[2024-01-24 14:07:00,940] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:07:00,942] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:07:00,942] [INFO] DQC Reference Directory: /var/lib/cwl/stg97aaf138-e5da-4d76-9ff1-3afc24a8619c/dqc_reference
[2024-01-24 14:07:02,263] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:07:02,264] [INFO] Task started: Prodigal
[2024-01-24 14:07:02,265] [INFO] Running command: gunzip -c /var/lib/cwl/stg6afa1b70-f21b-48e1-a138-a277a615290d/GCF_000024805.1_ASM2480v1_genomic.fna.gz | prodigal -d GCF_000024805.1_ASM2480v1_genomic.fna/cds.fna -a GCF_000024805.1_ASM2480v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:07:32,301] [INFO] Task succeeded: Prodigal
[2024-01-24 14:07:32,302] [INFO] Task started: HMMsearch
[2024-01-24 14:07:32,302] [INFO] Running command: hmmsearch --tblout GCF_000024805.1_ASM2480v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg97aaf138-e5da-4d76-9ff1-3afc24a8619c/dqc_reference/reference_markers.hmm GCF_000024805.1_ASM2480v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:07:32,642] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:07:32,643] [INFO] Found 6/6 markers.
[2024-01-24 14:07:32,706] [INFO] Query marker FASTA was written to GCF_000024805.1_ASM2480v1_genomic.fna/markers.fasta
[2024-01-24 14:07:32,707] [INFO] Task started: Blastn
[2024-01-24 14:07:32,707] [INFO] Running command: blastn -query GCF_000024805.1_ASM2480v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg97aaf138-e5da-4d76-9ff1-3afc24a8619c/dqc_reference/reference_markers.fasta -out GCF_000024805.1_ASM2480v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:07:33,544] [INFO] Task succeeded: Blastn
[2024-01-24 14:07:33,548] [INFO] Selected 33 target genomes.
[2024-01-24 14:07:33,548] [INFO] Target genome list was writen to GCF_000024805.1_ASM2480v1_genomic.fna/target_genomes.txt
[2024-01-24 14:07:33,565] [INFO] Task started: fastANI
[2024-01-24 14:07:33,566] [INFO] Running command: fastANI --query /var/lib/cwl/stg6afa1b70-f21b-48e1-a138-a277a615290d/GCF_000024805.1_ASM2480v1_genomic.fna.gz --refList GCF_000024805.1_ASM2480v1_genomic.fna/target_genomes.txt --output GCF_000024805.1_ASM2480v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:08:16,138] [INFO] Task succeeded: fastANI
[2024-01-24 14:08:16,139] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg97aaf138-e5da-4d76-9ff1-3afc24a8619c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:08:16,139] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg97aaf138-e5da-4d76-9ff1-3afc24a8619c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:08:16,161] [INFO] Found 32 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:08:16,161] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:08:16,162] [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	100.0	3147	3148	95	conclusive
Vulgatibacter incomptus	strain=DSM 27710	GCA_001263175.1	1391653	1391653	type	True	75.5975	225	3148	95	below_threshold
Geomonas propionica	strain=Red259	GCA_016458235.1	2798582	2798582	type	True	75.3491	118	3148	95	below_threshold
Geomonas anaerohicana	strain=Red421	GCA_016458305.1	2798583	2798583	type	True	75.3428	134	3148	95	below_threshold
Plesiocystis pacifica	strain=SIR-1	GCA_000170895.1	191768	191768	type	True	75.3166	711	3148	95	below_threshold
Geomonas ferrireducens	strain=S62	GCA_004917065.1	2570227	2570227	type	True	75.3136	104	3148	95	below_threshold
Lysobacter dokdonensis	strain=DS-58	GCA_000770795.1	414050	414050	type	True	75.2885	197	3148	95	below_threshold
Geomonas paludis	strain=Red736	GCA_014193585.1	2740185	2740185	type	True	75.2677	156	3148	95	below_threshold
Persicimonas caeni	strain=YN101	GCA_006517175.1	2292766	2292766	type	True	75.1931	336	3148	95	below_threshold
Nannocystis exedens	strain=ATCC 25963	GCA_900112715.1	54	54	type	True	75.1723	927	3148	95	below_threshold
Nannocystis exedens	strain=DSM 71	GCA_002343915.1	54	54	type	True	75.1711	971	3148	95	below_threshold
Corallococcus soli	strain=ZKHCc1 1396	GCA_014930455.1	2710757	2710757	type	True	75.1678	396	3148	95	below_threshold
