[2024-01-24 15:26:55,160] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:26:55,162] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:26:55,162] [INFO] DQC Reference Directory: /var/lib/cwl/stgfb8522c5-7565-458a-94e6-ca5f1fc08409/dqc_reference
[2024-01-24 15:26:56,584] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:26:56,585] [INFO] Task started: Prodigal
[2024-01-24 15:26:56,586] [INFO] Running command: gunzip -c /var/lib/cwl/stg7bc679e0-e7a8-4895-9906-c83aa10c2e9a/GCF_014268505.2_ASM1426850v2_genomic.fna.gz | prodigal -d GCF_014268505.2_ASM1426850v2_genomic.fna/cds.fna -a GCF_014268505.2_ASM1426850v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:27:15,622] [INFO] Task succeeded: Prodigal
[2024-01-24 15:27:15,622] [INFO] Task started: HMMsearch
[2024-01-24 15:27:15,622] [INFO] Running command: hmmsearch --tblout GCF_014268505.2_ASM1426850v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfb8522c5-7565-458a-94e6-ca5f1fc08409/dqc_reference/reference_markers.hmm GCF_014268505.2_ASM1426850v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:27:15,996] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:27:15,997] [INFO] Found 6/6 markers.
[2024-01-24 15:27:16,042] [INFO] Query marker FASTA was written to GCF_014268505.2_ASM1426850v2_genomic.fna/markers.fasta
[2024-01-24 15:27:16,042] [INFO] Task started: Blastn
[2024-01-24 15:27:16,042] [INFO] Running command: blastn -query GCF_014268505.2_ASM1426850v2_genomic.fna/markers.fasta -db /var/lib/cwl/stgfb8522c5-7565-458a-94e6-ca5f1fc08409/dqc_reference/reference_markers.fasta -out GCF_014268505.2_ASM1426850v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:27:17,039] [INFO] Task succeeded: Blastn
[2024-01-24 15:27:17,049] [INFO] Selected 19 target genomes.
[2024-01-24 15:27:17,049] [INFO] Target genome list was writen to GCF_014268505.2_ASM1426850v2_genomic.fna/target_genomes.txt
[2024-01-24 15:27:17,057] [INFO] Task started: fastANI
[2024-01-24 15:27:17,057] [INFO] Running command: fastANI --query /var/lib/cwl/stg7bc679e0-e7a8-4895-9906-c83aa10c2e9a/GCF_014268505.2_ASM1426850v2_genomic.fna.gz --refList GCF_014268505.2_ASM1426850v2_genomic.fna/target_genomes.txt --output GCF_014268505.2_ASM1426850v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:27:47,200] [INFO] Task succeeded: fastANI
[2024-01-24 15:27:47,201] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfb8522c5-7565-458a-94e6-ca5f1fc08409/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:27:47,201] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfb8522c5-7565-458a-94e6-ca5f1fc08409/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:27:47,217] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:27:47,217] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:27:47,217] [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 khorasanensis	strain=SWRI153	GCA_014268505.2	2745508	2745508	type	True	100.0	1854	1856	95	conclusive
Pseudomonas triticicola	strain=SWRI88	GCA_019145375.1	2842345	2842345	type	True	89.6876	1590	1856	95	below_threshold
Pseudomonas siliginis	strain=SWRI31	GCA_019145195.1	2842346	2842346	type	True	89.6362	1550	1856	95	below_threshold
Pseudomonas iranensis	strain=SWRI54	GCA_014268585.2	2745503	2745503	type	True	89.6352	1623	1856	95	below_threshold
Pseudomonas atacamensis	strain=M7D1	GCA_004801935.1	2565368	2565368	type	True	89.6336	1647	1856	95	below_threshold
Pseudomonas hamedanensis	strain=SWRI65	GCA_014268595.2	2745504	2745504	type	True	88.8706	1596	1856	95	below_threshold
Pseudomonas tensinigenes	strain=ZA 5.3	GCA_014268445.2	2745511	2745511	type	True	87.9154	1569	1856	95	below_threshold
Pseudomonas zeae	strain=OE 48.2	GCA_014268485.2	2745510	2745510	type	True	87.87	1570	1856	95	below_threshold
Pseudomonas granadensis	strain=LMG 27940	GCA_900105485.1	1421430	1421430	suspected-type	True	87.8632	1568	1856	95	below_threshold
Pseudomonas neuropathica	strain=P155	GCA_015461835.1	2730425	2730425	type	True	87.8479	1553	1856	95	below_threshold
Pseudomonas germanica	strain=FIT28	GCA_019614655.1	2815720	2815720	type	True	87.8129	1572	1856	95	below_threshold
Pseudomonas crudilactis	strain=UCMA 17988	GCA_013433315.1	2697028	2697028	type	True	87.7814	1552	1856	95	below_threshold
Pseudomonas koreensis	strain=DSM 16610	GCA_012986595.1	198620	198620	suspected-type	True	87.61	1529	1856	95	below_threshold
Pseudomonas baetica	strain=LMG 25716	GCA_002813455.1	674054	674054	type	True	87.5359	1519	1856	95	below_threshold
Pseudomonas baetica	strain=a390	GCA_003031005.1	674054	674054	type	True	87.5186	1496	1856	95	below_threshold
Pseudomonas pharyngis	strain=BML-PP036	GCA_021602345.1	2892333	2892333	type	True	87.1895	1492	1856	95	below_threshold
Pseudomonas sputi	strain=BML-PP014	GCA_021603585.1	2892325	2892325	type	True	87.0078	1484	1856	95	below_threshold
Pseudomonas pergaminensis	strain=1008	GCA_024112395.1	2853159	2853159	type	True	82.8217	1173	1856	95	below_threshold
