[2024-01-24 13:41:10,346] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:41:10,347] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:41:10,348] [INFO] DQC Reference Directory: /var/lib/cwl/stg92f8f232-61d7-4d45-bfe4-4190138a942b/dqc_reference
[2024-01-24 13:41:11,800] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:41:11,801] [INFO] Task started: Prodigal
[2024-01-24 13:41:11,801] [INFO] Running command: gunzip -c /var/lib/cwl/stge3065fe4-a2a3-4c4f-ae5d-94fcc70dbe26/GCF_000425625.1_ASM42562v1_genomic.fna.gz | prodigal -d GCF_000425625.1_ASM42562v1_genomic.fna/cds.fna -a GCF_000425625.1_ASM42562v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:41:27,049] [INFO] Task succeeded: Prodigal
[2024-01-24 13:41:27,049] [INFO] Task started: HMMsearch
[2024-01-24 13:41:27,050] [INFO] Running command: hmmsearch --tblout GCF_000425625.1_ASM42562v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg92f8f232-61d7-4d45-bfe4-4190138a942b/dqc_reference/reference_markers.hmm GCF_000425625.1_ASM42562v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:41:27,431] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:41:27,433] [INFO] Found 6/6 markers.
[2024-01-24 13:41:27,478] [INFO] Query marker FASTA was written to GCF_000425625.1_ASM42562v1_genomic.fna/markers.fasta
[2024-01-24 13:41:27,479] [INFO] Task started: Blastn
[2024-01-24 13:41:27,479] [INFO] Running command: blastn -query GCF_000425625.1_ASM42562v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg92f8f232-61d7-4d45-bfe4-4190138a942b/dqc_reference/reference_markers.fasta -out GCF_000425625.1_ASM42562v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:28,745] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:28,748] [INFO] Selected 20 target genomes.
[2024-01-24 13:41:28,749] [INFO] Target genome list was writen to GCF_000425625.1_ASM42562v1_genomic.fna/target_genomes.txt
[2024-01-24 13:41:28,759] [INFO] Task started: fastANI
[2024-01-24 13:41:28,759] [INFO] Running command: fastANI --query /var/lib/cwl/stge3065fe4-a2a3-4c4f-ae5d-94fcc70dbe26/GCF_000425625.1_ASM42562v1_genomic.fna.gz --refList GCF_000425625.1_ASM42562v1_genomic.fna/target_genomes.txt --output GCF_000425625.1_ASM42562v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:51,560] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:51,561] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg92f8f232-61d7-4d45-bfe4-4190138a942b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:51,561] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg92f8f232-61d7-4d45-bfe4-4190138a942b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:51,580] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:41:51,580] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:41:51,580] [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
Stutzerimonas azotifigens	strain=DSM 17556	GCA_000425625.1	291995	291995	type	True	100.0	1636	1643	95	conclusive
[Pseudomonas] nosocomialis	strain=A31/70	GCA_005876855.1	1056496	1056496	type	True	84.0313	1010	1643	95	below_threshold
[Pseudomonas] urumqiensis	strain=T3	GCA_003640395.1	638269	638269	type	True	83.0187	929	1643	95	below_threshold
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	82.941	823	1643	95	below_threshold
Pseudomonas thermotolerans	strain=DSM 14292	GCA_000364625.1	157784	157784	type	True	82.7321	722	1643	95	below_threshold
Stutzerimonas stutzeri	strain=CGMCC 1.1803	GCA_000219605.1	316	316	type	True	82.6602	941	1643	95	below_threshold
Stutzerimonas stutzeri	strain=FDAARGOS_875	GCA_016028655.1	316	316	type	True	82.66	944	1643	95	below_threshold
Pseudomonas sagittaria	strain=JCM 18195	GCA_900115715.1	1135990	1135990	type	True	82.4522	740	1643	95	below_threshold
Stutzerimonas frequens	strain=DNSP21	GCA_024448335.1	2968969	2968969	type	True	82.4343	903	1643	95	below_threshold
Pseudomonas alcaligenes	strain=NBRC 14159	GCA_000467105.1	43263	43263	type	True	82.4154	790	1643	95	below_threshold
Stutzerimonas frequens	strain=FDAARGOS_877	GCA_016028515.1	2968969	2968969	type	True	82.3984	915	1643	95	below_threshold
Pseudomonas aromaticivorans	strain=MAP12	GCA_019097855.1	2849492	2849492	type	True	82.3979	689	1643	95	below_threshold
Stutzerimonas frequens	strain=DNSP21	GCA_002890935.1	2968969	2968969	type	True	82.3979	915	1643	95	below_threshold
Pseudomonas alcaligenes	strain=NCTC10367	GCA_900455475.1	43263	43263	type	True	82.394	792	1643	95	below_threshold
Pseudomonas nitrititolerans	strain=GL14	GCA_003696285.1	2482751	2482751	type	True	82.1042	885	1643	95	below_threshold
Pseudomonas guguanensis	strain=JCM 18416	GCA_900104265.1	1198456	1198456	type	True	82.0717	853	1643	95	below_threshold
Pseudomonas hydrolytica	strain=DSWY01	GCA_021495345.2	2493633	2493633	type	True	82.0236	891	1643	95	below_threshold
Pseudomonas mangiferae	strain=DMKU BBB3-04	GCA_007109405.1	2593654	2593654	type	True	81.7565	792	1643	95	below_threshold
Pseudomonas guryensis	strain=SR9	GCA_014164785.1	2759165	2759165	type	True	81.4118	714	1643	95	below_threshold
Pseudomonas ullengensis	strain=UL070	GCA_014174475.1	2759166	2759166	type	True	81.3761	760	1643	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:51,583] [INFO] DFAST Taxonomy check result was written to GCF_000425625.1_ASM42562v1_genomic.fna/tc_result.tsv
