[2024-01-24 13:17:05,560] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:17:05,562] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:17:05,562] [INFO] DQC Reference Directory: /var/lib/cwl/stgc3faed66-4938-40b5-9216-38aa56491485/dqc_reference
[2024-01-24 13:17:06,926] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:17:06,927] [INFO] Task started: Prodigal
[2024-01-24 13:17:06,927] [INFO] Running command: gunzip -c /var/lib/cwl/stg877e012e-e54c-4b11-a11c-79b46811ac8b/GCF_003732545.1_ASM373254v1_genomic.fna.gz | prodigal -d GCF_003732545.1_ASM373254v1_genomic.fna/cds.fna -a GCF_003732545.1_ASM373254v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:17:17,602] [INFO] Task succeeded: Prodigal
[2024-01-24 13:17:17,603] [INFO] Task started: HMMsearch
[2024-01-24 13:17:17,603] [INFO] Running command: hmmsearch --tblout GCF_003732545.1_ASM373254v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc3faed66-4938-40b5-9216-38aa56491485/dqc_reference/reference_markers.hmm GCF_003732545.1_ASM373254v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:17:17,884] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:17:17,886] [INFO] Found 6/6 markers.
[2024-01-24 13:17:17,919] [INFO] Query marker FASTA was written to GCF_003732545.1_ASM373254v1_genomic.fna/markers.fasta
[2024-01-24 13:17:17,919] [INFO] Task started: Blastn
[2024-01-24 13:17:17,919] [INFO] Running command: blastn -query GCF_003732545.1_ASM373254v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc3faed66-4938-40b5-9216-38aa56491485/dqc_reference/reference_markers.fasta -out GCF_003732545.1_ASM373254v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:17:18,950] [INFO] Task succeeded: Blastn
[2024-01-24 13:17:18,953] [INFO] Selected 16 target genomes.
[2024-01-24 13:17:18,954] [INFO] Target genome list was writen to GCF_003732545.1_ASM373254v1_genomic.fna/target_genomes.txt
[2024-01-24 13:17:18,960] [INFO] Task started: fastANI
[2024-01-24 13:17:18,960] [INFO] Running command: fastANI --query /var/lib/cwl/stg877e012e-e54c-4b11-a11c-79b46811ac8b/GCF_003732545.1_ASM373254v1_genomic.fna.gz --refList GCF_003732545.1_ASM373254v1_genomic.fna/target_genomes.txt --output GCF_003732545.1_ASM373254v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:17:30,055] [INFO] Task succeeded: fastANI
[2024-01-24 13:17:30,055] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc3faed66-4938-40b5-9216-38aa56491485/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:17:30,056] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc3faed66-4938-40b5-9216-38aa56491485/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:17:30,069] [INFO] Found 16 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:17:30,069] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 13:17:30,069] [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
Salinisphaera halophila	strain=YIM 95161	GCA_003732545.1	1304158	1304158	type	True	100.0	1193	1200	95	inconclusive
Salinisphaera orenii	strain=MK-B5	GCA_003788635.1	856731	856731	type	True	96.8735	1052	1200	95	inconclusive
Salinisphaera shabanensis	strain=E1L3A	GCA_000215955.3	180542	180542	type	True	79.534	530	1200	95	below_threshold
Salinisphaera japonica	strain=YTM-1	GCA_003788585.1	1304270	1304270	type	True	78.6065	390	1200	95	below_threshold
Arhodomonas aquaeolei	strain=DSM 8974	GCA_000374645.1	2369	2369	type	True	76.7671	188	1200	95	below_threshold
Spiribacter aquaticus	strain=SP30	GCA_007625215.1	1935996	1935996	type	True	76.6913	99	1200	95	below_threshold
Solimonas fluminis	strain=HR-BB	GCA_002930645.1	2086571	2086571	type	True	76.6149	213	1200	95	below_threshold
Allochromatium tepidum	strain=NZ	GCA_018409545.1	553982	553982	type	True	76.5412	114	1200	95	below_threshold
Luteimonas viscosa	strain=XBU10	GCA_008244685.1	1132694	1132694	type	True	76.2738	177	1200	95	below_threshold
Luteimonas saliphila	strain=SJ-9	GCA_016774335.1	2804919	2804919	type	True	76.2527	180	1200	95	below_threshold
Solimonas terrae	strain=KIS83-12	GCA_011067135.1	1396819	1396819	type	True	76.1726	163	1200	95	below_threshold
Luteimonas wenzhouensis	strain=YD-1	GCA_007859305.1	2599615	2599615	type	True	76.1589	217	1200	95	below_threshold
Luteimonas weifangensis	strain=WF-2	GCA_003416885.1	2303539	2303539	type	True	76.0972	160	1200	95	below_threshold
Lysobacter chinensis	strain=TLK-CK17	GCA_021725675.1	2912247	2912247	type	True	75.9453	158	1200	95	below_threshold
Rubrivivax gelatinosus	strain=DSM 1709	GCA_016583525.1	28068	28068	suspected-type	True	75.5626	237	1200	95	below_threshold
Rubrivivax gelatinosus	strain=DSM 1709	GCA_004340905.1	28068	28068	suspected-type	True	75.5189	240	1200	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:17:30,071] [INFO] DFAST Taxonomy check result was written to GCF_003732545.1_ASM373254v1_genomic.fna/tc_result.tsv
