[2023-07-01 03:04:16,807] [INFO] DFAST_QC pipeline started.
[2023-07-01 03:04:16,813] [INFO] DFAST_QC version: 0.5.7
[2023-07-01 03:04:16,813] [INFO] DQC Reference Directory: /var/lib/cwl/stga567624a-7317-455e-836f-32e8e7104471/dqc_reference
[2023-07-01 03:04:19,701] [INFO] ===== Start taxonomy check using ANI =====
[2023-07-01 03:04:19,702] [INFO] Task started: Prodigal
[2023-07-01 03:04:19,702] [INFO] Running command: gunzip -c /var/lib/cwl/stgc8baedce-b4fe-45c7-a0cf-3fd356bada13/GCA_024641925.1_ASM2464192v1_genomic.fna.gz | prodigal -d GCA_024641925.1_ASM2464192v1_genomic.fna/cds.fna -a GCA_024641925.1_ASM2464192v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-07-01 03:04:35,876] [INFO] Task succeeded: Prodigal
[2023-07-01 03:04:35,876] [INFO] Task started: HMMsearch
[2023-07-01 03:04:35,876] [INFO] Running command: hmmsearch --tblout GCA_024641925.1_ASM2464192v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga567624a-7317-455e-836f-32e8e7104471/dqc_reference/reference_markers.hmm GCA_024641925.1_ASM2464192v1_genomic.fna/protein.faa > /dev/null
[2023-07-01 03:04:36,249] [INFO] Task succeeded: HMMsearch
[2023-07-01 03:04:36,250] [INFO] Found 6/6 markers.
[2023-07-01 03:04:36,292] [INFO] Query marker FASTA was written to GCA_024641925.1_ASM2464192v1_genomic.fna/markers.fasta
[2023-07-01 03:04:36,293] [INFO] Task started: Blastn
[2023-07-01 03:04:36,293] [INFO] Running command: blastn -query GCA_024641925.1_ASM2464192v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga567624a-7317-455e-836f-32e8e7104471/dqc_reference/reference_markers.fasta -out GCA_024641925.1_ASM2464192v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-07-01 03:04:37,338] [INFO] Task succeeded: Blastn
[2023-07-01 03:04:37,342] [INFO] Selected 23 target genomes.
[2023-07-01 03:04:37,346] [INFO] Target genome list was writen to GCA_024641925.1_ASM2464192v1_genomic.fna/target_genomes.txt
[2023-07-01 03:04:37,349] [INFO] Task started: fastANI
[2023-07-01 03:04:37,349] [INFO] Running command: fastANI --query /var/lib/cwl/stgc8baedce-b4fe-45c7-a0cf-3fd356bada13/GCA_024641925.1_ASM2464192v1_genomic.fna.gz --refList GCA_024641925.1_ASM2464192v1_genomic.fna/target_genomes.txt --output GCA_024641925.1_ASM2464192v1_genomic.fna/fastani_result.tsv --threads 1
[2023-07-01 03:04:58,264] [INFO] Task succeeded: fastANI
[2023-07-01 03:04:58,264] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga567624a-7317-455e-836f-32e8e7104471/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-07-01 03:04:58,265] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga567624a-7317-455e-836f-32e8e7104471/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-07-01 03:04:58,287] [INFO] Found 23 fastANI hits (0 hits with ANI > threshold)
[2023-07-01 03:04:58,287] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-07-01 03:04:58,288] [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
Ideonella dechloratans	strain=CCUG 30977	GCA_021049305.1	36863	36863	type	True	78.7479	391	1422	95	below_threshold
Ideonella azotifigens	strain=DSM 21438	GCA_006519715.1	513160	513160	type	True	78.7426	347	1422	95	below_threshold
Rubrivivax benzoatilyticus	strain=JA2	GCA_000190375.2	316997	316997	type	True	78.7369	435	1422	95	below_threshold
Rubrivivax benzoatilyticus	strain=JA2	GCA_000420125.1	316997	316997	type	True	78.6817	455	1422	95	below_threshold
Rubrivivax gelatinosus	strain=DSM 1709	GCA_016583525.1	28068	28068	suspected-type	True	78.6583	447	1422	95	below_threshold
Rubrivivax gelatinosus	strain=DSM 1709	GCA_004340905.1	28068	28068	suspected-type	True	78.6393	455	1422	95	below_threshold
Ideonella benzenivorans	strain=B7	GCA_020387415.1	2831643	2831643	type	True	78.3432	372	1422	95	below_threshold
