[2024-01-25 19:42:20,790] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:42:20,791] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:42:20,791] [INFO] DQC Reference Directory: /var/lib/cwl/stg59d546b9-df50-4517-b64c-eb497f946f92/dqc_reference
[2024-01-25 19:42:21,939] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:42:21,939] [INFO] Task started: Prodigal
[2024-01-25 19:42:21,940] [INFO] Running command: gunzip -c /var/lib/cwl/stg83670073-d76d-4b91-9111-eecaea146613/GCF_030159875.1_ASM3015987v1_genomic.fna.gz | prodigal -d GCF_030159875.1_ASM3015987v1_genomic.fna/cds.fna -a GCF_030159875.1_ASM3015987v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:42:27,957] [INFO] Task succeeded: Prodigal
[2024-01-25 19:42:27,957] [INFO] Task started: HMMsearch
[2024-01-25 19:42:27,957] [INFO] Running command: hmmsearch --tblout GCF_030159875.1_ASM3015987v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg59d546b9-df50-4517-b64c-eb497f946f92/dqc_reference/reference_markers.hmm GCF_030159875.1_ASM3015987v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:42:28,176] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:42:28,178] [INFO] Found 6/6 markers.
[2024-01-25 19:42:28,206] [INFO] Query marker FASTA was written to GCF_030159875.1_ASM3015987v1_genomic.fna/markers.fasta
[2024-01-25 19:42:28,206] [INFO] Task started: Blastn
[2024-01-25 19:42:28,206] [INFO] Running command: blastn -query GCF_030159875.1_ASM3015987v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg59d546b9-df50-4517-b64c-eb497f946f92/dqc_reference/reference_markers.fasta -out GCF_030159875.1_ASM3015987v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:42:28,889] [INFO] Task succeeded: Blastn
[2024-01-25 19:42:28,891] [INFO] Selected 19 target genomes.
[2024-01-25 19:42:28,892] [INFO] Target genome list was writen to GCF_030159875.1_ASM3015987v1_genomic.fna/target_genomes.txt
[2024-01-25 19:42:28,914] [INFO] Task started: fastANI
[2024-01-25 19:42:28,914] [INFO] Running command: fastANI --query /var/lib/cwl/stg83670073-d76d-4b91-9111-eecaea146613/GCF_030159875.1_ASM3015987v1_genomic.fna.gz --refList GCF_030159875.1_ASM3015987v1_genomic.fna/target_genomes.txt --output GCF_030159875.1_ASM3015987v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:42:42,289] [INFO] Task succeeded: fastANI
[2024-01-25 19:42:42,290] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg59d546b9-df50-4517-b64c-eb497f946f92/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:42:42,290] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg59d546b9-df50-4517-b64c-eb497f946f92/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:42:42,298] [INFO] Found 11 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 19:42:42,298] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:42:42,298] [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
Psychrosphaera saromensis	strain=SA4-48	GCA_002954545.1	716813	716813	type	True	99.9959	1189	1190	95	conclusive
Psychrosphaera saromensis	strain=KCTC 23240	GCA_014652155.1	716813	716813	type	True	99.9949	1187	1190	95	conclusive
Psychrosphaera aestuarii	strain=PSC101	GCA_017948405.1	1266052	1266052	type	True	78.3614	168	1190	95	below_threshold
Psychrosphaera ytuae	strain=MTZ26	GCA_017638545.1	2820710	2820710	type	True	77.9034	158	1190	95	below_threshold
Litorilituus lipolyticus	strain=RZ04	GCA_006439335.1	2491017	2491017	type	True	76.9571	71	1190	95	below_threshold
Pseudoalteromonas arctica	strain=A 37-1-2	GCA_000238395.4	394751	394751	type	True	76.8634	86	1190	95	below_threshold
Pseudoalteromonas marina	strain=DSM 17587	GCA_000238335.4	267375	267375	type	True	76.808	87	1190	95	below_threshold
Pseudoalteromonas arabiensis	strain=JCM 17292	GCA_001550155.1	874454	874454	type	True	76.5152	93	1190	95	below_threshold
Pseudocolwellia agarivorans	strain=QM50	GCA_002000085.1	1911682	1911682	type	True	76.5066	101	1190	95	below_threshold
Colwellia hornerae	strain=ACAM 607	GCA_007954355.1	89402	89402	type	True	76.4527	85	1190	95	below_threshold
Vibrio casei	strain=DSM 22364	GCA_002218025.2	673372	673372	type	True	76.2938	53	1190	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:42:42,300] [INFO] DFAST Taxonomy check result was written to GCF_030159875.1_ASM3015987v1_genomic.fna/tc_result.tsv
[2024-01-25 19:42:42,300] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:42:42,300] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:42:42,301] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg59d546b9-df50-4517-b64c-eb497f946f92/dqc_reference/checkm_data
