[2024-01-25 20:26:05,717] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:26:05,718] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:26:05,718] [INFO] DQC Reference Directory: /var/lib/cwl/stgaf8d25fa-4ff0-46f1-9c36-f99e1050b3bf/dqc_reference
[2024-01-25 20:26:06,846] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:26:06,847] [INFO] Task started: Prodigal
[2024-01-25 20:26:06,847] [INFO] Running command: gunzip -c /var/lib/cwl/stgc0eddb44-835c-4726-a492-076b95888a0b/GCF_000215955.2_SSPSH_V2_genomic.fna.gz | prodigal -d GCF_000215955.2_SSPSH_V2_genomic.fna/cds.fna -a GCF_000215955.2_SSPSH_V2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:26:16,914] [INFO] Task succeeded: Prodigal
[2024-01-25 20:26:16,915] [INFO] Task started: HMMsearch
[2024-01-25 20:26:16,915] [INFO] Running command: hmmsearch --tblout GCF_000215955.2_SSPSH_V2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgaf8d25fa-4ff0-46f1-9c36-f99e1050b3bf/dqc_reference/reference_markers.hmm GCF_000215955.2_SSPSH_V2_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:26:17,163] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:26:17,164] [INFO] Found 6/6 markers.
[2024-01-25 20:26:17,194] [INFO] Query marker FASTA was written to GCF_000215955.2_SSPSH_V2_genomic.fna/markers.fasta
[2024-01-25 20:26:17,194] [INFO] Task started: Blastn
[2024-01-25 20:26:17,194] [INFO] Running command: blastn -query GCF_000215955.2_SSPSH_V2_genomic.fna/markers.fasta -db /var/lib/cwl/stgaf8d25fa-4ff0-46f1-9c36-f99e1050b3bf/dqc_reference/reference_markers.fasta -out GCF_000215955.2_SSPSH_V2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:26:17,941] [INFO] Task succeeded: Blastn
[2024-01-25 20:26:17,944] [INFO] Selected 21 target genomes.
[2024-01-25 20:26:17,944] [INFO] Target genome list was writen to GCF_000215955.2_SSPSH_V2_genomic.fna/target_genomes.txt
[2024-01-25 20:26:17,973] [INFO] Task started: fastANI
[2024-01-25 20:26:17,973] [INFO] Running command: fastANI --query /var/lib/cwl/stgc0eddb44-835c-4726-a492-076b95888a0b/GCF_000215955.2_SSPSH_V2_genomic.fna.gz --refList GCF_000215955.2_SSPSH_V2_genomic.fna/target_genomes.txt --output GCF_000215955.2_SSPSH_V2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:26:31,786] [INFO] Task succeeded: fastANI
[2024-01-25 20:26:31,787] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgaf8d25fa-4ff0-46f1-9c36-f99e1050b3bf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:26:31,787] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgaf8d25fa-4ff0-46f1-9c36-f99e1050b3bf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:26:31,799] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:26:31,799] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:26:31,799] [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 shabanensis	strain=E1L3A	GCA_000215955.3	180542	180542	type	True	100.0	1231	1232	95	conclusive
Salinisphaera orenii	strain=MK-B5	GCA_003788635.1	856731	856731	type	True	79.6277	567	1232	95	below_threshold
Salinisphaera halophila	strain=YIM 95161	GCA_003732545.1	1304158	1304158	type	True	79.4802	529	1232	95	below_threshold
Salinisphaera japonica	strain=YTM-1	GCA_003788585.1	1304270	1304270	type	True	78.9299	329	1232	95	below_threshold
Thioalkalivibrio sulfidiphilus	strain=HL-EbGR7	GCA_000021985.1	1033854	1033854	type	True	77.0662	57	1232	95	below_threshold
Spiribacter aquaticus	strain=SP30	GCA_007625215.1	1935996	1935996	type	True	76.7771	64	1232	95	below_threshold
Thioalkalivibrio thiocyanodenitrificans	strain=ARhD 1	GCA_000378965.1	243063	243063	type	True	76.7181	61	1232	95	below_threshold
Thiohalobacter thiocyanaticus	strain=Hrh1	GCA_003932505.1	585455	585455	type	True	76.4059	69	1232	95	below_threshold
Alcanivorax marinus	strain=R8-12	GCA_025532125.1	1177169	1177169	type	True	76.3786	87	1232	95	below_threshold
Xanthomonas arboricola	strain=CFBP 2528	GCA_001013475.1	56448	56448	type	True	76.3043	86	1232	95	below_threshold
Plasticicumulans lactativorans	strain=DSM 25287	GCA_004341245.1	1133106	1133106	type	True	76.2724	92	1232	95	below_threshold
Luteimonas salinisoli	strain=SJ-92	GCA_013425525.1	2752307	2752307	type	True	76.1634	80	1232	95	below_threshold
Halomonas ethanolica	strain=MCCC 1A11081	GCA_021404305.1	2733486	2733486	type	True	76.0965	72	1232	95	below_threshold
Pseudomonas benzenivorans	strain=DSM 8628	GCA_900100495.1	556533	556533	type	True	76.0908	86	1232	95	below_threshold
Dyella choica	strain=4 M-K27	GCA_003977665.1	1927959	1927959	type	True	76.0342	54	1232	95	below_threshold
Dyella acidiphila	strain=7MK23	GCA_014863405.1	2775866	2775866	type	True	76.0189	81	1232	95	below_threshold
Halomonas taeanensis	strain=BH539	GCA_900100755.1	284577	284577	type	True	75.8855	72	1232	95	below_threshold
