[2024-01-24 15:26:54,828] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:26:54,830] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:26:54,831] [INFO] DQC Reference Directory: /var/lib/cwl/stgf0449d14-b607-4843-aa02-5fdd64a00e23/dqc_reference
[2024-01-24 15:26:56,353] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:26:56,354] [INFO] Task started: Prodigal
[2024-01-24 15:26:56,355] [INFO] Running command: gunzip -c /var/lib/cwl/stg2982b617-0aba-46c0-a9a9-c7cd8ec240c2/GCF_014268595.2_ASM1426859v2_genomic.fna.gz | prodigal -d GCF_014268595.2_ASM1426859v2_genomic.fna/cds.fna -a GCF_014268595.2_ASM1426859v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:27:19,811] [INFO] Task succeeded: Prodigal
[2024-01-24 15:27:19,812] [INFO] Task started: HMMsearch
[2024-01-24 15:27:19,812] [INFO] Running command: hmmsearch --tblout GCF_014268595.2_ASM1426859v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf0449d14-b607-4843-aa02-5fdd64a00e23/dqc_reference/reference_markers.hmm GCF_014268595.2_ASM1426859v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:27:20,232] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:27:20,233] [INFO] Found 6/6 markers.
[2024-01-24 15:27:20,282] [INFO] Query marker FASTA was written to GCF_014268595.2_ASM1426859v2_genomic.fna/markers.fasta
[2024-01-24 15:27:20,282] [INFO] Task started: Blastn
[2024-01-24 15:27:20,282] [INFO] Running command: blastn -query GCF_014268595.2_ASM1426859v2_genomic.fna/markers.fasta -db /var/lib/cwl/stgf0449d14-b607-4843-aa02-5fdd64a00e23/dqc_reference/reference_markers.fasta -out GCF_014268595.2_ASM1426859v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:27:21,334] [INFO] Task succeeded: Blastn
[2024-01-24 15:27:21,342] [INFO] Selected 20 target genomes.
[2024-01-24 15:27:21,342] [INFO] Target genome list was writen to GCF_014268595.2_ASM1426859v2_genomic.fna/target_genomes.txt
[2024-01-24 15:27:21,344] [INFO] Task started: fastANI
[2024-01-24 15:27:21,344] [INFO] Running command: fastANI --query /var/lib/cwl/stg2982b617-0aba-46c0-a9a9-c7cd8ec240c2/GCF_014268595.2_ASM1426859v2_genomic.fna.gz --refList GCF_014268595.2_ASM1426859v2_genomic.fna/target_genomes.txt --output GCF_014268595.2_ASM1426859v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:27:55,962] [INFO] Task succeeded: fastANI
[2024-01-24 15:27:55,962] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf0449d14-b607-4843-aa02-5fdd64a00e23/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:27:55,963] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf0449d14-b607-4843-aa02-5fdd64a00e23/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:27:55,978] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:27:55,978] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:27:55,978] [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 hamedanensis	strain=SWRI65	GCA_014268595.2	2745504	2745504	type	True	100.0	2013	2015	95	conclusive
Pseudomonas iranensis	strain=SWRI54	GCA_014268585.2	2745503	2745503	type	True	89.586	1676	2015	95	below_threshold
Pseudomonas siliginis	strain=SWRI31	GCA_019145195.1	2842346	2842346	type	True	89.5761	1568	2015	95	below_threshold
Pseudomonas atacamensis	strain=M7D1	GCA_004801935.1	2565368	2565368	type	True	89.4371	1670	2015	95	below_threshold
Pseudomonas triticicola	strain=SWRI88	GCA_019145375.1	2842345	2842345	type	True	89.4196	1635	2015	95	below_threshold
Pseudomonas khorasanensis	strain=SWRI153	GCA_014268505.2	2745508	2745508	type	True	88.6912	1620	2015	95	below_threshold
Pseudomonas granadensis	strain=LMG 27940	GCA_900105485.1	1421430	1421430	suspected-type	True	88.3135	1674	2015	95	below_threshold
Pseudomonas germanica	strain=FIT28	GCA_019614655.1	2815720	2815720	type	True	88.2514	1654	2015	95	below_threshold
Pseudomonas zeae	strain=OE 48.2	GCA_014268485.2	2745510	2745510	type	True	88.2085	1642	2015	95	below_threshold
Pseudomonas crudilactis	strain=UCMA 17988	GCA_013433315.1	2697028	2697028	type	True	88.1493	1640	2015	95	below_threshold
Pseudomonas neuropathica	strain=P155	GCA_015461835.1	2730425	2730425	type	True	88.0816	1646	2015	95	below_threshold
Pseudomonas monsensis	strain=PGSB 8459	GCA_014268495.2	2745509	2745509	type	True	87.9983	1596	2015	95	below_threshold
Pseudomonas koreensis	strain=CCUG 51519	GCA_008801535.1	198620	198620	suspected-type	True	87.9427	1536	2015	95	below_threshold
Pseudomonas koreensis	strain=DSM 16610	GCA_012986595.1	198620	198620	suspected-type	True	87.8823	1562	2015	95	below_threshold
Pseudomonas baetica	strain=a390	GCA_003031005.1	674054	674054	type	True	87.8377	1573	2015	95	below_threshold
Pseudomonas baetica	strain=LMG 25716	GCA_002813455.1	674054	674054	type	True	87.7978	1598	2015	95	below_threshold
Pseudomonas pharyngis	strain=BML-PP036	GCA_021602345.1	2892333	2892333	type	True	87.3746	1579	2015	95	below_threshold
Pseudomonas sputi	strain=BML-PP014	GCA_021603585.1	2892325	2892325	type	True	87.199	1537	2015	95	below_threshold
Pseudomonas pergaminensis	strain=1008	GCA_024112395.1	2853159	2853159	type	True	83.061	1218	2015	95	below_threshold
