[2023-06-17 06:44:56,393] [INFO] DFAST_QC pipeline started.
[2023-06-17 06:44:56,396] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 06:44:56,396] [INFO] DQC Reference Directory: /var/lib/cwl/stg5090ff0c-04a1-4c33-8a5c-1e69c50312f2/dqc_reference
[2023-06-17 06:44:57,710] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 06:44:57,711] [INFO] Task started: Prodigal
[2023-06-17 06:44:57,711] [INFO] Running command: gunzip -c /var/lib/cwl/stgdda97646-119c-4361-89a8-8f6cf109d248/GCA_009692535.1_ASM969253v1_genomic.fna.gz | prodigal -d GCA_009692535.1_ASM969253v1_genomic.fna/cds.fna -a GCA_009692535.1_ASM969253v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 06:45:06,882] [INFO] Task succeeded: Prodigal
[2023-06-17 06:45:06,882] [INFO] Task started: HMMsearch
[2023-06-17 06:45:06,882] [INFO] Running command: hmmsearch --tblout GCA_009692535.1_ASM969253v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5090ff0c-04a1-4c33-8a5c-1e69c50312f2/dqc_reference/reference_markers.hmm GCA_009692535.1_ASM969253v1_genomic.fna/protein.faa > /dev/null
[2023-06-17 06:45:07,188] [INFO] Task succeeded: HMMsearch
[2023-06-17 06:45:07,190] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgdda97646-119c-4361-89a8-8f6cf109d248/GCA_009692535.1_ASM969253v1_genomic.fna.gz]
[2023-06-17 06:45:07,252] [INFO] Query marker FASTA was written to GCA_009692535.1_ASM969253v1_genomic.fna/markers.fasta
[2023-06-17 06:45:07,252] [INFO] Task started: Blastn
[2023-06-17 06:45:07,253] [INFO] Running command: blastn -query GCA_009692535.1_ASM969253v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5090ff0c-04a1-4c33-8a5c-1e69c50312f2/dqc_reference/reference_markers.fasta -out GCA_009692535.1_ASM969253v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 06:45:08,060] [INFO] Task succeeded: Blastn
[2023-06-17 06:45:08,064] [INFO] Selected 33 target genomes.
[2023-06-17 06:45:08,065] [INFO] Target genome list was writen to GCA_009692535.1_ASM969253v1_genomic.fna/target_genomes.txt
[2023-06-17 06:45:08,067] [INFO] Task started: fastANI
[2023-06-17 06:45:08,067] [INFO] Running command: fastANI --query /var/lib/cwl/stgdda97646-119c-4361-89a8-8f6cf109d248/GCA_009692535.1_ASM969253v1_genomic.fna.gz --refList GCA_009692535.1_ASM969253v1_genomic.fna/target_genomes.txt --output GCA_009692535.1_ASM969253v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 06:45:36,470] [INFO] Task succeeded: fastANI
[2023-06-17 06:45:36,471] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5090ff0c-04a1-4c33-8a5c-1e69c50312f2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 06:45:36,471] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5090ff0c-04a1-4c33-8a5c-1e69c50312f2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 06:45:36,498] [INFO] Found 31 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 06:45:36,498] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-17 06:45:36,498] [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
Haliangium ochraceum	strain=DSM 14365	GCA_000024805.1	80816	80816	type	True	75.6021	309	1093	95	below_threshold
Anaeromyxobacter dehalogenans	strain=2CP-1	GCA_000022145.1	161493	161493	type	True	75.4023	280	1093	95	below_threshold
Myxococcus xanthus	strain=DSM 16526	GCA_900106535.1	34	34	type	True	75.1709	111	1093	95	below_threshold
Schlegelella thermodepolymerans	strain=DSM 15344	GCA_002933415.1	215580	215580	type	True	75.1026	98	1093	95	below_threshold
Schlegelella thermodepolymerans	strain=DSM 15344	GCA_003349825.1	215580	215580	type	True	75.101	99	1093	95	below_threshold
Schlegelella thermodepolymerans	strain=DSM 15344	GCA_015476235.1	215580	215580	type	True	75.0944	100	1093	95	below_threshold
Myxococcus virescens	strain=DSM 2260	GCA_900101905.1	83456	83456	type	True	75.0705	125	1093	95	below_threshold
Myxococcus virescens	strain=NBRC 100334	GCA_007989405.1	83456	83456	type	True	75.0613	127	1093	95	below_threshold
Methylobacterium oryzihabitans	strain=TER-1	GCA_004004555.2	2499852	2499852	type	True	75.0074	175	1093	95	below_threshold
Plesiocystis pacifica	strain=SIR-1	GCA_000170895.1	191768	191768	type	True	74.9926	241	1093	95	below_threshold