Pseudomonas brassicae	strain=MAFF 212427	GCA_010671725.1	2708063	2708063	type	True	81.4173	794	1856	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:27:47,219] [INFO] DFAST Taxonomy check result was written to GCF_014268505.2_ASM1426850v2_genomic.fna/tc_result.tsv
[2024-01-24 15:27:47,220] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:27:47,220] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:27:47,220] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfb8522c5-7565-458a-94e6-ca5f1fc08409/dqc_reference/checkm_data
[2024-01-24 15:27:47,221] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:27:47,273] [INFO] Task started: CheckM
[2024-01-24 15:27:47,274] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014268505.2_ASM1426850v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014268505.2_ASM1426850v2_genomic.fna/checkm_input GCF_014268505.2_ASM1426850v2_genomic.fna/checkm_result
[2024-01-24 15:28:43,212] [INFO] Task succeeded: CheckM
[2024-01-24 15:28:43,213] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:28:43,235] [INFO] ===== Completeness check finished =====
[2024-01-24 15:28:43,235] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:28:43,236] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014268505.2_ASM1426850v2_genomic.fna/markers.fasta)
[2024-01-24 15:28:43,236] [INFO] Task started: Blastn
[2024-01-24 15:28:43,236] [INFO] Running command: blastn -query GCF_014268505.2_ASM1426850v2_genomic.fna/markers.fasta -db /var/lib/cwl/stgfb8522c5-7565-458a-94e6-ca5f1fc08409/dqc_reference/reference_markers_gtdb.fasta -out GCF_014268505.2_ASM1426850v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:28:44,922] [INFO] Task succeeded: Blastn
[2024-01-24 15:28:44,926] [INFO] Selected 18 target genomes.
[2024-01-24 15:28:44,926] [INFO] Target genome list was writen to GCF_014268505.2_ASM1426850v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:28:44,937] [INFO] Task started: fastANI
[2024-01-24 15:28:44,937] [INFO] Running command: fastANI --query /var/lib/cwl/stg7bc679e0-e7a8-4895-9906-c83aa10c2e9a/GCF_014268505.2_ASM1426850v2_genomic.fna.gz --refList GCF_014268505.2_ASM1426850v2_genomic.fna/target_genomes_gtdb.txt --output GCF_014268505.2_ASM1426850v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:29:13,031] [INFO] Task succeeded: fastANI
[2024-01-24 15:29:13,046] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:29:13,047] [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_014268505.2	s__Pseudomonas_E sp014268505	100.0	1854	1856	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_004801935.1	s__Pseudomonas_E atacamensis	89.6448	1645	1856	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.5366	97.08	95.72	0.92	0.89	59	-
GCF_001605965.1	s__Pseudomonas_E koreensis_C	89.6202	1612	1856	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.5366	98.03	96.36	0.95	0.90	10	-
GCF_900105805.1	s__Pseudomonas_E moraviensis_A	89.5671	1626	1856	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.79	98.30	0.96	0.94	7	-
GCF_000817895.1	s__Pseudomonas_E fluorescens_AO	89.4152	1612	1856	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.16	98.16	0.95	0.95	2	-
GCF_002836515.1	s__Pseudomonas_E sp002836515	89.1507	1571	1856	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_014268595.2	s__Pseudomonas_E sp014270125	88.8706	1596	1856	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.71	97.59	0.94	0.93	4	-
GCF_000783395.1	s__Pseudomonas_E helmanticensis	87.9637	1553	1856	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_018138145.1	s__Pseudomonas_E koreensis_A	87.9284	1560	1856	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_900105485.1	s__Pseudomonas_E granadensis	87.8632	1568	1856	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.04	95.81	0.93	0.92	8	-
GCF_005938625.1	s__Pseudomonas_E fluorescens_BD	87.8559	1538	1856	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_900582195.1	s__Pseudomonas_E sp900582195	87.8557	1538	1856	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.42	98.42	0.95	0.95	2	-
GCF_013433315.1	s__Pseudomonas_E crudilactis	87.7899	1551	1856	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.42	98.37	0.96	0.95	4	-
GCF_016651305.1	s__Pseudomonas_E sp016651305	87.6332	1544	1856	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	87.5518	1510	1856	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_002813455.1	s__Pseudomonas_E baetica	87.5222	1521	1856	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_011369485.1	s__Pseudomonas_E sp011369485	87.5038	1504	1856	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_014472415.1	s__Pseudomonas_E sp014472415	87.4802	1502	1856	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 15:29:13,049] [INFO] GTDB search result was written to GCF_014268505.2_ASM1426850v2_genomic.fna/result_gtdb.tsv
[2024-01-24 15:29:13,049] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:29:13,054] [INFO] DFAST_QC result json was written to GCF_014268505.2_ASM1426850v2_genomic.fna/dqc_result.json
[2024-01-24 15:29:13,054] [INFO] DFAST_QC completed!
[2024-01-24 15:29:13,055] [INFO] Total running time: 0h2m18s