[2024-01-24 13:09:34,011] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:09:34,013] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:09:34,013] [INFO] DQC Reference Directory: /var/lib/cwl/stg9a13bd2a-f356-43fe-bb17-32eb2a13da8b/dqc_reference
[2024-01-24 13:09:35,239] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:09:35,240] [INFO] Task started: Prodigal
[2024-01-24 13:09:35,240] [INFO] Running command: gunzip -c /var/lib/cwl/stg32a5df05-3bb0-4e2a-a1db-8160a8b45bce/GCF_007993775.1_ASM799377v1_genomic.fna.gz | prodigal -d GCF_007993775.1_ASM799377v1_genomic.fna/cds.fna -a GCF_007993775.1_ASM799377v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:09:59,905] [INFO] Task succeeded: Prodigal
[2024-01-24 13:09:59,906] [INFO] Task started: HMMsearch
[2024-01-24 13:09:59,906] [INFO] Running command: hmmsearch --tblout GCF_007993775.1_ASM799377v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9a13bd2a-f356-43fe-bb17-32eb2a13da8b/dqc_reference/reference_markers.hmm GCF_007993775.1_ASM799377v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:10:00,275] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:10:00,276] [INFO] Found 6/6 markers.
[2024-01-24 13:10:00,331] [INFO] Query marker FASTA was written to GCF_007993775.1_ASM799377v1_genomic.fna/markers.fasta
[2024-01-24 13:10:00,331] [INFO] Task started: Blastn
[2024-01-24 13:10:00,331] [INFO] Running command: blastn -query GCF_007993775.1_ASM799377v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9a13bd2a-f356-43fe-bb17-32eb2a13da8b/dqc_reference/reference_markers.fasta -out GCF_007993775.1_ASM799377v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:10:01,085] [INFO] Task succeeded: Blastn
[2024-01-24 13:10:01,089] [INFO] Selected 23 target genomes.
[2024-01-24 13:10:01,089] [INFO] Target genome list was writen to GCF_007993775.1_ASM799377v1_genomic.fna/target_genomes.txt
[2024-01-24 13:10:01,116] [INFO] Task started: fastANI
[2024-01-24 13:10:01,116] [INFO] Running command: fastANI --query /var/lib/cwl/stg32a5df05-3bb0-4e2a-a1db-8160a8b45bce/GCF_007993775.1_ASM799377v1_genomic.fna.gz --refList GCF_007993775.1_ASM799377v1_genomic.fna/target_genomes.txt --output GCF_007993775.1_ASM799377v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:10:30,190] [INFO] Task succeeded: fastANI
[2024-01-24 13:10:30,191] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9a13bd2a-f356-43fe-bb17-32eb2a13da8b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:10:30,191] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9a13bd2a-f356-43fe-bb17-32eb2a13da8b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:10:30,210] [INFO] Found 22 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:10:30,210] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:10:30,211] [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
Persicimonas caeni	strain=YN101	GCA_007993775.1	2292766	2292766	type	True	100.0	2681	2682	95	conclusive
Persicimonas caeni	strain=YN101	GCA_006517175.1	2292766	2292766	type	True	100.0	2681	2682	95	conclusive
Bradymonas sediminis	strain=FA350	GCA_003258315.1	1548548	1548548	type	True	77.4825	487	2682	95	below_threshold
Bradymonas sediminis	strain=DSM 28820	GCA_004362595.1	1548548	1548548	type	True	77.2989	477	2682	95	below_threshold
Lujinxingia vulgaris	strain=TMQ4	GCA_007997015.1	2600176	2600176	type	True	76.6697	328	2682	95	below_threshold
Lujinxingia litoralis	strain=B210	GCA_003260125.1	2211119	2211119	type	True	76.4422	238	2682	95	below_threshold
