[2024-01-24 13:37:25,953] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:37:25,954] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:37:25,955] [INFO] DQC Reference Directory: /var/lib/cwl/stg74685e1e-ffbb-4fcc-a992-a2d2399245a2/dqc_reference
[2024-01-24 13:37:27,211] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:37:27,212] [INFO] Task started: Prodigal
[2024-01-24 13:37:27,212] [INFO] Running command: gunzip -c /var/lib/cwl/stg19a85acd-c2e3-471c-b8c2-d6bbc78a168f/GCF_013385305.1_ASM1338530v1_genomic.fna.gz | prodigal -d GCF_013385305.1_ASM1338530v1_genomic.fna/cds.fna -a GCF_013385305.1_ASM1338530v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:37:42,404] [INFO] Task succeeded: Prodigal
[2024-01-24 13:37:42,404] [INFO] Task started: HMMsearch
[2024-01-24 13:37:42,405] [INFO] Running command: hmmsearch --tblout GCF_013385305.1_ASM1338530v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg74685e1e-ffbb-4fcc-a992-a2d2399245a2/dqc_reference/reference_markers.hmm GCF_013385305.1_ASM1338530v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:37:42,770] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:37:42,771] [INFO] Found 6/6 markers.
[2024-01-24 13:37:42,816] [INFO] Query marker FASTA was written to GCF_013385305.1_ASM1338530v1_genomic.fna/markers.fasta
[2024-01-24 13:37:42,817] [INFO] Task started: Blastn
[2024-01-24 13:37:42,817] [INFO] Running command: blastn -query GCF_013385305.1_ASM1338530v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg74685e1e-ffbb-4fcc-a992-a2d2399245a2/dqc_reference/reference_markers.fasta -out GCF_013385305.1_ASM1338530v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:37:43,627] [INFO] Task succeeded: Blastn
[2024-01-24 13:37:43,633] [INFO] Selected 17 target genomes.
[2024-01-24 13:37:43,634] [INFO] Target genome list was writen to GCF_013385305.1_ASM1338530v1_genomic.fna/target_genomes.txt
[2024-01-24 13:37:43,639] [INFO] Task started: fastANI
[2024-01-24 13:37:43,639] [INFO] Running command: fastANI --query /var/lib/cwl/stg19a85acd-c2e3-471c-b8c2-d6bbc78a168f/GCF_013385305.1_ASM1338530v1_genomic.fna.gz --refList GCF_013385305.1_ASM1338530v1_genomic.fna/target_genomes.txt --output GCF_013385305.1_ASM1338530v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:38:04,918] [INFO] Task succeeded: fastANI
[2024-01-24 13:38:04,919] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg74685e1e-ffbb-4fcc-a992-a2d2399245a2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:38:04,919] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg74685e1e-ffbb-4fcc-a992-a2d2399245a2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:38:04,930] [INFO] Found 17 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 13:38:04,930] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:38:04,930] [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 agarici	strain=IPO3740	GCA_013385305.1	46677	46677	type	True	100.0	1782	1785	95	conclusive
Pseudomonas agarici	strain=LMG 2112	GCA_900109755.1	46677	46677	type	True	99.9842	1773	1785	95	conclusive
Pseudomonas agarici	strain=NCPPB 2289	GCA_000280785.1	46677	46677	type	True	99.9199	1764	1785	95	conclusive
Pseudomonas fuscovaginae	strain=LMG 2158	GCA_900108595.1	50340	50340	suspected-type	True	84.944	1182	1785	95	below_threshold
Pseudomonas batumici	strain=UCM B-321	GCA_000820515.1	226910	226910	type	True	84.8913	1105	1785	95	below_threshold
Pseudomonas chlororaphis subsp. aureofaciens	strain=DSM 6698	GCA_003851905.1	587851	587753	type	True	83.249	1043	1785	95	below_threshold
Pseudomonas ekonensis	strain=COR58	GCA_019145435.1	2842353	2842353	type	True	82.7567	992	1785	95	below_threshold
Pseudomonas kribbensis	strain=46-2	GCA_003352185.1	1628086	1628086	type	True	82.5544	951	1785	95	below_threshold
Pseudomonas libanensis	strain=DSM 17149	GCA_001439685.1	75588	75588	type	True	81.9789	938	1785	95	below_threshold
Pseudomonas zeae	strain=OE 48.2	GCA_014268485.2	2745510	2745510	type	True	81.9248	936	1785	95	below_threshold
Pseudomonas germanica	strain=FIT28	GCA_019614655.1	2815720	2815720	type	True	81.7752	934	1785	95	below_threshold
Pseudomonas bharatica	strain=CSV86	GCA_000319305.2	2692112	2692112	type	True	81.0739	824	1785	95	below_threshold
Pseudomonas coleopterorum	strain=LMG 28558	GCA_900105555.1	1605838	1605838	type	True	80.7364	677	1785	95	below_threshold
Pseudomonas capeferrum	strain=WCS358	GCA_022548835.1	1495066	1495066	type	True	80.5135	723	1785	95	below_threshold
Pseudomonas ceruminis	strain=BML-PP028	GCA_013373895.1	2740516	2740516	type	True	80.3566	702	1785	95	below_threshold
Pseudomonas ceruminis	strain=BML-PP028	GCA_021602025.1	2740516	2740516	type	True	80.3496	719	1785	95	below_threshold
Pseudomonas cavernicola	strain=K1S02-6	GCA_003596405.1	2320866	2320866	type	True	79.6667	607	1785	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:38:04,931] [INFO] DFAST Taxonomy check result was written to GCF_013385305.1_ASM1338530v1_genomic.fna/tc_result.tsv