[2024-01-24 13:17:30,072] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:17:30,072] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:17:30,072] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc3faed66-4938-40b5-9216-38aa56491485/dqc_reference/checkm_data
[2024-01-24 13:17:30,073] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:17:30,113] [INFO] Task started: CheckM
[2024-01-24 13:17:30,113] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003732545.1_ASM373254v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003732545.1_ASM373254v1_genomic.fna/checkm_input GCF_003732545.1_ASM373254v1_genomic.fna/checkm_result
[2024-01-24 13:18:04,296] [INFO] Task succeeded: CheckM
[2024-01-24 13:18:04,298] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:18:04,319] [INFO] ===== Completeness check finished =====
[2024-01-24 13:18:04,319] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:18:04,320] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003732545.1_ASM373254v1_genomic.fna/markers.fasta)
[2024-01-24 13:18:04,320] [INFO] Task started: Blastn
[2024-01-24 13:18:04,320] [INFO] Running command: blastn -query GCF_003732545.1_ASM373254v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc3faed66-4938-40b5-9216-38aa56491485/dqc_reference/reference_markers_gtdb.fasta -out GCF_003732545.1_ASM373254v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:18:06,149] [INFO] Task succeeded: Blastn
[2024-01-24 13:18:06,152] [INFO] Selected 11 target genomes.
[2024-01-24 13:18:06,152] [INFO] Target genome list was writen to GCF_003732545.1_ASM373254v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:18:06,166] [INFO] Task started: fastANI
[2024-01-24 13:18:06,166] [INFO] Running command: fastANI --query /var/lib/cwl/stg877e012e-e54c-4b11-a11c-79b46811ac8b/GCF_003732545.1_ASM373254v1_genomic.fna.gz --refList GCF_003732545.1_ASM373254v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003732545.1_ASM373254v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:18:14,505] [INFO] Task succeeded: fastANI
[2024-01-24 13:18:14,517] [INFO] Found 11 fastANI hits (2 hits with ANI > circumscription radius)
[2024-01-24 13:18:14,517] [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_003732545.1	s__Salinisphaera halophila	100.0	1193	1200	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Salinisphaeraceae;g__Salinisphaera	96.8739	N/A	N/A	N/A	N/A	1	inconclusive
GCF_003788635.1	s__Salinisphaera orenii	96.8926	1051	1200	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Salinisphaeraceae;g__Salinisphaera	96.8739	N/A	N/A	N/A	N/A	1	inconclusive
GCF_017744135.1	s__Salinisphaera sp017744135	81.2602	692	1200	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Salinisphaeraceae;g__Salinisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002729955.1	s__Salinisphaera sp002729955	80.243	622	1200	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Salinisphaeraceae;g__Salinisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002433465.1	s__Salinisphaera sp002433465	80.0051	509	1200	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Salinisphaeraceae;g__Salinisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000215955.2	s__Salinisphaera shabanensis	79.5294	531	1200	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Salinisphaeraceae;g__Salinisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000732535.1	s__Salinisphaera hydrothermalis	79.2043	421	1200	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Salinisphaeraceae;g__Salinisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003177035.1	s__Salinisphaera sp003177035	79.1041	450	1200	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Salinisphaeraceae;g__Salinisphaera	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003788585.1	s__Salinisphaera japonica	78.6171	389	1200	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Salinisphaeraceae;g__Salinisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003602005.1	s__Salinisphaera sp003602005	78.4428	390	1200	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Salinisphaeraceae;g__Salinisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016779605.1	s__Nevskia sp016779605	76.7141	216	1200	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Nevskia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:18:14,519] [INFO] GTDB search result was written to GCF_003732545.1_ASM373254v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:18:14,519] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:18:14,523] [INFO] DFAST_QC result json was written to GCF_003732545.1_ASM373254v1_genomic.fna/dqc_result.json
[2024-01-24 13:18:14,523] [INFO] DFAST_QC completed!
[2024-01-24 13:18:14,523] [INFO] Total running time: 0h1m9s