Corallococcus coralloides	strain=DSM 2259	GCA_000255295.1	184914	184914	type	True	75.4613	140	2682	95	below_threshold
Rhodovibrio salinarum	strain=DSM 9154	GCA_000515255.1	1087	1087	type	True	75.3027	64	2682	95	below_threshold
Haliangium ochraceum	strain=DSM 14365	GCA_000024805.1	80816	80816	type	True	75.2265	333	2682	95	below_threshold
Corallococcus interemptor	strain=AB047A	GCA_003668875.1	2316720	2316720	type	True	75.1812	140	2682	95	below_threshold
Rhodovibrio sodomensis	strain=DSM 9895	GCA_016583645.1	1088	1088	type	True	75.1782	111	2682	95	below_threshold
Plesiocystis pacifica	strain=SIR-1	GCA_000170895.1	191768	191768	type	True	75.0944	363	2682	95	below_threshold
Starkeya koreensis	strain=Jip08	GCA_023016525.1	266121	266121	type	True	75.0628	108	2682	95	below_threshold
Salsipaludibacter albus	strain=AS10	GCA_019798055.1	2849650	2849650	type	True	75.025	122	2682	95	below_threshold
Corallococcus terminator	strain=CA054A	GCA_003611635.1	2316733	2316733	type	True	74.9692	143	2682	95	below_threshold
Sphingomonas sanxanigenens	strain=NX02	GCA_000512205.2	397260	397260	type	True	74.9557	119	2682	95	below_threshold
Halomonas lactosivorans	strain=KCTC 52281	GCA_003254665.1	2185141	2185141	type	True	74.9485	118	2682	95	below_threshold
Methylorubrum rhodesianum	strain=DSM 5687	GCA_014199985.1	29427	29427	type	True	74.9372	114	2682	95	below_threshold
Kaistia adipata	strain=DSM 17808	GCA_000423225.1	166954	166954	type	True	74.9026	119	2682	95	below_threshold
Solimonas marina	strain=C16B3	GCA_012241385.1	2714601	2714601	type	True	74.8757	104	2682	95	below_threshold
Tistlia consotensis	strain=DSM 21585	GCA_900188055.1	1321365	1321365	type	True	74.8636	259	2682	95	below_threshold
Acuticoccus mangrovi	strain=B2012	GCA_016411865.1	2796142	2796142	type	True	74.8139	164	2682	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:10:30,212] [INFO] DFAST Taxonomy check result was written to GCF_007993775.1_ASM799377v1_genomic.fna/tc_result.tsv
[2024-01-24 13:10:30,213] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:10:30,213] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:10:30,213] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9a13bd2a-f356-43fe-bb17-32eb2a13da8b/dqc_reference/checkm_data
[2024-01-24 13:10:30,214] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:10:30,284] [INFO] Task started: CheckM
[2024-01-24 13:10:30,284] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007993775.1_ASM799377v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007993775.1_ASM799377v1_genomic.fna/checkm_input GCF_007993775.1_ASM799377v1_genomic.fna/checkm_result
[2024-01-24 13:11:35,151] [INFO] Task succeeded: CheckM
[2024-01-24 13:11:35,152] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:11:35,175] [INFO] ===== Completeness check finished =====
[2024-01-24 13:11:35,176] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:11:35,176] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007993775.1_ASM799377v1_genomic.fna/markers.fasta)
[2024-01-24 13:11:35,176] [INFO] Task started: Blastn
[2024-01-24 13:11:35,176] [INFO] Running command: blastn -query GCF_007993775.1_ASM799377v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9a13bd2a-f356-43fe-bb17-32eb2a13da8b/dqc_reference/reference_markers_gtdb.fasta -out GCF_007993775.1_ASM799377v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:11:36,400] [INFO] Task succeeded: Blastn
[2024-01-24 13:11:36,404] [INFO] Selected 15 target genomes.
