[2024-01-25 18:11:05,779] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:11:05,780] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:11:05,780] [INFO] DQC Reference Directory: /var/lib/cwl/stg74b459cc-4f78-43ec-92c6-9b9842bdfc30/dqc_reference
[2024-01-25 18:11:06,957] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:11:06,957] [INFO] Task started: Prodigal
[2024-01-25 18:11:06,958] [INFO] Running command: gunzip -c /var/lib/cwl/stg21a3381e-a508-47b9-9631-fd4e7d9b5fac/GCF_003788635.1_ASM378863v1_genomic.fna.gz | prodigal -d GCF_003788635.1_ASM378863v1_genomic.fna/cds.fna -a GCF_003788635.1_ASM378863v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:11:16,015] [INFO] Task succeeded: Prodigal
[2024-01-25 18:11:16,015] [INFO] Task started: HMMsearch
[2024-01-25 18:11:16,015] [INFO] Running command: hmmsearch --tblout GCF_003788635.1_ASM378863v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg74b459cc-4f78-43ec-92c6-9b9842bdfc30/dqc_reference/reference_markers.hmm GCF_003788635.1_ASM378863v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:11:16,223] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:11:16,224] [INFO] Found 6/6 markers.
[2024-01-25 18:11:16,252] [INFO] Query marker FASTA was written to GCF_003788635.1_ASM378863v1_genomic.fna/markers.fasta
[2024-01-25 18:11:16,252] [INFO] Task started: Blastn
[2024-01-25 18:11:16,253] [INFO] Running command: blastn -query GCF_003788635.1_ASM378863v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg74b459cc-4f78-43ec-92c6-9b9842bdfc30/dqc_reference/reference_markers.fasta -out GCF_003788635.1_ASM378863v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:11:17,139] [INFO] Task succeeded: Blastn
[2024-01-25 18:11:17,142] [INFO] Selected 17 target genomes.
[2024-01-25 18:11:17,142] [INFO] Target genome list was writen to GCF_003788635.1_ASM378863v1_genomic.fna/target_genomes.txt
[2024-01-25 18:11:17,151] [INFO] Task started: fastANI
[2024-01-25 18:11:17,151] [INFO] Running command: fastANI --query /var/lib/cwl/stg21a3381e-a508-47b9-9631-fd4e7d9b5fac/GCF_003788635.1_ASM378863v1_genomic.fna.gz --refList GCF_003788635.1_ASM378863v1_genomic.fna/target_genomes.txt --output GCF_003788635.1_ASM378863v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:11:28,628] [INFO] Task succeeded: fastANI
[2024-01-25 18:11:28,628] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg74b459cc-4f78-43ec-92c6-9b9842bdfc30/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:11:28,629] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg74b459cc-4f78-43ec-92c6-9b9842bdfc30/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:11:28,639] [INFO] Found 17 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 18:11:28,639] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-25 18:11:28,640] [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 orenii	strain=MK-B5	GCA_003788635.1	856731	856731	type	True	100.0	1195	1198	95	inconclusive
Salinisphaera halophila	strain=YIM 95161	GCA_003732545.1	1304158	1304158	type	True	96.8739	1045	1198	95	inconclusive
Salinisphaera shabanensis	strain=E1L3A	GCA_000215955.3	180542	180542	type	True	79.6328	546	1198	95	below_threshold
Salinisphaera japonica	strain=YTM-1	GCA_003788585.1	1304270	1304270	type	True	78.7765	390	1198	95	below_threshold
Thiohalobacter thiocyanaticus	strain=Hrh1	GCA_003932505.1	585455	585455	type	True	77.0664	148	1198	95	below_threshold
Solimonas fluminis	strain=HR-BB	GCA_002930645.1	2086571	2086571	type	True	76.8896	215	1198	95	below_threshold
Solimonas aquatica	strain=DSM 25927	GCA_900111015.1	489703	489703	type	True	76.6959	201	1198	95	below_threshold
Allochromatium tepidum	strain=NZ	GCA_018409545.1	553982	553982	type	True	76.6878	117	1198	95	below_threshold
Luteimonas colneyensis	strain=Sa2BVA3	GCA_014836665.1	2762230	2762230	type	True	76.4939	183	1198	95	below_threshold
Spiribacter aquaticus	strain=SP30	GCA_007625215.1	1935996	1935996	type	True	76.4728	113	1198	95	below_threshold
Frateuria flava	strain=MAH-13	GCA_017837635.1	2821489	2821489	type	True	76.4097	145	1198	95	below_threshold
Pseudomonas aromaticivorans	strain=MAP12	GCA_019097855.1	2849492	2849492	type	True	76.3432	171	1198	95	below_threshold
Solimonas terrae	strain=KIS83-12	GCA_011067135.1	1396819	1396819	type	True	76.2989	178	1198	95	below_threshold
Arenimonas caeni	strain=z29	GCA_003024235.1	2058085	2058085	type	True	76.2783	179	1198	95	below_threshold