[2024-01-24 13:38:04,932] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:38:04,932] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:38:04,932] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg74685e1e-ffbb-4fcc-a992-a2d2399245a2/dqc_reference/checkm_data
[2024-01-24 13:38:04,933] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:38:04,982] [INFO] Task started: CheckM
[2024-01-24 13:38:04,982] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013385305.1_ASM1338530v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013385305.1_ASM1338530v1_genomic.fna/checkm_input GCF_013385305.1_ASM1338530v1_genomic.fna/checkm_result
[2024-01-24 13:38:47,835] [INFO] Task succeeded: CheckM
[2024-01-24 13:38:47,836] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:38:47,854] [INFO] ===== Completeness check finished =====
[2024-01-24 13:38:47,854] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:38:47,854] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013385305.1_ASM1338530v1_genomic.fna/markers.fasta)
[2024-01-24 13:38:47,854] [INFO] Task started: Blastn
[2024-01-24 13:38:47,854] [INFO] Running command: blastn -query GCF_013385305.1_ASM1338530v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg74685e1e-ffbb-4fcc-a992-a2d2399245a2/dqc_reference/reference_markers_gtdb.fasta -out GCF_013385305.1_ASM1338530v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:38:49,197] [INFO] Task succeeded: Blastn
[2024-01-24 13:38:49,200] [INFO] Selected 15 target genomes.
[2024-01-24 13:38:49,201] [INFO] Target genome list was writen to GCF_013385305.1_ASM1338530v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:38:49,218] [INFO] Task started: fastANI
[2024-01-24 13:38:49,219] [INFO] Running command: fastANI --query /var/lib/cwl/stg19a85acd-c2e3-471c-b8c2-d6bbc78a168f/GCF_013385305.1_ASM1338530v1_genomic.fna.gz --refList GCF_013385305.1_ASM1338530v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013385305.1_ASM1338530v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:39:12,798] [INFO] Task succeeded: fastANI
[2024-01-24 13:39:12,807] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:39:12,808] [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_900109755.1	s__Pseudomonas_E agarici	99.9842	1773	1785	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.73	99.34	0.97	0.94	5	conclusive
GCF_013385635.1	s__Pseudomonas_E gingeri_A	89.0054	1319	1785	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.63	99.24	0.97	0.93	14	-
GCF_013386115.1	s__Pseudomonas_E gingeri_B	88.9773	1340	1785	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.74	98.43	0.94	0.92	9	-
GCF_001293465.1	s__Pseudomonas_E fuscovaginae_B	85.1139	1194	1785	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.24	99.24	0.95	0.95	2	-
GCF_014268755.2	s__Pseudomonas_E sp014268755	85.0301	1181	1785	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_900105475.1	s__Pseudomonas_E asplenii	84.9384	1164	1785	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.96	97.58	0.90	0.87	7	-
GCF_000820515.1	s__Pseudomonas_E batumici	84.9005	1104	1785	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_013385425.1	s__Pseudomonas_E gingeri_D	84.7913	1177	1785	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.70	98.70	0.93	0.93	2	-
GCF_002814235.1	s__Pseudomonas_E sp002814235	84.7757	1204	1785	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.25	95.56	0.91	0.90	3	-
GCF_904067045.1	s__Pseudomonas_E sp904067045	84.5962	1122	1785	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_013386165.1	s__Pseudomonas_E gingeri_C	84.4901	1173	1785	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.61	98.31	0.93	0.92	4	-
GCF_000282475.1	s__Pseudomonas_E sp000282475	82.5405	913	1785	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	95.45	95.45	0.83	0.83	2	-
GCF_004519405.1	s__Pseudomonas_E sp004519405	81.9078	917	1785	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.60	98.40	0.98	0.92	5	-
GCF_013522705.1	s__Pseudomonas_E sp002383725	81.852	920	1785	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.07	99.06	0.96	0.95	3	-
GCF_004339665.1	s__Azotobacter chroococcum	78.8108	504	1785	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Azotobacter	95.0	97.27	96.18	0.89	0.83	10	-
--------------------------------------------------------------------------------
[2024-01-24 13:39:12,809] [INFO] GTDB search result was written to GCF_013385305.1_ASM1338530v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:39:12,809] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:39:12,812] [INFO] DFAST_QC result json was written to GCF_013385305.1_ASM1338530v1_genomic.fna/dqc_result.json
[2024-01-24 13:39:12,813] [INFO] DFAST_QC completed!
[2024-01-24 13:39:12,813] [INFO] Total running time: 0h1m47s