[2024-01-24 12:44:43,210] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:44:43,213] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:44:43,213] [INFO] DQC Reference Directory: /var/lib/cwl/stg75948931-09a3-49a8-9e43-2d344bbeaffc/dqc_reference
[2024-01-24 12:44:44,612] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:44:44,613] [INFO] Task started: Prodigal
[2024-01-24 12:44:44,613] [INFO] Running command: gunzip -c /var/lib/cwl/stg54eaba7e-5066-4ecd-9e7a-b8a045f6b0c6/GCF_004348895.1_ASM434889v1_genomic.fna.gz | prodigal -d GCF_004348895.1_ASM434889v1_genomic.fna/cds.fna -a GCF_004348895.1_ASM434889v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:45:07,029] [INFO] Task succeeded: Prodigal
[2024-01-24 12:45:07,030] [INFO] Task started: HMMsearch
[2024-01-24 12:45:07,030] [INFO] Running command: hmmsearch --tblout GCF_004348895.1_ASM434889v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg75948931-09a3-49a8-9e43-2d344bbeaffc/dqc_reference/reference_markers.hmm GCF_004348895.1_ASM434889v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:45:07,440] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:45:07,441] [INFO] Found 6/6 markers.
[2024-01-24 12:45:07,512] [INFO] Query marker FASTA was written to GCF_004348895.1_ASM434889v1_genomic.fna/markers.fasta
[2024-01-24 12:45:07,513] [INFO] Task started: Blastn
[2024-01-24 12:45:07,513] [INFO] Running command: blastn -query GCF_004348895.1_ASM434889v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg75948931-09a3-49a8-9e43-2d344bbeaffc/dqc_reference/reference_markers.fasta -out GCF_004348895.1_ASM434889v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:45:08,475] [INFO] Task succeeded: Blastn
[2024-01-24 12:45:08,479] [INFO] Selected 21 target genomes.
[2024-01-24 12:45:08,479] [INFO] Target genome list was writen to GCF_004348895.1_ASM434889v1_genomic.fna/target_genomes.txt
[2024-01-24 12:45:08,488] [INFO] Task started: fastANI
[2024-01-24 12:45:08,488] [INFO] Running command: fastANI --query /var/lib/cwl/stg54eaba7e-5066-4ecd-9e7a-b8a045f6b0c6/GCF_004348895.1_ASM434889v1_genomic.fna.gz --refList GCF_004348895.1_ASM434889v1_genomic.fna/target_genomes.txt --output GCF_004348895.1_ASM434889v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:45:39,539] [INFO] Task succeeded: fastANI
[2024-01-24 12:45:39,540] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg75948931-09a3-49a8-9e43-2d344bbeaffc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:45:39,540] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg75948931-09a3-49a8-9e43-2d344bbeaffc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:45:39,559] [INFO] Found 21 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:45:39,560] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:45:39,560] [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 vancouverensis	strain=Dha-51	GCA_004348895.1	95300	95300	type	True	100.0	2102	2105	95	conclusive
Pseudomonas vancouverensis	strain=CCUG 49675	GCA_008801375.1	95300	95300	type	True	99.9993	2104	2105	95	conclusive
Pseudomonas jessenii	strain=DSM 17150	GCA_002236115.1	77298	77298	suspected-type	True	87.8518	1564	2105	95	below_threshold
Pseudomonas laurylsulfatiphila	strain=AP3_16	GCA_002934665.1	2011015	2011015	type	True	87.7976	1601	2105	95	below_threshold
Pseudomonas azerbaijanoriens	strain=SWRI123	GCA_019139795.1	2842350	2842350	type	True	87.7434	1539	2105	95	below_threshold
Pseudomonas laurylsulfativorans	strain=AP3_22	GCA_002906155.1	1943631	1943631	type	True	87.6976	1599	2105	95	below_threshold
Pseudomonas izuensis	strain=IzPS43_3003	GCA_009861505.1	2684212	2684212	type	True	86.6448	1529	2105	95	below_threshold
Pseudomonas reinekei	strain=MT1	GCA_001945365.1	395598	395598	type	True	86.5533	1449	2105	95	below_threshold
Pseudomonas reinekei	strain=CCUG 53116	GCA_008801455.1	395598	395598	type	True	86.5316	1448	2105	95	below_threshold
Pseudomonas sputi	strain=BML-PP014	GCA_021603585.1	2892325	2892325	type	True	86.0292	1347	2105	95	below_threshold
Pseudomonas pharyngis	strain=BML-PP036	GCA_021602345.1	2892333	2892333	type	True	85.9641	1423	2105	95	below_threshold
Pseudomonas neuropathica	strain=P155	GCA_015461835.1	2730425	2730425	type	True	85.2757	1401	2105	95	below_threshold
Pseudomonas tensinigenes	strain=ZA 5.3	GCA_014268445.2	2745511	2745511	type	True	85.2123	1405	2105	95	below_threshold
Pseudomonas germanica	strain=FIT28	GCA_019614655.1	2815720	2815720	type	True	85.1761	1410	2105	95	below_threshold
Pseudomonas iranensis	strain=SWRI54	GCA_014268585.2	2745503	2745503	type	True	85.1521	1344	2105	95	below_threshold
Pseudomonas hamedanensis	strain=SWRI65	GCA_014268595.2	2745504	2745504	type	True	84.78	1343	2105	95	below_threshold
Pseudomonas salmasensis	strain=SWRI126	GCA_014268375.2	2745514	2745514	type	True	83.2137	1165	2105	95	below_threshold
Pseudomonas lactis	strain=DSM 29167	GCA_001439845.1	1615674	1615674	type	True	83.1808	1148	2105	95	below_threshold
Pseudomonas fuscovaginae	strain=LMG 2158	GCA_900108595.1	50340	50340	suspected-type	True	82.976	1094	2105	95	below_threshold
Pseudomonas brassicae	strain=MAFF 212427	GCA_010671725.1	2708063	2708063	type	True	82.0875	848	2105	95	below_threshold
Pseudomonas peli	strain=DSM 17833	GCA_900099645.1	592361	592361	type	True	79.9672	599	2105	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:45:39,562] [INFO] DFAST Taxonomy check result was written to GCF_004348895.1_ASM434889v1_genomic.fna/tc_result.tsv
