[2024-01-25 20:16:50,642] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:16:50,645] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:16:50,645] [INFO] DQC Reference Directory: /var/lib/cwl/stg97c59980-1c82-4a22-ad3c-436cb1039213/dqc_reference
[2024-01-25 20:16:51,764] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:16:51,765] [INFO] Task started: Prodigal
[2024-01-25 20:16:51,765] [INFO] Running command: gunzip -c /var/lib/cwl/stgef9a8758-2501-4753-88c5-3d5a019ed2bc/GCF_011369485.1_ASM1136948v1_genomic.fna.gz | prodigal -d GCF_011369485.1_ASM1136948v1_genomic.fna/cds.fna -a GCF_011369485.1_ASM1136948v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:17:13,044] [INFO] Task succeeded: Prodigal
[2024-01-25 20:17:13,044] [INFO] Task started: HMMsearch
[2024-01-25 20:17:13,044] [INFO] Running command: hmmsearch --tblout GCF_011369485.1_ASM1136948v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg97c59980-1c82-4a22-ad3c-436cb1039213/dqc_reference/reference_markers.hmm GCF_011369485.1_ASM1136948v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:17:13,330] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:17:13,331] [INFO] Found 6/6 markers.
[2024-01-25 20:17:13,396] [INFO] Query marker FASTA was written to GCF_011369485.1_ASM1136948v1_genomic.fna/markers.fasta
[2024-01-25 20:17:13,396] [INFO] Task started: Blastn
[2024-01-25 20:17:13,397] [INFO] Running command: blastn -query GCF_011369485.1_ASM1136948v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg97c59980-1c82-4a22-ad3c-436cb1039213/dqc_reference/reference_markers.fasta -out GCF_011369485.1_ASM1136948v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:17:14,338] [INFO] Task succeeded: Blastn
[2024-01-25 20:17:14,341] [INFO] Selected 18 target genomes.
[2024-01-25 20:17:14,341] [INFO] Target genome list was writen to GCF_011369485.1_ASM1136948v1_genomic.fna/target_genomes.txt
[2024-01-25 20:17:14,350] [INFO] Task started: fastANI
[2024-01-25 20:17:14,350] [INFO] Running command: fastANI --query /var/lib/cwl/stgef9a8758-2501-4753-88c5-3d5a019ed2bc/GCF_011369485.1_ASM1136948v1_genomic.fna.gz --refList GCF_011369485.1_ASM1136948v1_genomic.fna/target_genomes.txt --output GCF_011369485.1_ASM1136948v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:17:43,169] [INFO] Task succeeded: fastANI
[2024-01-25 20:17:43,169] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg97c59980-1c82-4a22-ad3c-436cb1039213/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:17:43,170] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg97c59980-1c82-4a22-ad3c-436cb1039213/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:17:43,181] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 20:17:43,181] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 20:17:43,181] [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 tensinigenes	strain=ZA 5.3	GCA_014268445.2	2745511	2745511	type	True	89.2931	1716	2006	95	below_threshold
Pseudomonas zeae	strain=OE 48.2	GCA_014268485.2	2745510	2745510	type	True	89.2591	1707	2006	95	below_threshold
Pseudomonas crudilactis	strain=UCMA 17988	GCA_013433315.1	2697028	2697028	type	True	89.2527	1713	2006	95	below_threshold
Pseudomonas neuropathica	strain=P155	GCA_015461835.1	2730425	2730425	type	True	89.2433	1714	2006	95	below_threshold
Pseudomonas germanica	strain=FIT28	GCA_019614655.1	2815720	2815720	type	True	89.1077	1730	2006	95	below_threshold
Pseudomonas baetica	strain=LMG 25716	GCA_002813455.1	674054	674054	type	True	89.0348	1665	2006	95	below_threshold
Pseudomonas baetica	strain=a390	GCA_003031005.1	674054	674054	type	True	88.9841	1627	2006	95	below_threshold
Pseudomonas monsensis	strain=PGSB 8459	GCA_014268495.2	2745509	2745509	type	True	88.9793	1682	2006	95	below_threshold
Pseudomonas koreensis	strain=JCM 14769	GCA_014646955.1	198620	198620	suspected-type	True	88.9636	1651	2006	95	below_threshold
Pseudomonas koreensis	strain=CCUG 51519	GCA_008801535.1	198620	198620	suspected-type	True	88.9124	1647	2006	95	below_threshold
Pseudomonas koreensis	strain=DSM 16610	GCA_012986595.1	198620	198620	suspected-type	True	88.9051	1670	2006	95	below_threshold
Pseudomonas allokribbensis	strain=IzPS23	GCA_014863605.1	2774460	2774460	type	True	88.8286	1671	2006	95	below_threshold
Pseudomonas pharyngis	strain=BML-PP036	GCA_021602345.1	2892333	2892333	type	True	88.7448	1651	2006	95	below_threshold
Pseudomonas sputi	strain=BML-PP014	GCA_021603585.1	2892325	2892325	type	True	88.6259	1599	2006	95	below_threshold
Pseudomonas granadensis	strain=LMG 27940	GCA_900105485.1	1421430	1421430	suspected-type	True	87.8701	1571	2006	95	below_threshold
Pseudomonas hamedanensis	strain=SWRI65	GCA_014268595.2	2745504	2745504	type	True	87.7867	1585	2006	95	below_threshold
Pseudomonas spelaei	strain=CCM 7893	GCA_009724245.1	1055469	1055469	type	True	83.027	1211	2006	95	below_threshold
Pseudomonas brassicae	strain=MAFF 212427	GCA_010671725.1	2708063	2708063	type	True	81.5542	834	2006	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:17:43,184] [INFO] DFAST Taxonomy check result was written to GCF_011369485.1_ASM1136948v1_genomic.fna/tc_result.tsv
[2024-01-25 20:17:43,185] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:17:43,185] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:17:43,185] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg97c59980-1c82-4a22-ad3c-436cb1039213/dqc_reference/checkm_data
[2024-01-25 20:17:43,186] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:17:43,244] [INFO] Task started: CheckM
[2024-01-25 20:17:43,244] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_011369485.1_ASM1136948v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_011369485.1_ASM1136948v1_genomic.fna/checkm_input GCF_011369485.1_ASM1136948v1_genomic.fna/checkm_result
[2024-01-25 20:18:47,750] [INFO] Task succeeded: CheckM
[2024-01-25 20:18:47,751] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:18:47,768] [INFO] ===== Completeness check finished =====
[2024-01-25 20:18:47,768] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:18:47,769] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_011369485.1_ASM1136948v1_genomic.fna/markers.fasta)
[2024-01-25 20:18:47,769] [INFO] Task started: Blastn
[2024-01-25 20:18:47,769] [INFO] Running command: blastn -query GCF_011369485.1_ASM1136948v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg97c59980-1c82-4a22-ad3c-436cb1039213/dqc_reference/reference_markers_gtdb.fasta -out GCF_011369485.1_ASM1136948v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:18:49,557] [INFO] Task succeeded: Blastn
[2024-01-25 20:18:49,559] [INFO] Selected 23 target genomes.
