[2023-06-30 19:04:37,062] [INFO] DFAST_QC pipeline started.
[2023-06-30 19:04:37,071] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 19:04:37,071] [INFO] DQC Reference Directory: /var/lib/cwl/stg469054a0-1f54-4186-9cb6-69374daf51fc/dqc_reference
[2023-06-30 19:04:38,764] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 19:04:38,765] [INFO] Task started: Prodigal
[2023-06-30 19:04:38,765] [INFO] Running command: gunzip -c /var/lib/cwl/stg05de46e4-41ef-474f-a9ee-9743a175f177/GCA_007693585.1_ASM769358v1_genomic.fna.gz | prodigal -d GCA_007693585.1_ASM769358v1_genomic.fna/cds.fna -a GCA_007693585.1_ASM769358v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 19:04:52,539] [INFO] Task succeeded: Prodigal
[2023-06-30 19:04:52,540] [INFO] Task started: HMMsearch
[2023-06-30 19:04:52,540] [INFO] Running command: hmmsearch --tblout GCA_007693585.1_ASM769358v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg469054a0-1f54-4186-9cb6-69374daf51fc/dqc_reference/reference_markers.hmm GCA_007693585.1_ASM769358v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 19:04:52,894] [INFO] Task succeeded: HMMsearch
[2023-06-30 19:04:52,896] [INFO] Found 6/6 markers.
[2023-06-30 19:04:52,936] [INFO] Query marker FASTA was written to GCA_007693585.1_ASM769358v1_genomic.fna/markers.fasta
[2023-06-30 19:04:52,937] [INFO] Task started: Blastn
[2023-06-30 19:04:52,937] [INFO] Running command: blastn -query GCA_007693585.1_ASM769358v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg469054a0-1f54-4186-9cb6-69374daf51fc/dqc_reference/reference_markers.fasta -out GCA_007693585.1_ASM769358v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 19:04:53,607] [INFO] Task succeeded: Blastn
[2023-06-30 19:04:53,612] [INFO] Selected 39 target genomes.
[2023-06-30 19:04:53,613] [INFO] Target genome list was writen to GCA_007693585.1_ASM769358v1_genomic.fna/target_genomes.txt
[2023-06-30 19:04:53,616] [INFO] Task started: fastANI
[2023-06-30 19:04:53,617] [INFO] Running command: fastANI --query /var/lib/cwl/stg05de46e4-41ef-474f-a9ee-9743a175f177/GCA_007693585.1_ASM769358v1_genomic.fna.gz --refList GCA_007693585.1_ASM769358v1_genomic.fna/target_genomes.txt --output GCA_007693585.1_ASM769358v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 19:05:25,362] [INFO] Task succeeded: fastANI
[2023-06-30 19:05:25,363] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg469054a0-1f54-4186-9cb6-69374daf51fc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 19:05:25,364] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg469054a0-1f54-4186-9cb6-69374daf51fc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 19:05:25,386] [INFO] Found 29 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 19:05:25,387] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 19:05:25,387] [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
Lujinxingia vulgaris	strain=TMQ4	GCA_007997015.1	2600176	2600176	type	True	75.6506	68	1554	95	below_threshold
Lujinxingia sediminis	strain=SEH01	GCA_004005565.1	2480984	2480984	type	True	75.3899	55	1554	95	below_threshold
Lujinxingia litoralis	strain=B210	GCA_003260125.1	2211119	2211119	type	True	75.1975	57	1554	95	below_threshold
Mesorhizobium hawassense	strain=AC99b	GCA_003289945.1	1209954	1209954	type	True	75.0552	55	1554	95	below_threshold
Arhodomonas aquaeolei	strain=DSM 8974	GCA_000374645.1	2369	2369	type	True	75.0528	60	1554	95	below_threshold
Corallococcus terminator	strain=CA054A	GCA_003611635.1	2316733	2316733	type	True	74.9948	119	1554	95	below_threshold
Myxococcus eversor	strain=AB053B	GCA_010894455.1	2709661	2709661	type	True	74.9897	122	1554	95	below_threshold
Mesorhizobium atlanticum	strain=CNPSo 3140	GCA_003289965.1	2233532	2233532	type	True	74.9565	54	1554	95	below_threshold
Plasticicumulans lactativorans	strain=DSM 25287	GCA_004341245.1	1133106	1133106	type	True	74.907	98	1554	95	below_threshold
