213	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	97.70	97.56	0.93	0.91	3	-
GCA_003556835.1	s__PWQG01 sp003556835	76.3256	50	1213	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__PWQG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002706685.1	s__Pseudohongiella sp002706685	75.9067	59	1213	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__Pseudohongiella	95.0	99.93	99.90	0.98	0.96	5	-
GCA_002354805.1	s__Pseudohongiella sp002354805	75.8265	59	1213	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__Pseudohongiella	95.0	99.49	99.10	0.99	0.98	3	-
--------------------------------------------------------------------------------
[2023-06-27 03:26:21,445] [INFO] GTDB search result was written to GCA_002416505.1_ASM241650v1_genomic.fna/result_gtdb.tsv
[2023-06-27 03:26:21,445] [INFO] ===== GTDB Search completed =====
[2023-06-27 03:26:21,452] [INFO] DFAST_QC result json was written to GCA_002416505.1_ASM241650v1_genomic.fna/dqc_result.json
[2023-06-27 03:26:21,452] [INFO] DFAST_QC completed!
[2023-06-27 03:26:21,452] [INFO] Total running time: 0h1m23s