[2024-01-25 19:42:42,301] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:42:42,338] [INFO] Task started: CheckM
[2024-01-25 19:42:42,338] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030159875.1_ASM3015987v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030159875.1_ASM3015987v1_genomic.fna/checkm_input GCF_030159875.1_ASM3015987v1_genomic.fna/checkm_result
[2024-01-25 19:43:05,134] [INFO] Task succeeded: CheckM
[2024-01-25 19:43:05,136] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:43:05,189] [INFO] ===== Completeness check finished =====
[2024-01-25 19:43:05,189] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:43:05,189] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030159875.1_ASM3015987v1_genomic.fna/markers.fasta)
[2024-01-25 19:43:05,189] [INFO] Task started: Blastn
[2024-01-25 19:43:05,190] [INFO] Running command: blastn -query GCF_030159875.1_ASM3015987v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg59d546b9-df50-4517-b64c-eb497f946f92/dqc_reference/reference_markers_gtdb.fasta -out GCF_030159875.1_ASM3015987v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:43:06,281] [INFO] Task succeeded: Blastn
[2024-01-25 19:43:06,284] [INFO] Selected 16 target genomes.
[2024-01-25 19:43:06,284] [INFO] Target genome list was writen to GCF_030159875.1_ASM3015987v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:43:06,305] [INFO] Task started: fastANI
[2024-01-25 19:43:06,306] [INFO] Running command: fastANI --query /var/lib/cwl/stg83670073-d76d-4b91-9111-eecaea146613/GCF_030159875.1_ASM3015987v1_genomic.fna.gz --refList GCF_030159875.1_ASM3015987v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030159875.1_ASM3015987v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:43:17,666] [INFO] Task succeeded: fastANI
[2024-01-25 19:43:17,674] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:43:17,675] [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_002954545.1	s__Psychrosphaera saromensis	99.9959	1189	1190	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Psychrosphaera	95.0	99.99	99.99	1.00	1.00	2	conclusive
GCF_018860345.1	s__Psychrosphaera sp018860345	81.4972	654	1190	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Psychrosphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018861025.1	s__Psychrosphaera sp018861025	78.3617	206	1190	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Psychrosphaera	95.0	99.99	99.99	1.00	1.00	2	-
GCF_017948405.1	s__Psychrosphaera aestuarii	78.3614	168	1190	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Psychrosphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009728465.1	s__Psychrosphaera haliotis	78.0826	207	1190	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Psychrosphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017638545.1	s__Psychrosphaera sp017638545	77.9261	156	1190	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Psychrosphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002104475.1	s__Cognaticolwellia mytili	76.7799	99	1190	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009832865.1	s__Colwellia sp009832865	76.7681	112	1190	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018860585.1	s__Colwellia sp018860585	76.7001	110	1190	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002000085.1	s__Pseudocolwellia agarivorans	76.5257	100	1190	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudocolwellia	95.0	95.36	95.36	0.90	0.90	2	-
GCF_002104515.1	s__Cognaticolwellia polaris	76.5157	120	1190	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007954355.1	s__Colwellia_A hornerae	76.4527	85	1190	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia_A	95.0	100.00	100.00	0.99	0.99	3	-
GCF_002218025.2	s__Vibrio casei	76.2767	52	1190	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	99.63	99.33	0.95	0.89	5	-
--------------------------------------------------------------------------------
[2024-01-25 19:43:17,676] [INFO] GTDB search result was written to GCF_030159875.1_ASM3015987v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:43:17,677] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:43:17,680] [INFO] DFAST_QC result json was written to GCF_030159875.1_ASM3015987v1_genomic.fna/dqc_result.json
[2024-01-25 19:43:17,680] [INFO] DFAST_QC completed!
[2024-01-25 19:43:17,681] [INFO] Total running time: 0h0m57s