Luteimonas saliphila	strain=SJ-9	GCA_016774335.1	2804919	2804919	type	True	76.2654	191	1198	95	below_threshold
Rubrivivax gelatinosus	strain=DSM 1709	GCA_016583525.1	28068	28068	suspected-type	True	75.6472	238	1198	95	below_threshold
Rubrivivax gelatinosus	strain=DSM 1709	GCA_004340905.1	28068	28068	suspected-type	True	75.5825	242	1198	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:11:28,643] [INFO] DFAST Taxonomy check result was written to GCF_003788635.1_ASM378863v1_genomic.fna/tc_result.tsv
[2024-01-25 18:11:28,643] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:11:28,643] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:11:28,644] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg74b459cc-4f78-43ec-92c6-9b9842bdfc30/dqc_reference/checkm_data
[2024-01-25 18:11:28,644] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:11:28,683] [INFO] Task started: CheckM
[2024-01-25 18:11:28,683] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003788635.1_ASM378863v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003788635.1_ASM378863v1_genomic.fna/checkm_input GCF_003788635.1_ASM378863v1_genomic.fna/checkm_result
[2024-01-25 18:11:58,427] [INFO] Task succeeded: CheckM
[2024-01-25 18:11:58,428] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:11:58,447] [INFO] ===== Completeness check finished =====
[2024-01-25 18:11:58,447] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:11:58,447] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003788635.1_ASM378863v1_genomic.fna/markers.fasta)
[2024-01-25 18:11:58,448] [INFO] Task started: Blastn
[2024-01-25 18:11:58,448] [INFO] Running command: blastn -query GCF_003788635.1_ASM378863v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg74b459cc-4f78-43ec-92c6-9b9842bdfc30/dqc_reference/reference_markers_gtdb.fasta -out GCF_003788635.1_ASM378863v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:12:00,223] [INFO] Task succeeded: Blastn
[2024-01-25 18:12:00,227] [INFO] Selected 10 target genomes.
[2024-01-25 18:12:00,227] [INFO] Target genome list was writen to GCF_003788635.1_ASM378863v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:12:00,246] [INFO] Task started: fastANI
[2024-01-25 18:12:00,246] [INFO] Running command: fastANI --query /var/lib/cwl/stg21a3381e-a508-47b9-9631-fd4e7d9b5fac/GCF_003788635.1_ASM378863v1_genomic.fna.gz --refList GCF_003788635.1_ASM378863v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003788635.1_ASM378863v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:12:08,617] [INFO] Task succeeded: fastANI
[2024-01-25 18:12:08,624] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:12:08,625] [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_003788635.1	s__Salinisphaera orenii	100.0	1195	1198	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Salinisphaeraceae;g__Salinisphaera	96.8739	N/A	N/A	N/A	N/A	1	conclusive
GCF_003732545.1	s__Salinisphaera halophila	96.8739	1045	1198	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Salinisphaeraceae;g__Salinisphaera	96.8739	N/A	N/A	N/A	N/A	1	conclusive
GCF_017744135.1	s__Salinisphaera sp017744135	81.2285	693	1198	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	80.3652	637	1198	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	80.0355	525	1198	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	79.6238	547	1198	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	79.4225	451	1198	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Salinisphaeraceae;g__Salinisphaera	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000732535.1	s__Salinisphaera hydrothermalis	79.0624	446	1198	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Salinisphaeraceae;g__Salinisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003788585.1	s__Salinisphaera japonica	78.7868	389	1198	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	78.5376	402	1198	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Salinisphaeraceae;g__Salinisphaera	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:12:08,626] [INFO] GTDB search result was written to GCF_003788635.1_ASM378863v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:12:08,626] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:12:08,629] [INFO] DFAST_QC result json was written to GCF_003788635.1_ASM378863v1_genomic.fna/dqc_result.json
[2024-01-25 18:12:08,629] [INFO] DFAST_QC completed!
[2024-01-25 18:12:08,629] [INFO] Total running time: 0h1m3s