Azohydromonas lata	strain=NBRC 102462	GCA_001571085.1	45677	45677	type	True	78.3026	445	1422	95	below_threshold
Schlegelella thermodepolymerans	strain=DSM 15344	GCA_003349825.1	215580	215580	type	True	78.2969	373	1422	95	below_threshold
Hydrogenophaga crocea	strain=BA0156	GCA_011388215.1	2716225	2716225	type	True	78.2636	396	1422	95	below_threshold
Azohydromonas caseinilytica	strain=G-1-1-14	GCA_012927045.1	2728836	2728836	type	True	78.2355	461	1422	95	below_threshold
Schlegelella thermodepolymerans	strain=DSM 15344	GCA_002933415.1	215580	215580	type	True	78.2208	383	1422	95	below_threshold
Schlegelella thermodepolymerans	strain=DSM 15344	GCA_015476235.1	215580	215580	type	True	78.2169	380	1422	95	below_threshold
Sphaerotilus montanus	strain=DSM 21226	GCA_013410775.1	522889	522889	type	True	78.2074	365	1422	95	below_threshold
Pelomonas puraquae	strain=CCUG 52769	GCA_002205845.1	431059	431059	type	True	78.2003	423	1422	95	below_threshold
Paucibacter toxinivorans	strain=DSM 16998	GCA_004362525.1	270368	270368	type	True	78.1757	430	1422	95	below_threshold
Ramlibacter humi	strain=18x22-1	GCA_004681975.1	2530451	2530451	type	True	78.1754	385	1422	95	below_threshold
Sphaerotilus hippei	strain=DSM 566	GCA_003201595.1	744406	744406	type	True	78.1704	392	1422	95	below_threshold
Sphaerotilus montanus	strain=HS	GCA_013426955.1	522889	522889	type	True	78.1309	368	1422	95	below_threshold
Tepidimonas fonticaldi	strain=AT-A2	GCA_007556755.1	1101373	1101373	type	True	78.0364	260	1422	95	below_threshold
Schlegelella brevitalea	strain=DSM 7029	GCA_001017435.1	413882	413882	type	True	77.9946	338	1422	95	below_threshold
Ideonella paludis	strain=KCTC 32238	GCA_018069865.1	1233411	1233411	type	True	77.9721	307	1422	95	below_threshold
Aquabacterium soli	strain=SJQ9	GCA_003933735.1	2493092	2493092	type	True	77.9109	337	1422	95	below_threshold
--------------------------------------------------------------------------------
[2023-07-01 03:04:58,420] [INFO] DFAST Taxonomy check result was written to GCA_024641925.1_ASM2464192v1_genomic.fna/tc_result.tsv
[2023-07-01 03:04:58,420] [INFO] ===== Taxonomy check completed =====
[2023-07-01 03:04:58,421] [INFO] ===== Start completeness check using CheckM =====
[2023-07-01 03:04:58,421] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga567624a-7317-455e-836f-32e8e7104471/dqc_reference/checkm_data
[2023-07-01 03:04:58,423] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-07-01 03:04:58,475] [INFO] Task started: CheckM
[2023-07-01 03:04:58,476] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_024641925.1_ASM2464192v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_024641925.1_ASM2464192v1_genomic.fna/checkm_input GCA_024641925.1_ASM2464192v1_genomic.fna/checkm_result
[2023-07-01 03:06:13,477] [INFO] Task succeeded: CheckM
[2023-07-01 03:06:13,479] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 78.14%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-07-01 03:06:13,503] [INFO] ===== Completeness check finished =====
[2023-07-01 03:06:13,503] [INFO] ===== Start GTDB Search =====
[2023-07-01 03:06:13,504] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_024641925.1_ASM2464192v1_genomic.fna/markers.fasta)
[2023-07-01 03:06:13,504] [INFO] Task started: Blastn
[2023-07-01 03:06:13,504] [INFO] Running command: blastn -query GCA_024641925.1_ASM2464192v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga567624a-7317-455e-836f-32e8e7104471/dqc_reference/reference_markers_gtdb.fasta -out GCA_024641925.1_ASM2464192v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-07-01 03:06:15,481] [INFO] Task succeeded: Blastn
[2023-07-01 03:06:15,486] [INFO] Selected 23 target genomes.