[2024-01-24 13:11:36,404] [INFO] Target genome list was writen to GCF_007993775.1_ASM799377v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:11:36,433] [INFO] Task started: fastANI
[2024-01-24 13:11:36,434] [INFO] Running command: fastANI --query /var/lib/cwl/stg32a5df05-3bb0-4e2a-a1db-8160a8b45bce/GCF_007993775.1_ASM799377v1_genomic.fna.gz --refList GCF_007993775.1_ASM799377v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007993775.1_ASM799377v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:11:54,272] [INFO] Task succeeded: fastANI
[2024-01-24 13:11:54,284] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:11:54,285] [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_006517175.1	s__Persicimonas caeni	100.0	2681	2682	d__Bacteria;p__Myxococcota;c__Bradymonadia;o__Bradymonadales;f__Bradymonadaceae;g__Persicimonas	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_003258315.1	s__Bradymonas sediminis	77.4866	487	2682	d__Bacteria;p__Myxococcota;c__Bradymonadia;o__Bradymonadales;f__Bradymonadaceae;g__Bradymonas	95.0	99.99	99.99	1.00	1.00	2	-
GCA_007997015.1	s__Lujinxingia sp007997015	76.6634	329	2682	d__Bacteria;p__Myxococcota;c__Bradymonadia;o__Bradymonadales;f__Bradymonadaceae;g__Lujinxingia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004005565.1	s__Lujinxingia sediminis	76.5666	256	2682	d__Bacteria;p__Myxococcota;c__Bradymonadia;o__Bradymonadales;f__Bradymonadaceae;g__Lujinxingia	95.0	98.95	98.95	0.97	0.97	3	-
GCA_007997005.1	s__Lujinxingia sp007997005	76.5497	337	2682	d__Bacteria;p__Myxococcota;c__Bradymonadia;o__Bradymonadales;f__Bradymonadaceae;g__Lujinxingia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003260125.1	s__Lujinxingia litoralis	76.4344	239	2682	d__Bacteria;p__Myxococcota;c__Bradymonadia;o__Bradymonadales;f__Bradymonadaceae;g__Lujinxingia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013697635.1	s__JACCWM01 sp013697635	76.321	387	2682	d__Bacteria;p__Myxococcota;c__Bradymonadia;o__Bradymonadales;f__Bradymonadaceae;g__JACCWM01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007135085.1	s__SLJM01 sp007135085	75.8116	175	2682	d__Bacteria;p__Myxococcota;c__Bradymonadia;o__Bradymonadales;f__Bradymonadaceae;g__SLJM01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007120035.1	s__SKON01 sp007120035	75.7373	178	2682	d__Bacteria;p__Myxococcota;c__Bradymonadia;o__Bradymonadales;f__Bradymonadaceae;g__SKON01	95.0	99.72	99.66	0.90	0.87	5	-
GCA_007131755.1	s__SLJM01 sp007131755	75.7088	148	2682	d__Bacteria;p__Myxococcota;c__Bradymonadia;o__Bradymonadales;f__Bradymonadaceae;g__SLJM01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000024805.1	s__Haliangium ochraceum	75.2141	339	2682	d__Bacteria;p__Myxococcota;c__Polyangia;o__Haliangiales;f__Haliangiaceae;g__Haliangium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016711085.1	s__JADJTR01 sp016711085	74.959	82	2682	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__JADJTR01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000423225.1	s__Kaistia adipata	74.903	119	2682	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Kaistiaceae;g__Kaistia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001899075.1	s__Devosia_A sp001899075	74.7025	106	2682	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia_A	95.0	100.00	100.00	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:11:54,286] [INFO] GTDB search result was written to GCF_007993775.1_ASM799377v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:11:54,287] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:11:54,292] [INFO] DFAST_QC result json was written to GCF_007993775.1_ASM799377v1_genomic.fna/dqc_result.json
[2024-01-24 13:11:54,292] [INFO] DFAST_QC completed!
[2024-01-24 13:11:54,292] [INFO] Total running time: 0h2m20s