[2024-01-24 13:01:53,047] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:01:53,052] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:01:53,053] [INFO] DQC Reference Directory: /var/lib/cwl/stg7309f7dc-1cf7-49bb-8c5c-6081badfc68b/dqc_reference
[2024-01-24 13:01:54,418] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:01:54,419] [INFO] Task started: Prodigal
[2024-01-24 13:01:54,419] [INFO] Running command: gunzip -c /var/lib/cwl/stgf66c4e08-bd4b-4384-9d0a-d35257ecd9a5/GCF_003788585.1_ASM378858v1_genomic.fna.gz | prodigal -d GCF_003788585.1_ASM378858v1_genomic.fna/cds.fna -a GCF_003788585.1_ASM378858v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:02:04,370] [INFO] Task succeeded: Prodigal
[2024-01-24 13:02:04,371] [INFO] Task started: HMMsearch
[2024-01-24 13:02:04,371] [INFO] Running command: hmmsearch --tblout GCF_003788585.1_ASM378858v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7309f7dc-1cf7-49bb-8c5c-6081badfc68b/dqc_reference/reference_markers.hmm GCF_003788585.1_ASM378858v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:02:04,688] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:02:04,690] [INFO] Found 6/6 markers.
[2024-01-24 13:02:04,723] [INFO] Query marker FASTA was written to GCF_003788585.1_ASM378858v1_genomic.fna/markers.fasta
[2024-01-24 13:02:04,723] [INFO] Task started: Blastn
[2024-01-24 13:02:04,724] [INFO] Running command: blastn -query GCF_003788585.1_ASM378858v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7309f7dc-1cf7-49bb-8c5c-6081badfc68b/dqc_reference/reference_markers.fasta -out GCF_003788585.1_ASM378858v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:02:05,517] [INFO] Task succeeded: Blastn
[2024-01-24 13:02:05,522] [INFO] Selected 19 target genomes.
[2024-01-24 13:02:05,522] [INFO] Target genome list was writen to GCF_003788585.1_ASM378858v1_genomic.fna/target_genomes.txt
[2024-01-24 13:02:05,529] [INFO] Task started: fastANI
[2024-01-24 13:02:05,530] [INFO] Running command: fastANI --query /var/lib/cwl/stgf66c4e08-bd4b-4384-9d0a-d35257ecd9a5/GCF_003788585.1_ASM378858v1_genomic.fna.gz --refList GCF_003788585.1_ASM378858v1_genomic.fna/target_genomes.txt --output GCF_003788585.1_ASM378858v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:02:19,283] [INFO] Task succeeded: fastANI
[2024-01-24 13:02:19,284] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7309f7dc-1cf7-49bb-8c5c-6081badfc68b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:02:19,284] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7309f7dc-1cf7-49bb-8c5c-6081badfc68b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:02:19,302] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:02:19,302] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:02:19,303] [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 japonica	strain=YTM-1	GCA_003788585.1	1304270	1304270	type	True	100.0	1057	1057	95	conclusive
Salinisphaera shabanensis	strain=E1L3A	GCA_000215955.3	180542	180542	type	True	79.1435	326	1057	95	below_threshold
Salinisphaera orenii	strain=MK-B5	GCA_003788635.1	856731	856731	type	True	78.764	391	1057	95	below_threshold
Salinisphaera halophila	strain=YIM 95161	GCA_003732545.1	1304158	1304158	type	True	78.5037	398	1057	95	below_threshold
Allochromatium tepidum	strain=NZ	GCA_018409545.1	553982	553982	type	True	76.338	72	1057	95	below_threshold
Methylonatrum kenyense	strain=AMT 1	GCA_023195885.1	455253	455253	type	True	76.1982	53	1057	95	below_threshold
Lysobacter arseniciresistens	strain=ZS79	GCA_000768335.1	1385522	1385522	type	True	76.1758	75	1057	95	below_threshold
Thioalkalivibrio paradoxus	strain=ARh 1	GCA_000227685.3	108010	108010	type	True	76.1704	62	1057	95	below_threshold
Pseudomonas aromaticivorans	strain=MAP12	GCA_019097855.1	2849492	2849492	type	True	76.1313	85	1057	95	below_threshold
Arhodomonas aquaeolei	strain=DSM 8974	GCA_000374645.1	2369	2369	type	True	75.9469	104	1057	95	below_threshold
Algiphilus aromaticivorans	strain=DG1253	GCA_000733765.1	382454	382454	type	True	75.8596	86	1057	95	below_threshold
Rhodanobacter spathiphylli	strain=B39	GCA_000264295.1	347483	347483	type	True	75.7961	83	1057	95	below_threshold
Pseudomonas putida	strain=IPO3752	GCA_013387005.1	303	303	suspected-type	True	75.6297	53	1057	95	below_threshold
Pseudomonas faucium	strain=BML-PP048	GCA_021602585.1	2740518	2740518	type	True	75.5031	92	1057	95	below_threshold
