[2023-06-26 23:16:07,285] [INFO] DFAST_QC pipeline started.
[2023-06-26 23:16:07,287] [INFO] DFAST_QC version: 0.5.7
[2023-06-26 23:16:07,287] [INFO] DQC Reference Directory: /var/lib/cwl/stg0b214283-1798-4599-9fce-6e71b7a081de/dqc_reference
[2023-06-26 23:16:08,472] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-26 23:16:08,473] [INFO] Task started: Prodigal
[2023-06-26 23:16:08,474] [INFO] Running command: gunzip -c /var/lib/cwl/stgbef3bccb-aea6-448a-a0ed-0341273a88c9/GCA_026393115.1_ASM2639311v1_genomic.fna.gz | prodigal -d GCA_026393115.1_ASM2639311v1_genomic.fna/cds.fna -a GCA_026393115.1_ASM2639311v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-26 23:16:19,990] [INFO] Task succeeded: Prodigal
[2023-06-26 23:16:19,990] [INFO] Task started: HMMsearch
[2023-06-26 23:16:19,990] [INFO] Running command: hmmsearch --tblout GCA_026393115.1_ASM2639311v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0b214283-1798-4599-9fce-6e71b7a081de/dqc_reference/reference_markers.hmm GCA_026393115.1_ASM2639311v1_genomic.fna/protein.faa > /dev/null
[2023-06-26 23:16:20,188] [INFO] Task succeeded: HMMsearch
[2023-06-26 23:16:20,189] [INFO] Found 6/6 markers.
[2023-06-26 23:16:20,236] [INFO] Query marker FASTA was written to GCA_026393115.1_ASM2639311v1_genomic.fna/markers.fasta
[2023-06-26 23:16:20,237] [INFO] Task started: Blastn
[2023-06-26 23:16:20,237] [INFO] Running command: blastn -query GCA_026393115.1_ASM2639311v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0b214283-1798-4599-9fce-6e71b7a081de/dqc_reference/reference_markers.fasta -out GCA_026393115.1_ASM2639311v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-26 23:16:20,934] [INFO] Task succeeded: Blastn
[2023-06-26 23:16:20,938] [INFO] Selected 34 target genomes.
[2023-06-26 23:16:20,938] [INFO] Target genome list was writen to GCA_026393115.1_ASM2639311v1_genomic.fna/target_genomes.txt
[2023-06-26 23:16:20,944] [INFO] Task started: fastANI
[2023-06-26 23:16:20,944] [INFO] Running command: fastANI --query /var/lib/cwl/stgbef3bccb-aea6-448a-a0ed-0341273a88c9/GCA_026393115.1_ASM2639311v1_genomic.fna.gz --refList GCA_026393115.1_ASM2639311v1_genomic.fna/target_genomes.txt --output GCA_026393115.1_ASM2639311v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-26 23:16:46,559] [INFO] Task succeeded: fastANI
[2023-06-26 23:16:46,559] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0b214283-1798-4599-9fce-6e71b7a081de/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-26 23:16:46,559] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0b214283-1798-4599-9fce-6e71b7a081de/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-26 23:16:46,575] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold)
[2023-06-26 23:16:46,575] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-26 23:16:46,575] [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
Nocardioides cavernaquae	strain=K1W22B-1	GCA_003600895.1	2321396	2321396	type	True	76.4395	54	1154	95	below_threshold
Aeromicrobium fastidiosum	strain=DSM 10552	GCA_017876595.1	52699	52699	type	True	76.3188	52	1154	95	below_threshold
Nocardioides flavus Wang et al. 2016	strain=CGMCC 1.12791	GCA_014653115.1	2058780	2058780	type	True	76.244	57	1154	95	below_threshold
Thermobifida halotolerans	strain=DSM 44931	GCA_003574835.2	483545	483545	type	True	76.1745	54	1154	95	below_threshold
Cellulomonas palmilytica	strain=EW123	GCA_021590045.1	2608402	2608402	type	True	76.1257	56	1154	95	below_threshold