Anaeromyxobacter dehalogenans	strain=2CP-1	GCA_000022145.1	161493	161493	type	True	75.1546	570	3148	95	below_threshold
Wenzhouxiangella sediminis	strain=XDB06	GCA_003410055.1	1792836	1792836	type	True	75.1504	182	3148	95	below_threshold
Polyangium spumosum	strain=DSM 14734	GCA_009649845.1	889282	889282	type	True	75.1397	587	3148	95	below_threshold
Methylobrevis albus	strain=L22	GCA_015904235.1	2793297	2793297	type	True	75.1051	351	3148	95	below_threshold
Labilithrix luteola	strain=DSM 27648	GCA_001263205.1	1391654	1391654	type	True	75.0615	382	3148	95	below_threshold
Methylobacterium radiodurans	strain=17Sr1-43	GCA_003173735.1	2202828	2202828	type	True	75.0569	341	3148	95	below_threshold
Brachymonas denitrificans	strain=DSM 15123	GCA_900110225.1	28220	28220	type	True	75.0513	89	3148	95	below_threshold
Rhodoplanes roseus	strain=DSM 5909	GCA_003258865.1	29409	29409	type	True	75.0288	378	3148	95	below_threshold
Salinarimonas rosea	strain=DSM 21201	GCA_000429045.1	552063	552063	type	True	75.0269	441	3148	95	below_threshold
Oharaeibacter diazotrophicus	strain=SM30	GCA_011317485.1	1920512	1920512	type	True	75.0248	373	3148	95	below_threshold
Marinobacter bohaiensis	strain=T17	GCA_003258515.1	2201898	2201898	type	True	75.0238	118	3148	95	below_threshold
Sandaracinus amylolyticus	strain=DSM 53668	GCA_000737325.2	927083	927083	type	True	75.0207	794	3148	95	below_threshold
Chondromyces crocatus	strain=Cm c5	GCA_001189295.1	52	52	type	True	75.0131	439	3148	95	below_threshold
Sphingomonas citri	strain=RRHST34	GCA_019429485.1	2862499	2862499	type	True	75.0024	390	3148	95	below_threshold
Sphingomonas yunnanensis	strain=YIM 3	GCA_019898765.1	310400	310400	type	True	74.9992	374	3148	95	below_threshold
Saccharothrix variisporea	strain=DSM 43911	GCA_003634995.1	543527	543527	type	True	74.9922	473	3148	95	below_threshold
Oharaeibacter diazotrophicus	strain=DSM 102969	GCA_004362745.1	1920512	1920512	type	True	74.973	494	3148	95	below_threshold
Saccharothrix australiensis	strain=DSM 43800	GCA_003634935.1	2072	2072	type	True	74.8561	517	3148	95	below_threshold
Marinobacterium nitratireducens	strain=CGMCC 1.7286	GCA_014645375.1	518897	518897	type	True	74.7691	144	3148	95	below_threshold
Streptomyces virginiae	strain=NRRL ISP-5094	GCA_000720455.1	1961	1961	suspected-type	True	74.7663	403	3148	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:08:16,163] [INFO] DFAST Taxonomy check result was written to GCF_000024805.1_ASM2480v1_genomic.fna/tc_result.tsv
[2024-01-24 14:08:16,164] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:08:16,164] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:08:16,164] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg97aaf138-e5da-4d76-9ff1-3afc24a8619c/dqc_reference/checkm_data
[2024-01-24 14:08:16,165] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:08:16,248] [INFO] Task started: CheckM
[2024-01-24 14:08:16,249] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000024805.1_ASM2480v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000024805.1_ASM2480v1_genomic.fna/checkm_input GCF_000024805.1_ASM2480v1_genomic.fna/checkm_result
[2024-01-24 14:10:04,541] [INFO] Task succeeded: CheckM
[2024-01-24 14:10:04,543] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:10:04,565] [INFO] ===== Completeness check finished =====
[2024-01-24 14:10:04,565] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:10:04,565] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000024805.1_ASM2480v1_genomic.fna/markers.fasta)
[2024-01-24 14:10:04,566] [INFO] Task started: Blastn
[2024-01-24 14:10:04,566] [INFO] Running command: blastn -query GCF_000024805.1_ASM2480v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg97aaf138-e5da-4d76-9ff1-3afc24a8619c/dqc_reference/reference_markers_gtdb.fasta -out GCF_000024805.1_ASM2480v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:10:06,073] [INFO] Task succeeded: Blastn
[2024-01-24 14:10:06,076] [INFO] Selected 14 target genomes.
