[2024-01-25 18:59:50,824] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:59:50,826] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:59:50,826] [INFO] DQC Reference Directory: /var/lib/cwl/stg1eb5f5cb-ad0a-40d5-820f-e1105c9fba10/dqc_reference
[2024-01-25 18:59:51,981] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:59:51,982] [INFO] Task started: Prodigal
[2024-01-25 18:59:51,982] [INFO] Running command: gunzip -c /var/lib/cwl/stg3c9e4961-01ea-4f49-94fa-f18aa3a45acd/GCF_900475285.1_43222_B01_genomic.fna.gz | prodigal -d GCF_900475285.1_43222_B01_genomic.fna/cds.fna -a GCF_900475285.1_43222_B01_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:00:07,020] [INFO] Task succeeded: Prodigal
[2024-01-25 19:00:07,020] [INFO] Task started: HMMsearch
[2024-01-25 19:00:07,020] [INFO] Running command: hmmsearch --tblout GCF_900475285.1_43222_B01_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1eb5f5cb-ad0a-40d5-820f-e1105c9fba10/dqc_reference/reference_markers.hmm GCF_900475285.1_43222_B01_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:00:07,255] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:00:07,258] [INFO] Found 6/6 markers.
[2024-01-25 19:00:07,294] [INFO] Query marker FASTA was written to GCF_900475285.1_43222_B01_genomic.fna/markers.fasta
[2024-01-25 19:00:07,294] [INFO] Task started: Blastn
[2024-01-25 19:00:07,294] [INFO] Running command: blastn -query GCF_900475285.1_43222_B01_genomic.fna/markers.fasta -db /var/lib/cwl/stg1eb5f5cb-ad0a-40d5-820f-e1105c9fba10/dqc_reference/reference_markers.fasta -out GCF_900475285.1_43222_B01_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:00:08,156] [INFO] Task succeeded: Blastn
[2024-01-25 19:00:08,159] [INFO] Selected 15 target genomes.
[2024-01-25 19:00:08,160] [INFO] Target genome list was writen to GCF_900475285.1_43222_B01_genomic.fna/target_genomes.txt
[2024-01-25 19:00:08,167] [INFO] Task started: fastANI
[2024-01-25 19:00:08,167] [INFO] Running command: fastANI --query /var/lib/cwl/stg3c9e4961-01ea-4f49-94fa-f18aa3a45acd/GCF_900475285.1_43222_B01_genomic.fna.gz --refList GCF_900475285.1_43222_B01_genomic.fna/target_genomes.txt --output GCF_900475285.1_43222_B01_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:00:25,167] [INFO] Task succeeded: fastANI
[2024-01-25 19:00:25,167] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1eb5f5cb-ad0a-40d5-820f-e1105c9fba10/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:00:25,168] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1eb5f5cb-ad0a-40d5-820f-e1105c9fba10/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:00:25,178] [INFO] Found 15 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 19:00:25,178] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:00:25,178] [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 taetrolens	strain=NCTC10697	GCA_900475285.1	47884	47884	type	True	100.0	1611	1614	95	conclusive
Pseudomonas taetrolens	strain=DSM 21104	GCA_001042915.1	47884	47884	type	True	99.9832	1592	1614	95	conclusive
Pseudomonas deceptionensis	strain=LMG 25555	GCA_900106095.1	882211	882211	type	True	85.492	1164	1614	95	below_threshold
Pseudomonas deceptionensis	strain=DSM 26521	GCA_001042895.1	882211	882211	type	True	85.3859	1164	1614	95	below_threshold
Pseudomonas fragi	strain=NRRL B-727	GCA_900105835.1	296	296	type	True	85.0758	1134	1614	95	below_threshold
Pseudomonas fragi	strain=NBRC 3458	GCA_002091615.1	296	296	type	True	85.0204	1117	1614	95	below_threshold
Pseudomonas helleri	strain=DSM 29165	GCA_001043025.1	1608996	1608996	type	True	84.023	1074	1614	95	below_threshold
Pseudomonas pharyngis	strain=BML-PP036	GCA_021602345.1	2892333	2892333	type	True	81.4804	886	1614	95	below_threshold
Pseudomonas jessenii	strain=DSM 17150	GCA_002236115.1	77298	77298	suspected-type	True	81.4705	899	1614	95	below_threshold
Pseudomonas lurida	strain=LMG 21995	GCA_002563895.1	244566	244566	type	True	81.4525	873	1614	95	below_threshold
Pseudomonas reinekei	strain=MT1	GCA_001945365.1	395598	395598	type	True	81.4106	867	1614	95	below_threshold
Pseudomonas reinekei	strain=CCUG 53116	GCA_008801455.1	395598	395598	type	True	81.4033	873	1614	95	below_threshold
Pseudomonas sputi	strain=BML-PP014	GCA_021603585.1	2892325	2892325	type	True	81.3858	865	1614	95	below_threshold
Pseudomonas marginalis	strain=DSM 13124	GCA_007858155.1	298	298	suspected-type	True	81.3782	898	1614	95	below_threshold
Pseudomonas amygdali	strain=DSM 105780	GCA_022828345.1	47877	47877	pathovar	True	80.1293	631	1614	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:00:25,180] [INFO] DFAST Taxonomy check result was written to GCF_900475285.1_43222_B01_genomic.fna/tc_result.tsv