Oharaeibacter diazotrophicus	strain=DSM 102969	GCA_004362745.1	1920512	1920512	type	True	74.9708	212	1093	95	below_threshold
Lutibaculum baratangense	strain=AMV1	GCA_000496075.1	1358440	1358440	type	True	74.9667	110	1093	95	below_threshold
Rhodoplanes roseus	strain=DSM 5909	GCA_003258865.1	29409	29409	type	True	74.9478	149	1093	95	below_threshold
Geomonas azotofigens	strain=Red51	GCA_018919395.1	2843196	2843196	type	True	74.923	55	1093	95	below_threshold
Rhodoplanes elegans	strain=DSM 11907	GCA_003258805.1	29408	29408	type	True	74.9174	168	1093	95	below_threshold
Thauera aminoaromatica	strain=S2	GCA_000310185.1	164330	164330	type	True	74.9113	128	1093	95	below_threshold
Malikia granosa	strain=P1	GCA_002980595.1	263067	263067	type	True	74.8945	78	1093	95	below_threshold
Malikia spinosa	strain=83	GCA_002980625.1	86180	86180	type	True	74.8833	75	1093	95	below_threshold
Sulfurifustis variabilis	strain=skN76	GCA_002355415.1	1675686	1675686	type	True	74.8832	98	1093	95	below_threshold
Methylobrevis albus	strain=L22	GCA_015904235.1	2793297	2793297	type	True	74.8808	166	1093	95	below_threshold
Arenimonas composti	strain=DSM 18010	GCA_000426365.1	370776	370776	type	True	74.8665	142	1093	95	below_threshold
Bradymonas sediminis	strain=FA350	GCA_003258315.1	1548548	1548548	type	True	74.861	57	1093	95	below_threshold
Arenimonas composti	strain=TR7-09	GCA_000747175.1	370776	370776	type	True	74.8495	136	1093	95	below_threshold
Sphaerotilus natans	strain=ATCC 13338	GCA_900156335.1	34103	34103	type	True	74.8376	128	1093	95	below_threshold
Dokdonella fugitiva	strain=A3	GCA_004342425.1	328517	328517	type	True	74.8038	164	1093	95	below_threshold
Steroidobacter agariperforans	strain=KA5-B	GCA_004138335.1	268404	268404	type	True	74.8012	61	1093	95	below_threshold
Protaetiibacter larvae	strain=KACC 19322	GCA_008365275.1	2592654	2592654	type	True	74.7959	89	1093	95	below_threshold
Steroidobacter agaridevorans	strain=SA29-B	GCA_009932555.1	2695856	2695856	type	True	74.786	69	1093	95	below_threshold
Agrococcus jenensis	strain=DSM 9580	GCA_003752465.1	46353	46353	type	True	74.7834	176	1093	95	below_threshold
Nocardia thailandica	strain=NBRC 100428	GCA_000308795.1	257275	257275	type	True	74.7168	194	1093	95	below_threshold
Nocardia tenerifensis	strain=NBRC 101015	GCA_000308715.1	228006	228006	type	True	74.6902	151	1093	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-17 06:45:36,501] [INFO] DFAST Taxonomy check result was written to GCA_009692535.1_ASM969253v1_genomic.fna/tc_result.tsv
[2023-06-17 06:45:36,501] [INFO] ===== Taxonomy check completed =====
[2023-06-17 06:45:36,501] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 06:45:36,501] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5090ff0c-04a1-4c33-8a5c-1e69c50312f2/dqc_reference/checkm_data
[2023-06-17 06:45:36,502] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 06:45:36,539] [INFO] Task started: CheckM
[2023-06-17 06:45:36,539] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_009692535.1_ASM969253v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_009692535.1_ASM969253v1_genomic.fna/checkm_input GCA_009692535.1_ASM969253v1_genomic.fna/checkm_result
[2023-06-17 06:46:07,266] [INFO] Task succeeded: CheckM
[2023-06-17 06:46:07,267] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 50.38%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-17 06:46:07,290] [INFO] ===== Completeness check finished =====
[2023-06-17 06:46:07,290] [INFO] ===== Start GTDB Search =====
[2023-06-17 06:46:07,291] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_009692535.1_ASM969253v1_genomic.fna/markers.fasta)
[2023-06-17 06:46:07,291] [INFO] Task started: Blastn
[2023-06-17 06:46:07,291] [INFO] Running command: blastn -query GCA_009692535.1_ASM969253v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5090ff0c-04a1-4c33-8a5c-1e69c50312f2/dqc_reference/reference_markers_gtdb.fasta -out GCA_009692535.1_ASM969253v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 06:46:08,451] [INFO] Task succeeded: Blastn
[2023-06-17 06:46:08,456] [INFO] Selected 19 target genomes.
