[2024-01-24 14:14:32,058] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:14:32,060] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:14:32,060] [INFO] DQC Reference Directory: /var/lib/cwl/stg412ddb34-b3c8-4ae0-94d6-55de59f08ed9/dqc_reference
[2024-01-24 14:14:33,333] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:14:33,334] [INFO] Task started: Prodigal
[2024-01-24 14:14:33,334] [INFO] Running command: gunzip -c /var/lib/cwl/stg19ed54d9-a0c9-4e8f-b620-1e74105edc74/GCF_008692865.1_ASM869286v1_genomic.fna.gz | prodigal -d GCF_008692865.1_ASM869286v1_genomic.fna/cds.fna -a GCF_008692865.1_ASM869286v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:14:54,355] [INFO] Task succeeded: Prodigal
[2024-01-24 14:14:54,355] [INFO] Task started: HMMsearch
[2024-01-24 14:14:54,356] [INFO] Running command: hmmsearch --tblout GCF_008692865.1_ASM869286v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg412ddb34-b3c8-4ae0-94d6-55de59f08ed9/dqc_reference/reference_markers.hmm GCF_008692865.1_ASM869286v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:14:54,747] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:14:54,749] [INFO] Found 6/6 markers.
[2024-01-24 14:14:54,904] [INFO] Query marker FASTA was written to GCF_008692865.1_ASM869286v1_genomic.fna/markers.fasta
[2024-01-24 14:14:54,904] [INFO] Task started: Blastn
[2024-01-24 14:14:54,904] [INFO] Running command: blastn -query GCF_008692865.1_ASM869286v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg412ddb34-b3c8-4ae0-94d6-55de59f08ed9/dqc_reference/reference_markers.fasta -out GCF_008692865.1_ASM869286v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:14:55,740] [INFO] Task succeeded: Blastn
[2024-01-24 14:14:55,745] [INFO] Selected 17 target genomes.
[2024-01-24 14:14:55,745] [INFO] Target genome list was writen to GCF_008692865.1_ASM869286v1_genomic.fna/target_genomes.txt
[2024-01-24 14:14:55,768] [INFO] Task started: fastANI
[2024-01-24 14:14:55,768] [INFO] Running command: fastANI --query /var/lib/cwl/stg19ed54d9-a0c9-4e8f-b620-1e74105edc74/GCF_008692865.1_ASM869286v1_genomic.fna.gz --refList GCF_008692865.1_ASM869286v1_genomic.fna/target_genomes.txt --output GCF_008692865.1_ASM869286v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:15:22,047] [INFO] Task succeeded: fastANI
[2024-01-24 14:15:22,048] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg412ddb34-b3c8-4ae0-94d6-55de59f08ed9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:15:22,048] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg412ddb34-b3c8-4ae0-94d6-55de59f08ed9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:15:22,077] [INFO] Found 17 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:15:22,078] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:15:22,078] [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 proteolytica	strain=CCUG 51515T	GCA_008692865.1	219574	219574	type	True	100.0	2049	2058	95	conclusive
Pseudomonas proteolytica	strain=DSM 15321	GCA_007858275.1	219574	219574	type	True	99.9897	2036	2058	95	conclusive
Pseudomonas brenneri	strain=JCM 13307	GCA_014646715.1	129817	129817	type	True	92.2105	1629	2058	95	below_threshold
Pseudomonas brenneri	strain=DSM 15294	GCA_007858285.1	129817	129817	type	True	92.1881	1631	2058	95	below_threshold
Pseudomonas gessardii	strain=DSM 17152	GCA_001983165.1	78544	78544	type	True	91.6973	1584	2058	95	below_threshold
Pseudomonas gessardii	strain=DSM 17152	GCA_009671285.1	78544	78544	type	True	91.6973	1584	2058	95	below_threshold
Pseudomonas gessardii		GCA_900625085.1	78544	78544	type	True	91.6842	1587	2058	95	below_threshold
Pseudomonas marginalis	strain=DSM 13124	GCA_007858155.1	298	298	suspected-type	True	86.5129	1442	2058	95	below_threshold
Pseudomonas pergaminensis	strain=1008	GCA_024112395.1	2853159	2853159	type	True	86.4113	1422	2058	95	below_threshold
Pseudomonas spelaei	strain=CCM 7893	GCA_009724245.1	1055469	1055469	type	True	86.3453	1421	2058	95	below_threshold
Pseudomonas lurida	strain=LMG 21995	GCA_002563895.1	244566	244566	type	True	86.3044	1378	2058	95	below_threshold
Pseudomonas fluorescens	strain=NCTC10038	GCA_900475215.1	294	294	suspected-type	True	85.9607	1403	2058	95	below_threshold
Pseudomonas karstica	strain=CCM 7891	GCA_009707515.1	1055468	1055468	type	True	85.7067	1272	2058	95	below_threshold
Pseudomonas vranovensis	strain=DSM 16006	GCA_000425805.1	321661	321661	type	True	81.6162	972	2058	95	below_threshold
Stutzerimonas azotifigens	strain=DSM 17556	GCA_000425625.1	291995	291995	type	True	78.8353	572	2058	95	below_threshold
Pseudomonas oryzihabitans	strain=DSM 6835	GCA_012986195.1	47885	47885	suspected-type	True	78.5291	540	2058	95	below_threshold
Pseudomonas rhizoryzae	strain=RY24	GCA_005250615.1	2571129	2571129	type	True	78.2975	513	2058	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:15:22,080] [INFO] DFAST Taxonomy check result was written to GCF_008692865.1_ASM869286v1_genomic.fna/tc_result.tsv
[2024-01-24 14:15:22,080] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:15:22,080] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:15:22,081] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg412ddb34-b3c8-4ae0-94d6-55de59f08ed9/dqc_reference/checkm_data