[2024-01-24 14:10:06,076] [INFO] Target genome list was writen to GCF_000024805.1_ASM2480v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:10:06,089] [INFO] Task started: fastANI
[2024-01-24 14:10:06,089] [INFO] Running command: fastANI --query /var/lib/cwl/stg6afa1b70-f21b-48e1-a138-a277a615290d/GCF_000024805.1_ASM2480v1_genomic.fna.gz --refList GCF_000024805.1_ASM2480v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000024805.1_ASM2480v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:10:36,429] [INFO] Task succeeded: fastANI
[2024-01-24 14:10:36,441] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:10:36,441] [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_000024805.1	s__Haliangium ochraceum	100.0	3147	3148	d__Bacteria;p__Myxococcota;c__Polyangia;o__Haliangiales;f__Haliangiaceae;g__Haliangium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_900696455.1	s__UBA2376 sp900696455	76.6988	1007	3148	d__Bacteria;p__Myxococcota;c__Polyangia;o__Haliangiales;f__Haliangiaceae;g__UBA2376	95.0	98.40	97.29	0.91	0.90	3	-
GCA_018058095.1	s__JABFXX01 sp018058095	76.437	957	3148	d__Bacteria;p__Myxococcota;c__Polyangia;o__Haliangiales;f__Haliangiaceae;g__JABFXX01	95.0	99.29	99.24	0.92	0.91	3	-
GCA_016717005.1	s__UBA2376 sp016717005	76.3359	1126	3148	d__Bacteria;p__Myxococcota;c__Polyangia;o__Haliangiales;f__Haliangiaceae;g__UBA2376	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016707895.1	s__UBA2376 sp016707895	76.2962	1185	3148	d__Bacteria;p__Myxococcota;c__Polyangia;o__Haliangiales;f__Haliangiaceae;g__UBA2376	95.0	99.64	99.63	0.96	0.96	3	-
GCA_016794525.1	s__UBA2376 sp016794525	76.2703	1182	3148	d__Bacteria;p__Myxococcota;c__Polyangia;o__Haliangiales;f__Haliangiaceae;g__UBA2376	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011526095.1	s__WYBA01 sp011526095	76.1899	1129	3148	d__Bacteria;p__Myxococcota;c__Polyangia;o__Haliangiales;f__Haliangiaceae;g__WYBA01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018057825.1	s__UBA2376 sp018057825	76.1624	1017	3148	d__Bacteria;p__Myxococcota;c__Polyangia;o__Haliangiales;f__Haliangiaceae;g__UBA2376	95.0	99.99	99.98	0.98	0.98	3	-
GCA_016706545.1	s__JABFXX01 sp016706545	76.1171	777	3148	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	75.8992	614	3148	d__Bacteria;p__Myxococcota;c__Polyangia;o__Haliangiales;f__J016;g__J016	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016458225.1	s__Corallococcus sp016458225	75.171	409	3148	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Corallococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016794465.1	s__JAGNNG01 sp016794465	75.135	171	3148	d__Bacteria;p__Myxococcota;c__Polyangia;o__Palsa-1104;f__JAEUJZ01;g__JAGNNG01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004343155.1	s__Marichromatium gracile	75.0863	326	3148	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Marichromatium	95.0	98.88	96.74	0.96	0.94	6	-
GCA_012797735.1	s__JAAZOP01 sp012797735	75.0269	302	3148	d__Bacteria;p__Myxococcota;c__Polyangia;o__DRWM01;f__JAAZOP01;g__JAAZOP01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:10:36,442] [INFO] GTDB search result was written to GCF_000024805.1_ASM2480v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:10:36,443] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:10:36,447] [INFO] DFAST_QC result json was written to GCF_000024805.1_ASM2480v1_genomic.fna/dqc_result.json
[2024-01-24 14:10:36,448] [INFO] DFAST_QC completed!
[2024-01-24 14:10:36,448] [INFO] Total running time: 0h3m36s