[2023-07-01 03:06:15,486] [INFO] Target genome list was writen to GCA_024641925.1_ASM2464192v1_genomic.fna/target_genomes_gtdb.txt
[2023-07-01 03:06:15,492] [INFO] Task started: fastANI
[2023-07-01 03:06:15,492] [INFO] Running command: fastANI --query /var/lib/cwl/stgc8baedce-b4fe-45c7-a0cf-3fd356bada13/GCA_024641925.1_ASM2464192v1_genomic.fna.gz --refList GCA_024641925.1_ASM2464192v1_genomic.fna/target_genomes_gtdb.txt --output GCA_024641925.1_ASM2464192v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-07-01 03:06:35,141] [INFO] Task succeeded: fastANI
[2023-07-01 03:06:35,160] [INFO] Found 23 fastANI hits (0 hits with ANI > circumscription radius)
[2023-07-01 03:06:35,161] [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_014859905.1	s__Rubrivivax sp014859905	80.2141	361	1422	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rubrivivax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004016505.1	s__Rubrivivax rivuli	80.0686	599	1422	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rubrivivax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001295905.1	s__Rubrivivax sp001295905	80.0622	599	1422	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rubrivivax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001295865.1	s__Rubrivivax sp001295865	79.9906	598	1422	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rubrivivax	95.0	99.99	99.99	0.99	0.99	2	-
GCA_013822265.1	s__Rubrivivax sp013822265	79.9818	537	1422	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rubrivivax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903914615.1	s__Rubrivivax sp903914615	79.9619	522	1422	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rubrivivax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016709385.1	s__Rubrivivax sp016709385	79.9261	588	1422	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rubrivivax	95.0	99.31	99.15	0.91	0.88	11	-
GCA_016704535.1	s__Rubrivivax sp016704535	79.8165	546	1422	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rubrivivax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_904426505.1	s__Rubrivivax sp904426505	79.6455	561	1422	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rubrivivax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903822435.1	s__Rubrivivax sp903822435	79.5865	562	1422	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rubrivivax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017302505.1	s__Rubrivivax sp017302505	79.5839	451	1422	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rubrivivax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018780805.1	s__Rubrivivax sp018780805	79.3523	554	1422	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rubrivivax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016719535.1	s__Rubrivivax sp016719535	79.348	596	1422	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rubrivivax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903938815.1	s__Rubrivivax sp903938815	79.2368	548	1422	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rubrivivax	95.0	99.66	99.41	0.96	0.94	10	-
GCF_002198735.1	s__Aquabacterium_A sp002198735	78.9769	606	1422	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquabacterium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016790225.1	s__Rubrivivax sp016790225	78.9219	463	1422	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rubrivivax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018971105.1	s__Rubrivivax sp018971105	78.8445	383	1422	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rubrivivax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000969605.1	s__Aquincola tertiaricarbonis	78.742	528	1422	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquincola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016789865.1	s__Rubrivivax sp016789865	78.7304	457	1422	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rubrivivax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004340905.1	s__Rubrivivax gelatinosus	78.6499	454	1422	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rubrivivax	95.0	99.99	99.99	0.99	0.99	2	-
GCA_016788525.1	s__Rubrivivax sp016788525	78.4305	446	1422	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rubrivivax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007556755.1	s__Tepidimonas fonticaldi	78.0632	258	1422	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Tepidimonas	95.0	97.94	97.94	0.88	0.88	2	-
GCA_018780645.1	s__Paucibacter sp018780645	77.9757	416	1422	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paucibacter	95.0	95.57	95.57	0.86	0.86	2	-
--------------------------------------------------------------------------------
[2023-07-01 03:06:35,163] [INFO] GTDB search result was written to GCA_024641925.1_ASM2464192v1_genomic.fna/result_gtdb.tsv
[2023-07-01 03:06:35,163] [INFO] ===== GTDB Search completed =====
[2023-07-01 03:06:35,168] [INFO] DFAST_QC result json was written to GCA_024641925.1_ASM2464192v1_genomic.fna/dqc_result.json
[2023-07-01 03:06:35,168] [INFO] DFAST_QC completed!
[2023-07-01 03:06:35,169] [INFO] Total running time: 0h2m18s