Lysobacter maris	strain=KCTC 42381	GCA_006546735.2	1605891	1605891	type	True	75.8821	72	1232	95	below_threshold
Stenotrophomonas acidaminiphila	strain=DSM 13117	GCA_024221815.1	128780	128780	type	True	75.8477	82	1232	95	below_threshold
Marinobacterium arenosum	strain=CAU 1594	GCA_019795155.1	2862496	2862496	type	True	75.842	57	1232	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:26:31,800] [INFO] DFAST Taxonomy check result was written to GCF_000215955.2_SSPSH_V2_genomic.fna/tc_result.tsv
[2024-01-25 20:26:31,801] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:26:31,801] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:26:31,801] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgaf8d25fa-4ff0-46f1-9c36-f99e1050b3bf/dqc_reference/checkm_data
[2024-01-25 20:26:31,802] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:26:31,840] [INFO] Task started: CheckM
[2024-01-25 20:26:31,841] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000215955.2_SSPSH_V2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000215955.2_SSPSH_V2_genomic.fna/checkm_input GCF_000215955.2_SSPSH_V2_genomic.fna/checkm_result
[2024-01-25 20:27:02,447] [INFO] Task succeeded: CheckM
[2024-01-25 20:27:02,448] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:27:02,465] [INFO] ===== Completeness check finished =====
[2024-01-25 20:27:02,466] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:27:02,466] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000215955.2_SSPSH_V2_genomic.fna/markers.fasta)
[2024-01-25 20:27:02,466] [INFO] Task started: Blastn
[2024-01-25 20:27:02,466] [INFO] Running command: blastn -query GCF_000215955.2_SSPSH_V2_genomic.fna/markers.fasta -db /var/lib/cwl/stgaf8d25fa-4ff0-46f1-9c36-f99e1050b3bf/dqc_reference/reference_markers_gtdb.fasta -out GCF_000215955.2_SSPSH_V2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:27:03,858] [INFO] Task succeeded: Blastn
[2024-01-25 20:27:03,860] [INFO] Selected 10 target genomes.
[2024-01-25 20:27:03,860] [INFO] Target genome list was writen to GCF_000215955.2_SSPSH_V2_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:27:03,869] [INFO] Task started: fastANI
[2024-01-25 20:27:03,869] [INFO] Running command: fastANI --query /var/lib/cwl/stgc0eddb44-835c-4726-a492-076b95888a0b/GCF_000215955.2_SSPSH_V2_genomic.fna.gz --refList GCF_000215955.2_SSPSH_V2_genomic.fna/target_genomes_gtdb.txt --output GCF_000215955.2_SSPSH_V2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:27:11,635] [INFO] Task succeeded: fastANI
[2024-01-25 20:27:11,642] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:27:11,642] [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_000215955.2	s__Salinisphaera shabanensis	100.0	1231	1232	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_002729955.1	s__Salinisphaera sp002729955	84.2592	914	1232	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	83.8965	751	1232	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Salinisphaeraceae;g__Salinisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017744135.1	s__Salinisphaera sp017744135	81.8544	714	1232	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Salinisphaeraceae;g__Salinisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003788635.1	s__Salinisphaera orenii	79.6377	565	1232	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	79.4895	528	1232	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Salinisphaeraceae;g__Salinisphaera	96.8739	N/A	N/A	N/A	N/A	1	-
GCF_003177035.1	s__Salinisphaera sp003177035	78.6022	359	1232	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Salinisphaeraceae;g__Salinisphaera	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003602005.1	s__Salinisphaera sp003602005	78.0911	303	1232	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Salinisphaeraceae;g__Salinisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001013475.1	s__Xanthomonas arboricola	76.2655	88	1232	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	96.94	96.17	0.91	0.85	117	-
GCF_900100755.1	s__Halomonas_E taeanensis	75.8855	72	1232	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas_E	95.0	98.15	98.15	0.92	0.92	2	-
--------------------------------------------------------------------------------
[2024-01-25 20:27:11,645] [INFO] GTDB search result was written to GCF_000215955.2_SSPSH_V2_genomic.fna/result_gtdb.tsv
[2024-01-25 20:27:11,645] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:27:11,649] [INFO] DFAST_QC result json was written to GCF_000215955.2_SSPSH_V2_genomic.fna/dqc_result.json
[2024-01-25 20:27:11,649] [INFO] DFAST_QC completed!
[2024-01-25 20:27:11,649] [INFO] Total running time: 0h1m6s