[2023-06-17 06:46:08,456] [INFO] Target genome list was writen to GCA_009692535.1_ASM969253v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 06:46:08,472] [INFO] Task started: fastANI
[2023-06-17 06:46:08,472] [INFO] Running command: fastANI --query /var/lib/cwl/stgdda97646-119c-4361-89a8-8f6cf109d248/GCA_009692535.1_ASM969253v1_genomic.fna.gz --refList GCA_009692535.1_ASM969253v1_genomic.fna/target_genomes_gtdb.txt --output GCA_009692535.1_ASM969253v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 06:46:34,517] [INFO] Task succeeded: fastANI
[2023-06-17 06:46:34,540] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-17 06:46:34,540] [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
GCA_009692535.1	s__SHYZ01 sp009692535	100.0	1077	1093	d__Bacteria;p__Myxococcota;c__Polyangia;o__Haliangiales;f__SHYZ01;g__SHYZ01	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_011526095.1	s__WYBA01 sp011526095	75.9605	543	1093	d__Bacteria;p__Myxococcota;c__Polyangia;o__Haliangiales;f__Haliangiaceae;g__WYBA01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018058095.1	s__JABFXX01 sp018058095	75.9559	356	1093	d__Bacteria;p__Myxococcota;c__Polyangia;o__Haliangiales;f__Haliangiaceae;g__JABFXX01	95.0	99.29	99.24	0.92	0.91	3	-
GCA_016720595.1	s__JABFXX01 sp016720595	75.8533	318	1093	d__Bacteria;p__Myxococcota;c__Polyangia;o__Haliangiales;f__Haliangiaceae;g__JABFXX01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016707895.1	s__UBA2376 sp016707895	75.8269	498	1093	d__Bacteria;p__Myxococcota;c__Polyangia;o__Haliangiales;f__Haliangiaceae;g__UBA2376	95.0	99.64	99.63	0.96	0.96	3	-
GCA_016717005.1	s__UBA2376 sp016717005	75.8096	486	1093	d__Bacteria;p__Myxococcota;c__Polyangia;o__Haliangiales;f__Haliangiaceae;g__UBA2376	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016794525.1	s__UBA2376 sp016794525	75.7736	500	1093	d__Bacteria;p__Myxococcota;c__Polyangia;o__Haliangiales;f__Haliangiaceae;g__UBA2376	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016794545.1	s__JABFXX01 sp016794545	75.7636	420	1093	d__Bacteria;p__Myxococcota;c__Polyangia;o__Haliangiales;f__Haliangiaceae;g__JABFXX01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013813765.1	s__JABFXX01 sp013813765	75.7306	312	1093	d__Bacteria;p__Myxococcota;c__Polyangia;o__Haliangiales;f__Haliangiaceae;g__JABFXX01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013812655.1	s__JABFXX01 sp013812655	75.7087	341	1093	d__Bacteria;p__Myxococcota;c__Polyangia;o__Haliangiales;f__Haliangiaceae;g__JABFXX01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003696105.1	s__J016 sp003696105	75.7031	317	1093	d__Bacteria;p__Myxococcota;c__Polyangia;o__Haliangiales;f__J016;g__J016	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013368795.1	s__JABFXX01 sp013368795	75.6814	398	1093	d__Bacteria;p__Myxococcota;c__Polyangia;o__Haliangiales;f__Haliangiaceae;g__JABFXX01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017881315.1	s__JADGRB01 sp017881315	75.6007	166	1093	d__Bacteria;p__Myxococcota;c__Polyangia;o__Palsa-1104_A;f__Fen-1088;g__JADGRB01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016210055.1	s__JACQUZ01 sp016210055	75.5882	116	1093	d__Bacteria;p__Myxococcota;c__Polyangia;o__Haliangiales;f__SHYZ01;g__JACQUZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016706545.1	s__JABFXX01 sp016706545	75.3786	239	1093	d__Bacteria;p__Myxococcota;c__Polyangia;o__Haliangiales;f__Haliangiaceae;g__JABFXX01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014879945.1	s__JAEUJQ01 sp014879945	75.2925	217	1093	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__JAEUJQ01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000418325.1	s__Sorangium cellulosum_D	75.0847	457	1093	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__Sorangium	95.0	95.45	95.45	0.82	0.82	2	-
GCA_002297645.1	s__Dokdonella_A sp002297645	74.9031	119	1093	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dokdonella_A	95.0	99.81	99.81	0.89	0.89	2	-
GCA_017881025.1	s__Schlegelella_A sp017881025	74.8228	179	1093	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Schlegelella_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-17 06:46:34,542] [INFO] GTDB search result was written to GCA_009692535.1_ASM969253v1_genomic.fna/result_gtdb.tsv
[2023-06-17 06:46:34,543] [INFO] ===== GTDB Search completed =====
[2023-06-17 06:46:34,548] [INFO] DFAST_QC result json was written to GCA_009692535.1_ASM969253v1_genomic.fna/dqc_result.json
[2023-06-17 06:46:34,548] [INFO] DFAST_QC completed!
[2023-06-17 06:46:34,548] [INFO] Total running time: 0h1m38s