Nocardioides psychrotolerans	strain=NBRC 108563	GCA_007992415.1	1005945	1005945	type	True	76.0982	55	1154	95	below_threshold
Actinotalea solisilvae	strain=KACC 19191	GCA_016464425.1	2072922	2072922	type	True	76.0635	51	1154	95	below_threshold
Nocardioides psychrotolerans	strain=CGMCC 1.11156	GCA_900113685.1	1005945	1005945	type	True	76.0618	55	1154	95	below_threshold
Aeromicrobium endophyticum	strain=M2KJ-4	GCA_003586285.1	2292704	2292704	type	True	76.0327	59	1154	95	below_threshold
Thermobifida cellulosilytica	strain=TB100	GCA_001517975.1	144786	144786	type	True	75.9272	60	1154	95	below_threshold
Actinoplanes humidus	strain=NBRC 14915	GCA_016862215.1	113566	113566	type	True	75.9204	61	1154	95	below_threshold
Lentzea aerocolonigenes	strain=DSM 40034	GCA_024171805.1	68170	68170	type	True	75.8668	71	1154	95	below_threshold
Lentzea aerocolonigenes	strain=NRRL B-3298	GCA_000719205.1	68170	68170	type	True	75.8499	72	1154	95	below_threshold
Nonomuraea rhizosphaerae	strain=CGMCC 4.7431	GCA_019396405.1	2665663	2665663	type	True	75.8463	64	1154	95	below_threshold
Pseudonocardia hydrocarbonoxydans	strain=NBRC 14498	GCA_006539565.1	76726	76726	type	True	75.8232	73	1154	95	below_threshold
Actinomadura macrotermitis	strain=RB68	GCA_009604375.1	2585200	2585200	type	True	75.7708	72	1154	95	below_threshold
Lentzea alba	strain=NEAU-D13	GCA_011067745.1	2714351	2714351	type	True	75.7615	71	1154	95	below_threshold
Gordonia rhizosphera	strain=NBRC 16068	GCA_000298195.1	83341	83341	type	True	75.6887	51	1154	95	below_threshold
Nonomuraea aurantiaca	strain=NEAU-L178	GCA_020215705.1	2878562	2878562	type	True	75.662	68	1154	95	below_threshold
Pseudonocardia alaniniphila	strain=Y-16303	GCA_022524485.1	75291	75291	type	True	75.6233	63	1154	95	below_threshold
Pseudonocardia acidicola	strain=K10HN5	GCA_012911935.1	2724939	2724939	type	True	75.4567	80	1154	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-26 23:16:46,577] [INFO] DFAST Taxonomy check result was written to GCA_026393115.1_ASM2639311v1_genomic.fna/tc_result.tsv
[2023-06-26 23:16:46,578] [INFO] ===== Taxonomy check completed =====
[2023-06-26 23:16:46,578] [INFO] ===== Start completeness check using CheckM =====
[2023-06-26 23:16:46,578] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0b214283-1798-4599-9fce-6e71b7a081de/dqc_reference/checkm_data
[2023-06-26 23:16:46,579] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-26 23:16:46,616] [INFO] Task started: CheckM
[2023-06-26 23:16:46,617] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_026393115.1_ASM2639311v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_026393115.1_ASM2639311v1_genomic.fna/checkm_input GCA_026393115.1_ASM2639311v1_genomic.fna/checkm_result
[2023-06-26 23:17:22,749] [INFO] Task succeeded: CheckM
[2023-06-26 23:17:22,750] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-26 23:17:22,874] [INFO] ===== Completeness check finished =====
[2023-06-26 23:17:22,874] [INFO] ===== Start GTDB Search =====
[2023-06-26 23:17:22,874] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_026393115.1_ASM2639311v1_genomic.fna/markers.fasta)
[2023-06-26 23:17:22,874] [INFO] Task started: Blastn
[2023-06-26 23:17:22,875] [INFO] Running command: blastn -query GCA_026393115.1_ASM2639311v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0b214283-1798-4599-9fce-6e71b7a081de/dqc_reference/reference_markers_gtdb.fasta -out GCA_026393115.1_ASM2639311v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-26 23:17:23,860] [INFO] Task succeeded: Blastn
[2023-06-26 23:17:23,864] [INFO] Selected 29 target genomes.