Myxococcus llanfairpwllgwyngyllgogerychwyrndrobwllllantysiliogogogochensis	strain=AM401	GCA_006636215.1	2590453	2590453	type	True	74.8815	118	1554	95	below_threshold
Xylophilus rhododendri	strain=KACC 21265	GCA_009906855.1	2697032	2697032	type	True	74.8489	78	1554	95	below_threshold
Nocardioides plantarum	strain=DSM 11054	GCA_006346395.1	29299	29299	type	True	74.7995	96	1554	95	below_threshold
Tessaracoccus flavescens	strain=SST-39T	GCA_001998865.1	399497	399497	type	True	74.7786	53	1554	95	below_threshold
Arenimonas metalli	strain=CF5-1	GCA_000747155.1	948077	948077	type	True	74.7762	72	1554	95	below_threshold
Longimicrobium terrae	strain=CECT 8660	GCA_014198875.1	1639882	1639882	type	True	74.7758	95	1554	95	below_threshold
Longimicrobium terrae	strain=DSM 29007	GCA_014202995.1	1639882	1639882	type	True	74.7715	96	1554	95	below_threshold
Longispora albida	strain=DSM 44784	GCA_000379825.1	203523	203523	type	True	74.7656	99	1554	95	below_threshold
Longimicrobium terrae	strain=CB-286315	GCA_013000925.1	1639882	1639882	type	True	74.7643	98	1554	95	below_threshold
Agromyces atrinae	strain=DSM 23870	GCA_013407835.1	592376	592376	type	True	74.749	62	1554	95	below_threshold
Catellatospora tritici	strain=NEAU-YM18	GCA_019083965.1	2851566	2851566	type	True	74.7022	128	1554	95	below_threshold
Aromatoleum tolulyticum	strain=ATCC 51758	GCA_900156155.1	34027	34027	type	True	74.6974	54	1554	95	below_threshold
Aromatoleum petrolei	strain=ToN1	GCA_012910985.1	76116	76116	type	True	74.658	56	1554	95	below_threshold
Aromatoleum petrolei	strain=ToN1	GCA_017894385.1	76116	76116	type	True	74.6545	58	1554	95	below_threshold
Actinoplanes digitatis	strain=DSM 43149	GCA_014205335.1	1868	1868	type	True	74.6377	150	1554	95	below_threshold
Plantibacter flavus	strain=VKM Ac-2504	GCA_900177615.1	150123	150123	type	True	74.6087	66	1554	95	below_threshold
Plantibacter flavus	strain=DSM 14012	GCA_003755125.1	150123	150123	type	True	74.6048	68	1554	95	below_threshold
Achromobacter denitrificans	strain=LMG 1231	GCA_902859715.1	32002	32002	type	True	74.5299	70	1554	95	below_threshold
Achromobacter denitrificans	strain=FDAARGOS_786	GCA_013267395.1	32002	32002	type	True	74.5299	70	1554	95	below_threshold
Achromobacter denitrificans	strain=NBRC 15125	GCA_001571365.1	32002	32002	type	True	74.5274	71	1554	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 19:05:25,389] [INFO] DFAST Taxonomy check result was written to GCA_007693585.1_ASM769358v1_genomic.fna/tc_result.tsv
[2023-06-30 19:05:25,390] [INFO] ===== Taxonomy check completed =====
[2023-06-30 19:05:25,390] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 19:05:25,390] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg469054a0-1f54-4186-9cb6-69374daf51fc/dqc_reference/checkm_data
[2023-06-30 19:05:25,391] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 19:05:25,442] [INFO] Task started: CheckM
[2023-06-30 19:05:25,442] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_007693585.1_ASM769358v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_007693585.1_ASM769358v1_genomic.fna/checkm_input GCA_007693585.1_ASM769358v1_genomic.fna/checkm_result
[2023-06-30 19:06:57,422] [INFO] Task succeeded: CheckM
[2023-06-30 19:06:57,423] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 19:06:57,446] [INFO] ===== Completeness check finished =====
[2023-06-30 19:06:57,446] [INFO] ===== Start GTDB Search =====
[2023-06-30 19:06:57,447] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_007693585.1_ASM769358v1_genomic.fna/markers.fasta)
[2023-06-30 19:06:57,447] [INFO] Task started: Blastn
[2023-06-30 19:06:57,447] [INFO] Running command: blastn -query GCA_007693585.1_ASM769358v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg469054a0-1f54-4186-9cb6-69374daf51fc/dqc_reference/reference_markers_gtdb.fasta -out GCA_007693585.1_ASM769358v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 19:06:58,333] [INFO] Task succeeded: Blastn
[2023-06-30 19:06:58,338] [INFO] Selected 30 target genomes.
