[2024-01-25 20:01:20,915] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:01:20,917] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:01:20,917] [INFO] DQC Reference Directory: /var/lib/cwl/stga38af0dc-7188-4316-adf5-601f1c5375c4/dqc_reference
[2024-01-25 20:01:22,080] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:01:22,081] [INFO] Task started: Prodigal
[2024-01-25 20:01:22,081] [INFO] Running command: gunzip -c /var/lib/cwl/stg092a32bb-ba68-445c-8b64-18614dfc310e/GCF_000498575.2_MS-3_genomic.fna.gz | prodigal -d GCF_000498575.2_MS-3_genomic.fna/cds.fna -a GCF_000498575.2_MS-3_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:01:36,488] [INFO] Task succeeded: Prodigal
[2024-01-25 20:01:36,488] [INFO] Task started: HMMsearch
[2024-01-25 20:01:36,488] [INFO] Running command: hmmsearch --tblout GCF_000498575.2_MS-3_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga38af0dc-7188-4316-adf5-601f1c5375c4/dqc_reference/reference_markers.hmm GCF_000498575.2_MS-3_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:01:36,795] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:01:36,796] [INFO] Found 6/6 markers.
[2024-01-25 20:01:36,840] [INFO] Query marker FASTA was written to GCF_000498575.2_MS-3_genomic.fna/markers.fasta
[2024-01-25 20:01:36,841] [INFO] Task started: Blastn
[2024-01-25 20:01:36,841] [INFO] Running command: blastn -query GCF_000498575.2_MS-3_genomic.fna/markers.fasta -db /var/lib/cwl/stga38af0dc-7188-4316-adf5-601f1c5375c4/dqc_reference/reference_markers.fasta -out GCF_000498575.2_MS-3_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:01:37,665] [INFO] Task succeeded: Blastn
[2024-01-25 20:01:37,668] [INFO] Selected 19 target genomes.
[2024-01-25 20:01:37,669] [INFO] Target genome list was writen to GCF_000498575.2_MS-3_genomic.fna/target_genomes.txt
[2024-01-25 20:01:37,695] [INFO] Task started: fastANI
[2024-01-25 20:01:37,695] [INFO] Running command: fastANI --query /var/lib/cwl/stg092a32bb-ba68-445c-8b64-18614dfc310e/GCF_000498575.2_MS-3_genomic.fna.gz --refList GCF_000498575.2_MS-3_genomic.fna/target_genomes.txt --output GCF_000498575.2_MS-3_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:01:59,682] [INFO] Task succeeded: fastANI
[2024-01-25 20:01:59,682] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga38af0dc-7188-4316-adf5-601f1c5375c4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:01:59,683] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga38af0dc-7188-4316-adf5-601f1c5375c4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:01:59,694] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:01:59,694] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:01:59,694] [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 taeanensis	strain=MS-3	GCA_000498575.2	574962	574962	type	True	100.0	1807	1808	95	conclusive
Pseudomonas benzenivorans	strain=DSM 8628	GCA_900100495.1	556533	556533	type	True	84.281	1147	1808	95	below_threshold
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	84.1294	1134	1808	95	below_threshold
Pseudomonas tumuqii	strain=LAMW06	GCA_013184545.1	2715755	2715755	type	True	83.7772	1108	1808	95	below_threshold
Pseudomonas borbori	strain=DSM 17834	GCA_900115555.1	289003	289003	type	True	83.7392	1092	1808	95	below_threshold
Pseudomonas cavernae	strain=K2W31S-8	GCA_003595175.1	2320867	2320867	type	True	81.8014	902	1808	95	below_threshold
Pseudomonas peli	strain=DSM 17833	GCA_012986145.1	592361	592361	type	True	81.6525	882	1808	95	below_threshold
Pseudomonas peli	strain=DSM 17833	GCA_900099645.1	592361	592361	type	True	81.6082	879	1808	95	below_threshold
Pseudomonas insulae	strain=UL073	GCA_016901015.1	2809017	2809017	type	True	81.036	841	1808	95	below_threshold
Pseudomonas cavernicola	strain=K1S02-6	GCA_003596405.1	2320866	2320866	type	True	81.0355	903	1808	95	below_threshold
Pseudomonas argentinensis	strain=CCUG 50743	GCA_008801645.1	289370	289370	type	True	80.9764	764	1808	95	below_threshold
Pseudomonas argentinensis	strain=LMG 22563	GCA_900113905.1	289370	289370	type	True	80.9735	761	1808	95	below_threshold
Pseudomonas sagittaria	strain=JCM 18195	GCA_900115715.1	1135990	1135990	type	True	80.8718	689	1808	95	below_threshold
Pseudomonas aromaticivorans	strain=MAP12	GCA_019097855.1	2849492	2849492	type	True	80.8396	596	1808	95	below_threshold
Pseudomonas otitidis	strain=DSM 17224	GCA_900111835.1	319939	319939	suspected-type	True	80.5403	846	1808	95	below_threshold
Pseudomonas ekonensis	strain=COR58	GCA_019145435.1	2842353	2842353	type	True	80.3694	750	1808	95	below_threshold
Pseudomonas sichuanensis	strain=WCHPs060039	GCA_003231305.1	2213015	2213015	type	True	80.0074	710	1808	95	below_threshold
Pseudomonas thivervalensis	strain=DSM 13194	GCA_001269655.1	86265	86265	type	True	79.7846	657	1808	95	below_threshold