[2023-06-26 23:17:23,864] [INFO] Target genome list was writen to GCA_026393115.1_ASM2639311v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-26 23:17:23,921] [INFO] Task started: fastANI
[2023-06-26 23:17:23,921] [INFO] Running command: fastANI --query /var/lib/cwl/stgbef3bccb-aea6-448a-a0ed-0341273a88c9/GCA_026393115.1_ASM2639311v1_genomic.fna.gz --refList GCA_026393115.1_ASM2639311v1_genomic.fna/target_genomes_gtdb.txt --output GCA_026393115.1_ASM2639311v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-26 23:17:43,529] [INFO] Task succeeded: fastANI
[2023-06-26 23:17:43,543] [INFO] Found 17 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-26 23:17:43,543] [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_903927265.1	s__CAIYMF01 sp903927265	89.6339	891	1154	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__CAIYMF01;g__CAIYMF01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009699025.1	s__CAIYMF01 sp009699025	78.4696	206	1154	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__CAIYMF01;g__CAIYMF01	95.0	97.39	97.39	0.70	0.70	2	-
GCA_016717115.1	s__UBA10649 sp016717115	76.6604	101	1154	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__S36-B12;g__UBA10649	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016125335.1	s__WLRQ01 sp016125335	76.4701	131	1154	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__CAIYMF01;g__WLRQ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016125355.1	s__UBA10649 sp016125355	76.3425	101	1154	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__S36-B12;g__UBA10649	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017876595.1	s__Aeromicrobium fastidiosum	76.3188	52	1154	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Aeromicrobium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001427795.1	s__Nocardioides sp001427795	76.2165	53	1154	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	1.00	1.00	2	-
GCA_017848795.1	s__JAFIHG01 sp017848795	76.1882	88	1154	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__CAIYMF01;g__JAFIHG01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007829035.1	s__Rudaeicoccus suwonensis	76.1312	57	1154	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Rudaeicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014108865.1	s__Nocardioides sp014108865	76.1085	67	1154	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900113685.1	s__Nocardioides psychrotolerans	76.0618	55	1154	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.99	99.99	1.00	1.00	2	-
GCF_000519005.1	s__Nocardioides sp000519005	75.8939	71	1154	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	98.89	98.89	0.90	0.90	2	-
GCF_006539565.1	s__Pseudonocardia hydrocarbonoxydans	75.8232	73	1154	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014207745.1	s__Nonomuraea muscovyensis	75.7925	78	1154	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011067745.1	s__Lentzea alba	75.7615	71	1154	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Lentzea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900323885.1	s__Nonomuraea parvosata	75.6339	91	1154	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	98.64	97.29	0.94	0.90	3	-
GCF_012911935.1	s__Pseudonocardia sp012911935	75.4478	81	1154	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-26 23:17:43,545] [INFO] GTDB search result was written to GCA_026393115.1_ASM2639311v1_genomic.fna/result_gtdb.tsv
[2023-06-26 23:17:43,546] [INFO] ===== GTDB Search completed =====
[2023-06-26 23:17:43,550] [INFO] DFAST_QC result json was written to GCA_026393115.1_ASM2639311v1_genomic.fna/dqc_result.json
[2023-06-26 23:17:43,550] [INFO] DFAST_QC completed!
[2023-06-26 23:17:43,550] [INFO] Total running time: 0h1m36s