[2024-01-25 20:14:20,687] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:14:20,688] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:14:20,689] [INFO] DQC Reference Directory: /var/lib/cwl/stg6aa7b544-1a05-48bb-88dd-ba71037e071c/dqc_reference
[2024-01-25 20:14:21,788] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:14:21,789] [INFO] Task started: Prodigal
[2024-01-25 20:14:21,789] [INFO] Running command: gunzip -c /var/lib/cwl/stge7ebe913-17cc-423b-992f-b6b56573685c/GCF_904063065.1_V4_genomic.fna.gz | prodigal -d GCF_904063065.1_V4_genomic.fna/cds.fna -a GCF_904063065.1_V4_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:14:35,749] [INFO] Task succeeded: Prodigal
[2024-01-25 20:14:35,750] [INFO] Task started: HMMsearch
[2024-01-25 20:14:35,750] [INFO] Running command: hmmsearch --tblout GCF_904063065.1_V4_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6aa7b544-1a05-48bb-88dd-ba71037e071c/dqc_reference/reference_markers.hmm GCF_904063065.1_V4_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:14:36,049] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:14:36,051] [INFO] Found 6/6 markers.
[2024-01-25 20:14:36,098] [INFO] Query marker FASTA was written to GCF_904063065.1_V4_genomic.fna/markers.fasta
[2024-01-25 20:14:36,099] [INFO] Task started: Blastn
[2024-01-25 20:14:36,099] [INFO] Running command: blastn -query GCF_904063065.1_V4_genomic.fna/markers.fasta -db /var/lib/cwl/stg6aa7b544-1a05-48bb-88dd-ba71037e071c/dqc_reference/reference_markers.fasta -out GCF_904063065.1_V4_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:14:36,980] [INFO] Task succeeded: Blastn
[2024-01-25 20:14:36,983] [INFO] Selected 13 target genomes.
[2024-01-25 20:14:36,984] [INFO] Target genome list was writen to GCF_904063065.1_V4_genomic.fna/target_genomes.txt
[2024-01-25 20:14:36,988] [INFO] Task started: fastANI
[2024-01-25 20:14:36,988] [INFO] Running command: fastANI --query /var/lib/cwl/stge7ebe913-17cc-423b-992f-b6b56573685c/GCF_904063065.1_V4_genomic.fna.gz --refList GCF_904063065.1_V4_genomic.fna/target_genomes.txt --output GCF_904063065.1_V4_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:14:52,299] [INFO] Task succeeded: fastANI
[2024-01-25 20:14:52,300] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6aa7b544-1a05-48bb-88dd-ba71037e071c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:14:52,300] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6aa7b544-1a05-48bb-88dd-ba71037e071c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:14:52,311] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:14:52,311] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:14:52,311] [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 paraversuta	strain=V4/DAB/S4/2a	GCA_904063065.1	2750624	2750624	type	True	100.0	1644	1646	95	conclusive
Pseudomonas versuta	strain=L10.10	GCA_001294575.1	1788301	1788301	type	True	91.4788	1410	1646	95	below_threshold
Pseudomonas deceptionensis	strain=DSM 26521	GCA_001042895.1	882211	882211	type	True	86.2947	1258	1646	95	below_threshold
Pseudomonas deceptionensis	strain=LMG 25555	GCA_900106095.1	882211	882211	type	True	86.2877	1268	1646	95	below_threshold
Pseudomonas fragi	strain=NRRL B-727	GCA_900105835.1	296	296	type	True	85.8006	1228	1646	95	below_threshold
Pseudomonas psychrophila	strain=DSM 17535	GCA_001043005.1	122355	122355	type	True	85.4702	1233	1646	95	below_threshold
Pseudomonas psychrophila	strain=CCUG 53877	GCA_008801485.1	122355	122355	type	True	85.4386	1239	1646	95	below_threshold
Pseudomonas helleri	strain=DSM 29165	GCA_001043025.1	1608996	1608996	type	True	84.6158	1125	1646	95	below_threshold
Pseudomonas sputi	strain=BML-PP014	GCA_021603585.1	2892325	2892325	type	True	81.7106	890	1646	95	below_threshold
Pseudomonas pharyngis	strain=BML-PP036	GCA_021602345.1	2892333	2892333	type	True	81.7074	921	1646	95	below_threshold
Pseudomonas karstica	strain=CCM 7891	GCA_009707515.1	1055468	1055468	type	True	81.408	872	1646	95	below_threshold
Pseudomonas faucium	strain=BML-PP048	GCA_013373935.1	2740518	2740518	type	True	79.8284	751	1646	95	below_threshold