[2024-01-25 19:00:25,180] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:00:25,180] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:00:25,181] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1eb5f5cb-ad0a-40d5-820f-e1105c9fba10/dqc_reference/checkm_data
[2024-01-25 19:00:25,181] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:00:25,227] [INFO] Task started: CheckM
[2024-01-25 19:00:25,227] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900475285.1_43222_B01_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900475285.1_43222_B01_genomic.fna/checkm_input GCF_900475285.1_43222_B01_genomic.fna/checkm_result
[2024-01-25 19:01:11,835] [INFO] Task succeeded: CheckM
[2024-01-25 19:01:11,836] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:01:11,855] [INFO] ===== Completeness check finished =====
[2024-01-25 19:01:11,855] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:01:11,855] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900475285.1_43222_B01_genomic.fna/markers.fasta)
[2024-01-25 19:01:11,855] [INFO] Task started: Blastn
[2024-01-25 19:01:11,856] [INFO] Running command: blastn -query GCF_900475285.1_43222_B01_genomic.fna/markers.fasta -db /var/lib/cwl/stg1eb5f5cb-ad0a-40d5-820f-e1105c9fba10/dqc_reference/reference_markers_gtdb.fasta -out GCF_900475285.1_43222_B01_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:01:13,481] [INFO] Task succeeded: Blastn
[2024-01-25 19:01:13,485] [INFO] Selected 18 target genomes.
[2024-01-25 19:01:13,485] [INFO] Target genome list was writen to GCF_900475285.1_43222_B01_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:01:13,523] [INFO] Task started: fastANI
[2024-01-25 19:01:13,523] [INFO] Running command: fastANI --query /var/lib/cwl/stg3c9e4961-01ea-4f49-94fa-f18aa3a45acd/GCF_900475285.1_43222_B01_genomic.fna.gz --refList GCF_900475285.1_43222_B01_genomic.fna/target_genomes_gtdb.txt --output GCF_900475285.1_43222_B01_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:01:35,280] [INFO] Task succeeded: fastANI
[2024-01-25 19:01:35,290] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:01:35,291] [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_900475285.1	s__Pseudomonas_E taetrolens	100.0	1612	1614	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.99	99.98	0.99	0.99	4	conclusive
GCF_900106095.1	s__Pseudomonas_E deceptionensis	85.5098	1166	1614	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	85.0875	1133	1614	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_904063065.1	s__Pseudomonas_E paraversuta	84.8881	1154	1614	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.24	99.22	0.95	0.95	9	-
GCF_002269505.1	s__Pseudomonas_E fragi_D	84.8768	1102	1614	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	84.7652	1121	1614	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_000282975.1	s__Pseudomonas_E psychrophila_A	83.7287	1028	1614	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_001043055.1	s__Pseudomonas_E weihenstephanensis	83.7162	1035	1614	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.02	97.13	0.92	0.88	6	-
GCF_009600315.1	s__Pseudomonas_E helleri_A	83.4948	1034	1614	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.82	99.80	0.94	0.93	4	-
GCF_007858365.1	s__Pseudomonas_E saxonica	83.3705	1049	1614	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.82	98.82	0.90	0.90	2	-
GCF_000282415.1	s__Pseudomonas_E sp000282415	81.7034	849	1614	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.45	97.21	0.89	0.87	6	-
GCF_018502625.1	s__Pseudomonas_E fluorescens_BW	81.6558	883	1614	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_016650695.1	s__Pseudomonas_E sp016650695	81.6016	863	1614	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_002303925.1	s__Pseudomonas_E sp002303925	81.5746	864	1614	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_000802965.1	s__Pseudomonas_E fluorescens_A	81.5275	857	1614	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_002091715.1	s__Pseudomonas_E migulae	81.5235	865	1614	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.54	99.09	0.95	0.90	3	-
GCF_002236115.1	s__Pseudomonas_E jessenii	81.4569	899	1614	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_016909445.1	s__Pseudomonas_E stutzeri_A	81.3193	873	1614	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.88	96.88	0.84	0.84	2	-
--------------------------------------------------------------------------------
[2024-01-25 19:01:35,292] [INFO] GTDB search result was written to GCF_900475285.1_43222_B01_genomic.fna/result_gtdb.tsv
[2024-01-25 19:01:35,292] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:01:35,305] [INFO] DFAST_QC result json was written to GCF_900475285.1_43222_B01_genomic.fna/dqc_result.json
[2024-01-25 19:01:35,305] [INFO] DFAST_QC completed!
[2024-01-25 19:01:35,306] [INFO] Total running time: 0h1m44s