[2024-01-24 14:05:34,153] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:05:34,155] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:05:34,155] [INFO] DQC Reference Directory: /var/lib/cwl/stg9bf43162-7f06-4cf6-954c-3a29c89bed33/dqc_reference
[2024-01-24 14:05:35,364] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:05:35,365] [INFO] Task started: Prodigal
[2024-01-24 14:05:35,366] [INFO] Running command: gunzip -c /var/lib/cwl/stgb6e999c6-83f1-4590-9d1e-04b629cd0667/GCF_004786035.1_ASM478603v1_genomic.fna.gz | prodigal -d GCF_004786035.1_ASM478603v1_genomic.fna/cds.fna -a GCF_004786035.1_ASM478603v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:06:19,439] [INFO] Task succeeded: Prodigal
[2024-01-24 14:06:19,440] [INFO] Task started: HMMsearch
[2024-01-24 14:06:19,440] [INFO] Running command: hmmsearch --tblout GCF_004786035.1_ASM478603v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9bf43162-7f06-4cf6-954c-3a29c89bed33/dqc_reference/reference_markers.hmm GCF_004786035.1_ASM478603v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:06:19,738] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:06:19,739] [INFO] Found 6/6 markers.
[2024-01-24 14:06:19,788] [INFO] Query marker FASTA was written to GCF_004786035.1_ASM478603v1_genomic.fna/markers.fasta
[2024-01-24 14:06:19,789] [INFO] Task started: Blastn
[2024-01-24 14:06:19,789] [INFO] Running command: blastn -query GCF_004786035.1_ASM478603v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9bf43162-7f06-4cf6-954c-3a29c89bed33/dqc_reference/reference_markers.fasta -out GCF_004786035.1_ASM478603v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:20,726] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:20,729] [INFO] Selected 12 target genomes.
[2024-01-24 14:06:20,730] [INFO] Target genome list was writen to GCF_004786035.1_ASM478603v1_genomic.fna/target_genomes.txt
[2024-01-24 14:06:20,738] [INFO] Task started: fastANI
[2024-01-24 14:06:20,738] [INFO] Running command: fastANI --query /var/lib/cwl/stgb6e999c6-83f1-4590-9d1e-04b629cd0667/GCF_004786035.1_ASM478603v1_genomic.fna.gz --refList GCF_004786035.1_ASM478603v1_genomic.fna/target_genomes.txt --output GCF_004786035.1_ASM478603v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:06:41,718] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:41,719] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9bf43162-7f06-4cf6-954c-3a29c89bed33/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:06:41,719] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9bf43162-7f06-4cf6-954c-3a29c89bed33/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:06:41,730] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:06:41,731] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:06:41,731] [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 viciae	strain=11K1	GCA_004786035.1	2505979	2505979	type	True	100.0	2233	2234	95	conclusive
Pseudomonas bijieensis	strain=L22-9	GCA_013347965.1	2681983	2681983	type	True	90.5908	1805	2234	95	below_threshold
Pseudomonas kilonensis	strain=DSM 13647	GCA_001269885.1	132476	132476	type	True	90.3021	1724	2234	95	below_threshold
Pseudomonas brassicacearum	strain=JCM 11938	GCA_012034345.1	930166	930166	suspected-type	True	90.1066	1788	2234	95	below_threshold
Pseudomonas brassicacearum subsp. brassicacearum	strain=CCUG 51508	GCA_008801605.1	86264	930166	type	True	90.1008	1790	2234	95	below_threshold
Pseudomonas thivervalensis	strain=DSM 13194	GCA_001269655.1	86265	86265	type	True	89.4698	1753	2234	95	below_threshold
Pseudomonas rhizophila	strain=S211	GCA_003033885.1	2045200	2045200	type	True	89.0812	1651	2234	95	below_threshold
Pseudomonas tehranensis	strain=SWRI196	GCA_014268615.1	2745502	2745502	type	True	88.5453	1417	2234	95	below_threshold
Pseudomonas pharyngis	strain=BML-PP036	GCA_021602345.1	2892333	2892333	type	True	84.4013	1334	2234	95	below_threshold
Pseudomonas sputi	strain=BML-PP014	GCA_021603585.1	2892325	2892325	type	True	84.3839	1311	2234	95	below_threshold
Pseudomonas germanica	strain=FIT28	GCA_019614655.1	2815720	2815720	type	True	83.7529	1294	2234	95	below_threshold
Pseudomonas pergaminensis	strain=1008	GCA_024112395.1	2853159	2853159	type	True	83.3417	1216	2234	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:06:41,732] [INFO] DFAST Taxonomy check result was written to GCF_004786035.1_ASM478603v1_genomic.fna/tc_result.tsv