Pseudomonas faucium	strain=BML-PP048	GCA_013373935.1	2740518	2740518	type	True	75.4213	90	1057	95	below_threshold
Variovorax boronicumulans	strain=NBRC 103145	GCA_001591345.1	436515	436515	type	True	75.1706	95	1057	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:02:19,305] [INFO] DFAST Taxonomy check result was written to GCF_003788585.1_ASM378858v1_genomic.fna/tc_result.tsv
[2024-01-24 13:02:19,305] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:02:19,306] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:02:19,306] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7309f7dc-1cf7-49bb-8c5c-6081badfc68b/dqc_reference/checkm_data
[2024-01-24 13:02:19,307] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:02:19,343] [INFO] Task started: CheckM
[2024-01-24 13:02:19,343] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003788585.1_ASM378858v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003788585.1_ASM378858v1_genomic.fna/checkm_input GCF_003788585.1_ASM378858v1_genomic.fna/checkm_result
[2024-01-24 13:02:51,842] [INFO] Task succeeded: CheckM
[2024-01-24 13:02:51,844] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:02:51,868] [INFO] ===== Completeness check finished =====
[2024-01-24 13:02:51,868] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:02:51,869] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003788585.1_ASM378858v1_genomic.fna/markers.fasta)
[2024-01-24 13:02:51,869] [INFO] Task started: Blastn
[2024-01-24 13:02:51,869] [INFO] Running command: blastn -query GCF_003788585.1_ASM378858v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7309f7dc-1cf7-49bb-8c5c-6081badfc68b/dqc_reference/reference_markers_gtdb.fasta -out GCF_003788585.1_ASM378858v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:02:53,173] [INFO] Task succeeded: Blastn
[2024-01-24 13:02:53,176] [INFO] Selected 10 target genomes.
[2024-01-24 13:02:53,176] [INFO] Target genome list was writen to GCF_003788585.1_ASM378858v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:02:53,185] [INFO] Task started: fastANI
[2024-01-24 13:02:53,185] [INFO] Running command: fastANI --query /var/lib/cwl/stgf66c4e08-bd4b-4384-9d0a-d35257ecd9a5/GCF_003788585.1_ASM378858v1_genomic.fna.gz --refList GCF_003788585.1_ASM378858v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003788585.1_ASM378858v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:03:00,968] [INFO] Task succeeded: fastANI
[2024-01-24 13:03:00,976] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:03:00,976] [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_003788585.1	s__Salinisphaera japonica	100.0	1057	1057	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Salinisphaeraceae;g__Salinisphaera	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002715985.1	s__Salinisphaera sp002715985	89.5638	630	1057	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Salinisphaeraceae;g__Salinisphaera	95.0	99.39	99.39	0.77	0.77	2	-
GCA_002320455.1	s__Salinisphaera sp002320455	82.6773	670	1057	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	79.5649	518	1057	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	79.0272	496	1057	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	78.9522	453	1057	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Salinisphaeraceae;g__Salinisphaera	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003788635.1	s__Salinisphaera orenii	78.7473	393	1057	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Salinisphaeraceae;g__Salinisphaera	96.8739	N/A	N/A	N/A	N/A	1	-
GCF_003732545.1	s__Salinisphaera halophila	78.5331	395	1057	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Salinisphaeraceae;g__Salinisphaera	96.8739	N/A	N/A	N/A	N/A	1	-
GCF_000184745.1	s__Variovorax paradoxus_C	75.1969	84	1057	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Variovorax	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:03:00,979] [INFO] GTDB search result was written to GCF_003788585.1_ASM378858v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:03:00,979] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:03:00,984] [INFO] DFAST_QC result json was written to GCF_003788585.1_ASM378858v1_genomic.fna/dqc_result.json
[2024-01-24 13:03:00,984] [INFO] DFAST_QC completed!
[2024-01-24 13:03:00,984] [INFO] Total running time: 0h1m8s