[2024-01-24 12:45:39,563] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:45:39,563] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:45:39,563] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg75948931-09a3-49a8-9e43-2d344bbeaffc/dqc_reference/checkm_data
[2024-01-24 12:45:39,565] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:45:39,624] [INFO] Task started: CheckM
[2024-01-24 12:45:39,624] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004348895.1_ASM434889v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004348895.1_ASM434889v1_genomic.fna/checkm_input GCF_004348895.1_ASM434889v1_genomic.fna/checkm_result
[2024-01-24 12:46:42,948] [INFO] Task succeeded: CheckM
[2024-01-24 12:46:42,950] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:46:42,975] [INFO] ===== Completeness check finished =====
[2024-01-24 12:46:42,976] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:46:42,976] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004348895.1_ASM434889v1_genomic.fna/markers.fasta)
[2024-01-24 12:46:42,977] [INFO] Task started: Blastn
[2024-01-24 12:46:42,977] [INFO] Running command: blastn -query GCF_004348895.1_ASM434889v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg75948931-09a3-49a8-9e43-2d344bbeaffc/dqc_reference/reference_markers_gtdb.fasta -out GCF_004348895.1_ASM434889v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:46:44,450] [INFO] Task succeeded: Blastn
[2024-01-24 12:46:44,455] [INFO] Selected 20 target genomes.
[2024-01-24 12:46:44,455] [INFO] Target genome list was writen to GCF_004348895.1_ASM434889v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:46:44,503] [INFO] Task started: fastANI
[2024-01-24 12:46:44,504] [INFO] Running command: fastANI --query /var/lib/cwl/stg54eaba7e-5066-4ecd-9e7a-b8a045f6b0c6/GCF_004348895.1_ASM434889v1_genomic.fna.gz --refList GCF_004348895.1_ASM434889v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004348895.1_ASM434889v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:47:13,818] [INFO] Task succeeded: fastANI
[2024-01-24 12:47:13,834] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:47:13,835] [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_004348895.1	s__Pseudomonas_E vancouverensis	100.0	2102	2105	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	100.00	100.00	1.00	1.00	3	conclusive
GCF_000282455.1	s__Pseudomonas_E sp000282455	87.9602	1474	2105	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_009764265.1	s__Pseudomonas_E sp009764265	87.9546	1600	2105	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	95.48	95.48	0.85	0.85	2	-
GCF_902498135.1	s__Pseudomonas_E fluorescens_BH	87.9237	1530	2105	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.39	98.07	0.87	0.86	3	-
GCF_000967965.1	s__Pseudomonas_E fluorescens_O	87.8948	1567	2105	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.01	99.01	0.96	0.96	2	-
GCF_002236115.1	s__Pseudomonas_E jessenii	87.8518	1564	2105	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.88	96.89	0.89	0.84	18	-
GCF_002934665.1	s__Pseudomonas_E laurylsulfatiphila	87.7989	1600	2105	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.04	95.74	0.86	0.82	13	-
GCF_002303925.1	s__Pseudomonas_E sp002303925	87.7559	1511	2105	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.04	99.04	0.91	0.91	2	-
GCF_016909445.1	s__Pseudomonas_E stutzeri_A	87.741	1534	2105	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.88	96.88	0.84	0.84	2	-
GCF_002906155.1	s__Pseudomonas_E laurylsulfativorans	87.7015	1598	2105	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_003053605.1	s__Pseudomonas_E sp003053605	87.608	1506	2105	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.75	96.54	0.88	0.80	4	-
GCF_003050925.1	s__Pseudomonas_E sp003050925	87.5155	1467	2105	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.23	96.92	0.93	0.89	3	-
GCF_002113375.1	s__Pseudomonas_E sp002113375	87.4989	1500	2105	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_900187615.1	s__Pseudomonas_E sp900187615	87.1043	1432	2105	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.27	99.27	0.93	0.93	2	-
GCF_001984065.1	s__Pseudomonas_E sp001984065	86.7205	1447	2105	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_004364415.1	s__Pseudomonas_E mandelii_D	86.0385	1466	2105	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_900187425.1	s__Pseudomonas_E sp900187425	86.0317	1446	2105	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	95.77	95.75	0.84	0.83	4	-
GCF_902497995.1	s__Pseudomonas_E fluorescens_BK	85.7269	1329	2105	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.06	99.06	0.89	0.89	2	-
GCF_017980685.1	s__Pseudomonas_E iridis	85.1302	1305	2105	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.83	96.38	0.88	0.86	9	-
GCF_002158995.1	s__Pseudomonas_E caspiana	80.5907	796	2105	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 12:47:13,837] [INFO] GTDB search result was written to GCF_004348895.1_ASM434889v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:47:13,838] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:47:13,843] [INFO] DFAST_QC result json was written to GCF_004348895.1_ASM434889v1_genomic.fna/dqc_result.json
[2024-01-24 12:47:13,843] [INFO] DFAST_QC completed!
[2024-01-24 12:47:13,843] [INFO] Total running time: 0h2m31s