Pseudomonas pharyngis	strain=BML-PP036	GCA_021602345.1	2892333	2892333	type	True	79.7037	680	1808	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:01:59,695] [INFO] DFAST Taxonomy check result was written to GCF_000498575.2_MS-3_genomic.fna/tc_result.tsv
[2024-01-25 20:01:59,696] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:01:59,696] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:01:59,696] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga38af0dc-7188-4316-adf5-601f1c5375c4/dqc_reference/checkm_data
[2024-01-25 20:01:59,697] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:01:59,749] [INFO] Task started: CheckM
[2024-01-25 20:01:59,749] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000498575.2_MS-3_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000498575.2_MS-3_genomic.fna/checkm_input GCF_000498575.2_MS-3_genomic.fna/checkm_result
[2024-01-25 20:02:42,731] [INFO] Task succeeded: CheckM
[2024-01-25 20:02:42,732] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:02:42,758] [INFO] ===== Completeness check finished =====
[2024-01-25 20:02:42,758] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:02:42,759] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000498575.2_MS-3_genomic.fna/markers.fasta)
[2024-01-25 20:02:42,759] [INFO] Task started: Blastn
[2024-01-25 20:02:42,759] [INFO] Running command: blastn -query GCF_000498575.2_MS-3_genomic.fna/markers.fasta -db /var/lib/cwl/stga38af0dc-7188-4316-adf5-601f1c5375c4/dqc_reference/reference_markers_gtdb.fasta -out GCF_000498575.2_MS-3_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:02:44,135] [INFO] Task succeeded: Blastn
[2024-01-25 20:02:44,138] [INFO] Selected 17 target genomes.
[2024-01-25 20:02:44,138] [INFO] Target genome list was writen to GCF_000498575.2_MS-3_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:02:44,156] [INFO] Task started: fastANI
[2024-01-25 20:02:44,156] [INFO] Running command: fastANI --query /var/lib/cwl/stg092a32bb-ba68-445c-8b64-18614dfc310e/GCF_000498575.2_MS-3_genomic.fna.gz --refList GCF_000498575.2_MS-3_genomic.fna/target_genomes_gtdb.txt --output GCF_000498575.2_MS-3_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:03:05,074] [INFO] Task succeeded: fastANI
[2024-01-25 20:03:05,087] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:03:05,087] [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_000498575.2	s__Pseudomonas_E taeanensis	100.0	1807	1808	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_007993865.1	s__Pseudomonas_E sp007993865	92.0391	1371	1808	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_002025205.1	s__Pseudomonas_E sp002025205	84.4054	1222	1808	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_900100495.1	s__Pseudomonas_E benzenivorans	84.2588	1150	1808	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_013184545.1	s__Pseudomonas_E sp013184545	83.8011	1106	1808	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_900115555.1	s__Pseudomonas_E borbori	83.7314	1094	1808	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002354655.1	s__Pseudomonas_E sp002354655	83.5057	1087	1808	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.84	99.84	0.95	0.95	2	-
GCA_002840155.1	s__Pseudomonas_E sp002840155	81.9689	929	1808	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_004327355.1	s__Pseudomonas_E dryadis	81.8729	812	1808	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.58	99.16	0.96	0.92	3	-
GCF_009763245.1	s__Pseudomonas_E sp009763245	81.8023	880	1808	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_005502935.1	s__Pseudomonas_E sp005502935	81.7157	848	1808	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	95.95	95.95	0.83	0.83	2	-
GCA_018816095.1	s__Pseudomonas_E sp018816095	81.2276	726	1808	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.20	96.15	0.83	0.82	4	-
GCF_003596405.1	s__Pseudomonas_E sp003596405	81.0501	901	1808	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_016901015.1	s__Pseudomonas_E sp016901015	81.0298	843	1808	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_002286785.1	s__Pseudomonas_M sp002286785	80.6408	875	1808	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_M	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019145475.1	s__Pseudomonas_E sp019145475	79.7601	687	1808	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_001579805.1	s__Pseudomonas_E azotoformans_A	79.3827	625	1808	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.75	96.24	0.87	0.84	8	-
--------------------------------------------------------------------------------
[2024-01-25 20:03:05,089] [INFO] GTDB search result was written to GCF_000498575.2_MS-3_genomic.fna/result_gtdb.tsv
[2024-01-25 20:03:05,089] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:03:05,095] [INFO] DFAST_QC result json was written to GCF_000498575.2_MS-3_genomic.fna/dqc_result.json
[2024-01-25 20:03:05,095] [INFO] DFAST_QC completed!
[2024-01-25 20:03:05,095] [INFO] Total running time: 0h1m44s