[2023-06-30 19:06:58,339] [INFO] Target genome list was writen to GCA_007693585.1_ASM769358v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 19:06:58,352] [INFO] Task started: fastANI
[2023-06-30 19:06:58,352] [INFO] Running command: fastANI --query /var/lib/cwl/stg05de46e4-41ef-474f-a9ee-9743a175f177/GCA_007693585.1_ASM769358v1_genomic.fna.gz --refList GCA_007693585.1_ASM769358v1_genomic.fna/target_genomes_gtdb.txt --output GCA_007693585.1_ASM769358v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 19:07:25,789] [INFO] Task succeeded: fastANI
[2023-06-30 19:07:25,812] [INFO] Found 23 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 19:07:25,812] [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_007693585.1	s__REDH01 sp007693585	100.0	1537	1554	d__Bacteria;p__Myxococcota;c__Bradymonadia;o__REDH01;f__REDH01;g__REDH01	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_007997015.1	s__Lujinxingia sp007997015	75.6326	69	1554	d__Bacteria;p__Myxococcota;c__Bradymonadia;o__Bradymonadales;f__Bradymonadaceae;g__Lujinxingia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007120035.1	s__SKON01 sp007120035	75.4022	84	1554	d__Bacteria;p__Myxococcota;c__Bradymonadia;o__Bradymonadales;f__Bradymonadaceae;g__SKON01	95.0	99.72	99.66	0.90	0.87	5	-
GCF_019091085.1	s__Mesorhizobium sp019091085	75.1616	56	1554	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000374645.1	s__Arhodomonas aquaeolei	75.0528	60	1554	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrococcales;f__Nitrococcaceae;g__Arhodomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015075635.1	s__JADJKB01 sp015075635	74.9965	143	1554	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__JADJKB01	95.0	96.31	96.31	0.86	0.86	2	-
GCF_010894455.1	s__Myxococcus eversor	74.9897	122	1554	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Myxococcus	95.0	99.18	99.18	0.94	0.94	2	-
GCA_018606725.1	s__JAGYID01 sp018606725	74.9891	68	1554	d__Bacteria;p__Acidobacteriota;c__Mor1;o__Gp22-AA2;f__Gp22-AA2;g__JAGYID01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003044305.1	s__Archangium sp003044305	74.9629	147	1554	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Archangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016591715.1	s__Mesorhizobium sp016591715	74.9595	57	1554	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002789955.1	s__UM-FILTER-63-12 sp002789955	74.9568	75	1554	d__Bacteria;p__Myxococcota;c__Bradymonadia;o__UBA4248;f__UBA4248;g__UM-FILTER-63-12	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012960515.1	s__Rubricoccus sp012960515	74.9246	70	1554	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Rhodothermales;f__Rubricoccaceae;g__Rubricoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013336725.1	s__Myxococcus sp013336725	74.9075	125	1554	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Myxococcus	95.0	98.23	98.12	0.95	0.94	5	-
GCF_004341245.1	s__Plasticicumulans_A lactativorans	74.907	98	1554	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Competibacterales;f__Competibacteraceae;g__Plasticicumulans_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012797735.1	s__JAAZOP01 sp012797735	74.8793	128	1554	d__Bacteria;p__Myxococcota;c__Polyangia;o__DRWM01;f__JAAZOP01;g__JAAZOP01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005804885.1	s__SYOX01 sp005804885	74.8658	166	1554	d__Bacteria;p__Myxococcota;c__Bradymonadia;o__Bradymonadales;f__GCA-2716585;g__SYOX01	95.0	99.96	99.96	0.96	0.96	2	-
GCF_009906855.1	s__Xylophilus rhododendri	74.8489	78	1554	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Xylophilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001598255.1	s__Mitsuaria chitosanitabida	74.8119	89	1554	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Mitsuaria	95.0	99.05	99.05	0.96	0.96	2	-
GCF_018397995.1	s__NBRC-107566 sp018397995	74.8026	100	1554	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__NBRC-107566	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013694495.1	s__JACDCH01 sp013694495	74.7858	94	1554	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__JACDCH01;g__JACDCH01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013362815.1	s__Hamadaea sp013362815	74.7219	78	1554	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Hamadaea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018001935.1	s__JAGNHB01 sp018001935	74.7196	58	1554	d__Bacteria;p__Acidobacteriota;c__UBA6911;o__JAAYUB01;f__JAAYUB01;g__JAGNHB01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013289985.1	s__CAIMXF01 sp013289985	74.6792	83	1554	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__CAIMXF01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 19:07:25,815] [INFO] GTDB search result was written to GCA_007693585.1_ASM769358v1_genomic.fna/result_gtdb.tsv
[2023-06-30 19:07:25,815] [INFO] ===== GTDB Search completed =====
[2023-06-30 19:07:25,824] [INFO] DFAST_QC result json was written to GCA_007693585.1_ASM769358v1_genomic.fna/dqc_result.json
[2023-06-30 19:07:25,825] [INFO] DFAST_QC completed!
[2023-06-30 19:07:25,825] [INFO] Total running time: 0h2m49s