[2024-01-24 14:06:41,733] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:06:41,733] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:06:41,733] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9bf43162-7f06-4cf6-954c-3a29c89bed33/dqc_reference/checkm_data
[2024-01-24 14:06:41,734] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:06:41,795] [INFO] Task started: CheckM
[2024-01-24 14:06:41,796] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004786035.1_ASM478603v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004786035.1_ASM478603v1_genomic.fna/checkm_input GCF_004786035.1_ASM478603v1_genomic.fna/checkm_result
[2024-01-24 14:08:38,768] [INFO] Task succeeded: CheckM
[2024-01-24 14:08:38,770] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:08:38,789] [INFO] ===== Completeness check finished =====
[2024-01-24 14:08:38,789] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:08:38,789] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004786035.1_ASM478603v1_genomic.fna/markers.fasta)
[2024-01-24 14:08:38,789] [INFO] Task started: Blastn
[2024-01-24 14:08:38,790] [INFO] Running command: blastn -query GCF_004786035.1_ASM478603v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9bf43162-7f06-4cf6-954c-3a29c89bed33/dqc_reference/reference_markers_gtdb.fasta -out GCF_004786035.1_ASM478603v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:08:40,411] [INFO] Task succeeded: Blastn
[2024-01-24 14:08:40,414] [INFO] Selected 12 target genomes.
[2024-01-24 14:08:40,414] [INFO] Target genome list was writen to GCF_004786035.1_ASM478603v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:08:40,422] [INFO] Task started: fastANI
[2024-01-24 14:08:40,422] [INFO] Running command: fastANI --query /var/lib/cwl/stgb6e999c6-83f1-4590-9d1e-04b629cd0667/GCF_004786035.1_ASM478603v1_genomic.fna.gz --refList GCF_004786035.1_ASM478603v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004786035.1_ASM478603v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:09:02,723] [INFO] Task succeeded: fastANI
[2024-01-24 14:09:02,733] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:09:02,733] [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_004786035.1	s__Pseudomonas_E viciae	100.0	2233	2234	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_017968885.1	s__Pseudomonas_E sp017968885	92.9059	1966	2234	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_000585995.1	s__Pseudomonas_E brassicacearum_A	90.4014	1820	2234	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	95.55	95.52	0.86	0.84	3	-
GCF_001269885.1	s__Pseudomonas_E kilonensis	90.2998	1725	2234	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.12	95.91	0.90	0.87	15	-
GCF_008801605.1	s__Pseudomonas_E brassicacearum	90.1022	1790	2234	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.43	96.48	0.95	0.86	21	-
GCF_001623525.1	s__Pseudomonas_E fluorescens_Q	89.9648	1776	2234	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.03	97.11	0.90	0.89	14	-
GCF_900581005.1	s__Pseudomonas_E sp900581005	89.961	1729	2234	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_009601685.2	s__Pseudomonas_E kilonensis_B	89.9555	1774	2234	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.30	99.26	0.94	0.93	4	-
GCF_018325905.1	s__Pseudomonas_E sp018325905	89.8308	1753	2234	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_001307275.1	s__Pseudomonas_E fluorescens_AA	89.7031	1841	2234	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.99	95.90	0.90	0.85	18	-
GCF_003033885.1	s__Pseudomonas_E sp003033885	89.0875	1649	2234	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.90	98.67	0.93	0.91	8	-
GCF_900113505.1	s__Pseudomonas_E sp900113505	88.7115	1646	2234	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.10	95.53	0.86	0.83	12	-
--------------------------------------------------------------------------------
[2024-01-24 14:09:02,735] [INFO] GTDB search result was written to GCF_004786035.1_ASM478603v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:09:02,735] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:09:02,738] [INFO] DFAST_QC result json was written to GCF_004786035.1_ASM478603v1_genomic.fna/dqc_result.json
[2024-01-24 14:09:02,738] [INFO] DFAST_QC completed!
[2024-01-24 14:09:02,738] [INFO] Total running time: 0h3m29s