[2024-01-24 13:41:51,583] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:51,583] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:51,584] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg92f8f232-61d7-4d45-bfe4-4190138a942b/dqc_reference/checkm_data
[2024-01-24 13:41:51,585] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:51,638] [INFO] Task started: CheckM
[2024-01-24 13:41:51,638] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000425625.1_ASM42562v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000425625.1_ASM42562v1_genomic.fna/checkm_input GCF_000425625.1_ASM42562v1_genomic.fna/checkm_result
[2024-01-24 13:42:34,639] [INFO] Task succeeded: CheckM
[2024-01-24 13:42:34,640] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:42:34,664] [INFO] ===== Completeness check finished =====
[2024-01-24 13:42:34,664] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:42:34,664] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000425625.1_ASM42562v1_genomic.fna/markers.fasta)
[2024-01-24 13:42:34,665] [INFO] Task started: Blastn
[2024-01-24 13:42:34,665] [INFO] Running command: blastn -query GCF_000425625.1_ASM42562v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg92f8f232-61d7-4d45-bfe4-4190138a942b/dqc_reference/reference_markers_gtdb.fasta -out GCF_000425625.1_ASM42562v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:42:36,947] [INFO] Task succeeded: Blastn
[2024-01-24 13:42:36,952] [INFO] Selected 20 target genomes.
[2024-01-24 13:42:36,952] [INFO] Target genome list was writen to GCF_000425625.1_ASM42562v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:42:37,001] [INFO] Task started: fastANI
[2024-01-24 13:42:37,001] [INFO] Running command: fastANI --query /var/lib/cwl/stge3065fe4-a2a3-4c4f-ae5d-94fcc70dbe26/GCF_000425625.1_ASM42562v1_genomic.fna.gz --refList GCF_000425625.1_ASM42562v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000425625.1_ASM42562v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:42:58,442] [INFO] Task succeeded: fastANI
[2024-01-24 13:42:58,465] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:42:58,465] [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_000425625.1	s__Pseudomonas_N azotifigens	100.0	1636	1643	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_N	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_005876855.1	s__Pseudomonas_R nosocomialis	83.9937	1014	1643	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_R	95.0	98.98	98.95	0.91	0.90	3	-
GCF_002890915.1	s__Pseudomonas_A stutzeri_AF	83.9908	993	1643	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	98.35	98.08	0.91	0.89	3	-
GCF_015070855.1	s__Pseudomonas_A lopnurensis	83.8047	1005	1643	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	98.76	98.41	0.83	0.83	4	-
GCF_003640395.1	s__Pseudomonas_N urumqiensis	83.0198	931	1643	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_N	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003205495.1	s__Pseudomonas_E alcaligenes_B	82.9563	803	1643	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_018398425.1	s__Pseudomonas_E lalucatii	82.9133	826	1643	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.68	99.28	0.97	0.92	4	-
GCF_000219605.1	s__Pseudomonas_A stutzeri	82.6724	940	1643	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	97.69	96.98	0.90	0.83	156	-
GCF_009799925.1	s__Pseudomonas_E sp009799925	82.492	801	1643	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900766265.1	s__Pseudomonas_R sp900766265	82.4399	933	1643	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_R	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000467105.1	s__Pseudomonas_E alcaligenes	82.3885	793	1643	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.23	96.43	0.89	0.81	8	-
GCF_902506505.1	s__Pseudomonas_E sp902506505	82.3851	799	1643	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	95.45	95.45	0.88	0.88	2	-
GCF_005508865.1	s__Pseudomonas_E sp005508865	82.346	803	1643	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_003205815.1	s__Pseudomonas_A sp003205815	82.2725	913	1643	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	97.18	96.58	0.91	0.87	27	-
GCF_014490745.1	s__Pseudomonas_E alcaligenes_C	82.1063	802	1643	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_900156545.1	s__Pseudomonas_E alcaligenes_A	82.1026	769	1643	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	95.95	95.95	0.92	0.92	2	-
GCA_002339675.1	s__Pseudomonas_A stutzeri_O	81.955	935	1643	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004521985.1	s__Pseudomonas_E khazarica	81.8783	865	1643	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.35	98.01	0.91	0.87	12	-
GCF_007109405.1	s__VJOY01 sp007109405	81.7742	790	1643	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__VJOY01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014174475.1	s__Pseudomonas_E sp014174475	81.3544	763	1643	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:42:58,467] [INFO] GTDB search result was written to GCF_000425625.1_ASM42562v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:42:58,468] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:42:58,472] [INFO] DFAST_QC result json was written to GCF_000425625.1_ASM42562v1_genomic.fna/dqc_result.json
[2024-01-24 13:42:58,473] [INFO] DFAST_QC completed!
[2024-01-24 13:42:58,473] [INFO] Total running time: 0h1m48s