[2024-01-24 14:15:22,082] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:15:22,142] [INFO] Task started: CheckM
[2024-01-24 14:15:22,143] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008692865.1_ASM869286v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008692865.1_ASM869286v1_genomic.fna/checkm_input GCF_008692865.1_ASM869286v1_genomic.fna/checkm_result
[2024-01-24 14:16:23,999] [INFO] Task succeeded: CheckM
[2024-01-24 14:16:24,000] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:16:24,020] [INFO] ===== Completeness check finished =====
[2024-01-24 14:16:24,020] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:16:24,021] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008692865.1_ASM869286v1_genomic.fna/markers.fasta)
[2024-01-24 14:16:24,021] [INFO] Task started: Blastn
[2024-01-24 14:16:24,021] [INFO] Running command: blastn -query GCF_008692865.1_ASM869286v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg412ddb34-b3c8-4ae0-94d6-55de59f08ed9/dqc_reference/reference_markers_gtdb.fasta -out GCF_008692865.1_ASM869286v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:16:25,488] [INFO] Task succeeded: Blastn
[2024-01-24 14:16:25,492] [INFO] Selected 21 target genomes.
[2024-01-24 14:16:25,492] [INFO] Target genome list was writen to GCF_008692865.1_ASM869286v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:16:25,516] [INFO] Task started: fastANI
[2024-01-24 14:16:25,516] [INFO] Running command: fastANI --query /var/lib/cwl/stg19ed54d9-a0c9-4e8f-b620-1e74105edc74/GCF_008692865.1_ASM869286v1_genomic.fna.gz --refList GCF_008692865.1_ASM869286v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008692865.1_ASM869286v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:16:57,743] [INFO] Task succeeded: fastANI
[2024-01-24 14:16:57,762] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:16:57,763] [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_007858275.1	s__Pseudomonas_E proteolytica	99.9897	2036	2058	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.69	98.38	0.90	0.86	19	conclusive
GCF_016925675.1	s__Pseudomonas_E sp012985665	94.9697	1717	2058	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.30	97.44	0.92	0.88	4	-
GCF_012985465.1	s__Pseudomonas_E sp012985465	92.4746	1689	2058	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.03	98.94	0.91	0.90	5	-
GCF_007858285.1	s__Pseudomonas_E brenneri	92.2075	1629	2058	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.23	97.33	0.94	0.88	10	-
GCF_003626995.1	s__Pseudomonas_E fluorescens_BA	91.8536	1644	2058	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.95	98.57	0.93	0.88	19	-
GCF_000730425.1	s__Pseudomonas_E fluorescens_X	91.7528	1590	2058	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.75	99.75	0.93	0.93	2	-
GCF_001983165.1	s__Pseudomonas_E gessardii	91.6973	1584	2058	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.96	98.08	0.94	0.88	9	-
GCF_001439695.1	s__Pseudomonas_E veronii	86.6286	1394	2058	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.79	98.13	0.89	0.82	43	-
GCF_003852315.1	s__Pseudomonas_E sp003014915	86.0382	1414	2058	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.48	96.20	0.95	0.91	10	-
GCF_003851685.1	s__Pseudomonas_E sp003851685	86.0379	1345	2058	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_001439845.1	s__Pseudomonas_E lactis	85.9809	1433	2058	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.24	95.50	0.88	0.81	30	-
GCF_900105675.1	s__Pseudomonas_E synxantha	85.9119	1424	2058	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.7053	98.15	96.46	0.93	0.84	14	-
GCF_902497995.1	s__Pseudomonas_E fluorescens_BK	83.6859	1100	2058	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_008801475.1	s__Pseudomonas_E moorei	83.3624	1124	2058	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	100.00	100.00	1.00	1.00	2	-
GCF_017980685.1	s__Pseudomonas_E iridis	83.1939	1122	2058	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_015680235.1	s__Pseudomonas_E guariconensis_A	81.0072	889	2058	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.95	98.73	0.91	0.90	4	-
GCF_018449655.1	s__Pseudomonas_E sp018449655	80.6237	808	2058	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_002158995.1	s__Pseudomonas_E caspiana	80.5961	762	2058	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_004803755.1	s__Pseudomonas_E sp004803755	80.5673	848	2058	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_017589465.1	s__Pseudomonas sp017589465	79.7003	730	2058	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:16:57,764] [INFO] GTDB search result was written to GCF_008692865.1_ASM869286v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:16:57,765] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:16:57,770] [INFO] DFAST_QC result json was written to GCF_008692865.1_ASM869286v1_genomic.fna/dqc_result.json
[2024-01-24 14:16:57,770] [INFO] DFAST_QC completed!
[2024-01-24 14:16:57,770] [INFO] Total running time: 0h2m26s