[2024-01-25 20:18:49,560] [INFO] Target genome list was writen to GCF_011369485.1_ASM1136948v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:18:49,588] [INFO] Task started: fastANI
[2024-01-25 20:18:49,588] [INFO] Running command: fastANI --query /var/lib/cwl/stgef9a8758-2501-4753-88c5-3d5a019ed2bc/GCF_011369485.1_ASM1136948v1_genomic.fna.gz --refList GCF_011369485.1_ASM1136948v1_genomic.fna/target_genomes_gtdb.txt --output GCF_011369485.1_ASM1136948v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:19:28,470] [INFO] Task succeeded: fastANI
[2024-01-25 20:19:28,483] [INFO] Found 23 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:19:28,484] [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_011369485.1	s__Pseudomonas_E sp011369485	100.0	2004	2006	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_016651305.1	s__Pseudomonas_E sp016651305	90.6308	1742	2006	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_018326005.1	s__Pseudomonas_E sp002901475	89.9841	1716	2006	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.45	98.45	0.94	0.94	2	-
GCF_003053805.1	s__Pseudomonas_E sp003053805	89.3664	1694	2006	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.38	98.38	0.96	0.96	2	-
GCF_018138145.1	s__Pseudomonas_E koreensis_A	89.3408	1723	2006	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.53	97.00	0.95	0.94	5	-
GCF_014268445.2	s__Pseudomonas_E sp900187515	89.2913	1717	2006	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.92	96.07	0.93	0.91	8	-
GCF_003732425.1	s__Pseudomonas_E fluorescens_BE	89.2792	1675	2006	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_000783395.1	s__Pseudomonas_E helmanticensis	89.2696	1712	2006	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	95.23	95.21	0.89	0.89	3	-
GCF_015461835.1	s__Pseudomonas_E neuropathica	89.2433	1714	2006	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.00	95.48	0.91	0.90	7	-
GCF_902497745.1	s__Pseudomonas_E fluorescens_BM	89.2369	1734	2006	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_005938625.1	s__Pseudomonas_E fluorescens_BD	89.2119	1705	2006	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_009764645.1	s__Pseudomonas_E sp009764645	89.1784	1538	2006	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_001269815.1	s__Pseudomonas_E sp001269815	89.1282	1626	2006	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.38	97.36	0.89	0.88	4	-
GCF_009834515.1	s__Pseudomonas_E sp009834515	89.1258	1720	2006	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_000282515.1	s__Pseudomonas_E sp000282515	89.1227	1618	2006	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.31	97.31	0.87	0.87	2	-
GCF_016650635.1	s__Pseudomonas_E sp016650635	89.0919	1713	2006	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.85	97.85	0.86	0.86	2	-
GCF_002813455.1	s__Pseudomonas_E baetica	89.0348	1665	2006	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.98	95.55	0.93	0.86	4	-
GCF_000282275.2	s__Pseudomonas_E sp000282275	89.0056	1679	2006	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_014268495.2	s__Pseudomonas_E fluorescens_BC	88.9784	1682	2006	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.66	98.66	0.95	0.95	2	-
GCF_002878485.1	s__Pseudomonas_E sp002878485	88.9552	1616	2006	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_014863585.1	s__Pseudomonas_E gozinkensis	88.9226	1686	2006	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_017980685.1	s__Pseudomonas_E iridis	88.5738	1549	2006	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.83	96.38	0.88	0.86	9	-
GCA_902825215.1	s__Pseudomonas_E fluorescens_G	88.0251	1576	2006	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.46	97.46	0.85	0.85	2	-
--------------------------------------------------------------------------------
[2024-01-25 20:19:28,485] [INFO] GTDB search result was written to GCF_011369485.1_ASM1136948v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:19:28,486] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:19:28,489] [INFO] DFAST_QC result json was written to GCF_011369485.1_ASM1136948v1_genomic.fna/dqc_result.json
[2024-01-25 20:19:28,490] [INFO] DFAST_QC completed!
[2024-01-25 20:19:28,490] [INFO] Total running time: 0h2m38s