Pseudomonas faucium	strain=BML-PP048	GCA_021602585.1	2740518	2740518	type	True	79.7469	786	1646	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:14:52,315] [INFO] DFAST Taxonomy check result was written to GCF_904063065.1_V4_genomic.fna/tc_result.tsv
[2024-01-25 20:14:52,315] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:14:52,315] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:14:52,316] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6aa7b544-1a05-48bb-88dd-ba71037e071c/dqc_reference/checkm_data
[2024-01-25 20:14:52,317] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:14:52,367] [INFO] Task started: CheckM
[2024-01-25 20:14:52,368] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_904063065.1_V4_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_904063065.1_V4_genomic.fna/checkm_input GCF_904063065.1_V4_genomic.fna/checkm_result
[2024-01-25 20:15:33,568] [INFO] Task succeeded: CheckM
[2024-01-25 20:15:33,569] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:15:33,610] [INFO] ===== Completeness check finished =====
[2024-01-25 20:15:33,610] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:15:33,611] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_904063065.1_V4_genomic.fna/markers.fasta)
[2024-01-25 20:15:33,611] [INFO] Task started: Blastn
[2024-01-25 20:15:33,611] [INFO] Running command: blastn -query GCF_904063065.1_V4_genomic.fna/markers.fasta -db /var/lib/cwl/stg6aa7b544-1a05-48bb-88dd-ba71037e071c/dqc_reference/reference_markers_gtdb.fasta -out GCF_904063065.1_V4_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:15:35,179] [INFO] Task succeeded: Blastn
[2024-01-25 20:15:35,182] [INFO] Selected 10 target genomes.
[2024-01-25 20:15:35,182] [INFO] Target genome list was writen to GCF_904063065.1_V4_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:15:35,209] [INFO] Task started: fastANI
[2024-01-25 20:15:35,209] [INFO] Running command: fastANI --query /var/lib/cwl/stge7ebe913-17cc-423b-992f-b6b56573685c/GCF_904063065.1_V4_genomic.fna.gz --refList GCF_904063065.1_V4_genomic.fna/target_genomes_gtdb.txt --output GCF_904063065.1_V4_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:15:47,944] [INFO] Task succeeded: fastANI
[2024-01-25 20:15:47,951] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:15:47,951] [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_904063065.1	s__Pseudomonas_E paraversuta	100.0	1644	1646	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.24	99.22	0.95	0.95	9	conclusive
GCF_001294575.1	s__Pseudomonas_E versuta	91.4674	1411	1646	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.68	99.38	0.97	0.97	3	-
GCF_900106095.1	s__Pseudomonas_E deceptionensis	86.2935	1267	1646	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_900105835.1	s__Pseudomonas_E fragi	85.8152	1226	1646	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.76	96.96	0.94	0.89	28	-
GCF_002269505.1	s__Pseudomonas_E fragi_D	85.7005	1198	1646	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.09	96.09	0.88	0.88	2	-
GCF_900618535.1	s__Pseudomonas_E bubulae	85.5244	1211	1646	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.12	98.96	0.92	0.87	18	-
GCF_001043005.1	s__Pseudomonas_E psychrophila	85.4524	1235	1646	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.62	99.23	0.96	0.92	7	-
GCF_900475285.1	s__Pseudomonas_E taetrolens	84.9205	1151	1646	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.99	99.98	0.99	0.99	4	-
GCF_001043025.1	s__Pseudomonas_E helleri	84.6058	1127	1646	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.29	96.40	0.86	0.80	22	-
GCF_902497875.1	s__Pseudomonas_E fluorescens_BR	81.6191	944	1646	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:15:47,953] [INFO] GTDB search result was written to GCF_904063065.1_V4_genomic.fna/result_gtdb.tsv
[2024-01-25 20:15:47,954] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:15:47,957] [INFO] DFAST_QC result json was written to GCF_904063065.1_V4_genomic.fna/dqc_result.json
[2024-01-25 20:15:47,957] [INFO] DFAST_QC completed!
[2024-01-25 20:15:47,957] [INFO] Total running time: 0h1m27s