Pseudomonas brassicae	strain=MAFF 212427	GCA_010671725.1	2708063	2708063	type	True	81.8214	824	2015	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:27:55,980] [INFO] DFAST Taxonomy check result was written to GCF_014268595.2_ASM1426859v2_genomic.fna/tc_result.tsv
[2024-01-24 15:27:55,980] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:27:55,980] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:27:55,981] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf0449d14-b607-4843-aa02-5fdd64a00e23/dqc_reference/checkm_data
[2024-01-24 15:27:55,982] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:27:56,080] [INFO] Task started: CheckM
[2024-01-24 15:27:56,080] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014268595.2_ASM1426859v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014268595.2_ASM1426859v2_genomic.fna/checkm_input GCF_014268595.2_ASM1426859v2_genomic.fna/checkm_result
[2024-01-24 15:29:03,424] [INFO] Task succeeded: CheckM
[2024-01-24 15:29:03,426] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:29:03,469] [INFO] ===== Completeness check finished =====
[2024-01-24 15:29:03,469] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:29:03,469] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014268595.2_ASM1426859v2_genomic.fna/markers.fasta)
[2024-01-24 15:29:03,470] [INFO] Task started: Blastn
[2024-01-24 15:29:03,470] [INFO] Running command: blastn -query GCF_014268595.2_ASM1426859v2_genomic.fna/markers.fasta -db /var/lib/cwl/stgf0449d14-b607-4843-aa02-5fdd64a00e23/dqc_reference/reference_markers_gtdb.fasta -out GCF_014268595.2_ASM1426859v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:29:05,293] [INFO] Task succeeded: Blastn
[2024-01-24 15:29:05,297] [INFO] Selected 19 target genomes.
[2024-01-24 15:29:05,297] [INFO] Target genome list was writen to GCF_014268595.2_ASM1426859v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:29:05,302] [INFO] Task started: fastANI
[2024-01-24 15:29:05,302] [INFO] Running command: fastANI --query /var/lib/cwl/stg2982b617-0aba-46c0-a9a9-c7cd8ec240c2/GCF_014268595.2_ASM1426859v2_genomic.fna.gz --refList GCF_014268595.2_ASM1426859v2_genomic.fna/target_genomes_gtdb.txt --output GCF_014268595.2_ASM1426859v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:29:38,296] [INFO] Task succeeded: fastANI
[2024-01-24 15:29:38,311] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:29:38,311] [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_014268595.2	s__Pseudomonas_E sp014270125	100.0	2014	2015	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.71	97.59	0.94	0.93	4	conclusive
GCF_001605965.1	s__Pseudomonas_E koreensis_C	89.5434	1660	2015	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	89.4418	1671	2015	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_004801935.1	s__Pseudomonas_E atacamensis	89.4323	1670	2015	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_000817895.1	s__Pseudomonas_E fluorescens_AO	89.3523	1664	2015	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_003732425.1	s__Pseudomonas_E fluorescens_BE	88.3395	1625	2015	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_900105485.1	s__Pseudomonas_E granadensis	88.3266	1673	2015	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_004011755.1	s__Pseudomonas_E sp004011755	88.3259	1686	2015	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.20	98.13	0.94	0.93	4	-
GCF_018138145.1	s__Pseudomonas_E koreensis_A	88.246	1664	2015	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_013433315.1	s__Pseudomonas_E crudilactis	88.1575	1639	2015	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_005938625.1	s__Pseudomonas_E fluorescens_BD	88.1422	1606	2015	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_003053805.1	s__Pseudomonas_E sp003053805	88.1357	1657	2015	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_004124275.1	s__Pseudomonas_E sp004124275	88.1192	1619	2015	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_001297015.1	s__Pseudomonas_E sp001297015	88.1015	1622	2015	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.81	98.77	0.95	0.94	9	-
GCF_014268495.2	s__Pseudomonas_E fluorescens_BC	88.0125	1598	2015	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_016651305.1	s__Pseudomonas_E sp016651305	87.913	1612	2015	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	87.8171	1566	2015	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_002813455.1	s__Pseudomonas_E baetica	87.7998	1599	2015	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_016650635.1	s__Pseudomonas_E sp016650635	87.665	1622	2015	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.85	97.85	0.86	0.86	2	-
--------------------------------------------------------------------------------
[2024-01-24 15:29:38,313] [INFO] GTDB search result was written to GCF_014268595.2_ASM1426859v2_genomic.fna/result_gtdb.tsv
[2024-01-24 15:29:38,313] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:29:38,319] [INFO] DFAST_QC result json was written to GCF_014268595.2_ASM1426859v2_genomic.fna/dqc_result.json
[2024-01-24 15:29:38,319] [INFO] DFAST_QC completed!
[2024-01-24 15:29:38,320] [INFO] Total running time: 0h2m43s