[2024-01-24 14:19:01,155] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:19:01,161] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:19:01,162] [INFO] DQC Reference Directory: /var/lib/cwl/stg45e03f40-3a14-4aad-bbc7-b7ee833ceca7/dqc_reference
[2024-01-24 14:19:02,597] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:19:02,598] [INFO] Task started: Prodigal
[2024-01-24 14:19:02,599] [INFO] Running command: gunzip -c /var/lib/cwl/stg2515ca9b-6c44-4656-8752-2d85572ac017/GCF_000214175.1_ASM21417v1_genomic.fna.gz | prodigal -d GCF_000214175.1_ASM21417v1_genomic.fna/cds.fna -a GCF_000214175.1_ASM21417v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:19:25,063] [INFO] Task succeeded: Prodigal
[2024-01-24 14:19:25,063] [INFO] Task started: HMMsearch
[2024-01-24 14:19:25,063] [INFO] Running command: hmmsearch --tblout GCF_000214175.1_ASM21417v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg45e03f40-3a14-4aad-bbc7-b7ee833ceca7/dqc_reference/reference_markers.hmm GCF_000214175.1_ASM21417v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:19:25,358] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:19:25,360] [INFO] Found 6/6 markers.
[2024-01-24 14:19:25,416] [INFO] Query marker FASTA was written to GCF_000214175.1_ASM21417v1_genomic.fna/markers.fasta
[2024-01-24 14:19:25,417] [INFO] Task started: Blastn
[2024-01-24 14:19:25,417] [INFO] Running command: blastn -query GCF_000214175.1_ASM21417v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg45e03f40-3a14-4aad-bbc7-b7ee833ceca7/dqc_reference/reference_markers.fasta -out GCF_000214175.1_ASM21417v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:19:26,349] [INFO] Task succeeded: Blastn
[2024-01-24 14:19:26,353] [INFO] Selected 20 target genomes.
[2024-01-24 14:19:26,353] [INFO] Target genome list was writen to GCF_000214175.1_ASM21417v1_genomic.fna/target_genomes.txt
[2024-01-24 14:19:26,361] [INFO] Task started: fastANI
[2024-01-24 14:19:26,361] [INFO] Running command: fastANI --query /var/lib/cwl/stg2515ca9b-6c44-4656-8752-2d85572ac017/GCF_000214175.1_ASM21417v1_genomic.fna.gz --refList GCF_000214175.1_ASM21417v1_genomic.fna/target_genomes.txt --output GCF_000214175.1_ASM21417v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:19:43,794] [INFO] Task succeeded: fastANI
[2024-01-24 14:19:43,795] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg45e03f40-3a14-4aad-bbc7-b7ee833ceca7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:19:43,795] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg45e03f40-3a14-4aad-bbc7-b7ee833ceca7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:19:43,811] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:19:43,811] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:19:43,812] [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
Hoyosella subflava	strain=DQS3-9A1	GCA_000214175.1	639313	639313	type	True	100.0	1619	1619	95	conclusive
Hoyosella altamirensis	strain=DSM 45258	GCA_014191505.1	616997	616997	type	True	92.5527	1370	1619	95	below_threshold
Hoyosella lacisalsi	strain=G463	GCA_014841105.1	2742202	2742202	type	True	77.6809	271	1619	95	below_threshold
Hoyosella suaedae	strain=LNNU 331112	GCA_008312885.1	2605429	2605429	type	True	77.5917	277	1619	95	below_threshold
Prescottella equi	strain=NCTC1621	GCA_900455845.1	43767	43767	type	True	77.109	183	1619	95	below_threshold
Mycobacterium pallens	strain=JCM 16370	GCA_019456675.1	370524	370524	type	True	76.8542	128	1619	95	below_threshold
Prescottella equi	strain=NBRC 101255	GCA_001552575.1	43767	43767	type	True	76.8291	176	1619	95	below_threshold
Prescottella equi	strain=DSM 20307	GCA_002094305.1	43767	43767	type	True	76.82	180	1619	95	below_threshold
Rhodococcus spelaei	strain=C9-5	GCA_006704125.1	2546320	2546320	type	True	76.6947	173	1619	95	below_threshold
Gordonia namibiensis	strain=NBRC 108229	GCA_000298235.1	168480	168480	type	True	76.658	133	1619	95	below_threshold
Nocardia stercoris	strain=NEAU-LL90	GCA_003696265.1	2483361	2483361	type	True	76.6487	141	1619	95	below_threshold
Rhodococcus tukisamuensis	strain=NBRC 100609	GCA_001894985.1	168276	168276	type	True	76.6268	188	1619	95	below_threshold
Rhodococcus tukisamuensis	strain=JCM 11308	GCA_900101735.1	168276	168276	type	True	76.6146	189	1619	95	below_threshold
Cellulomonas soli	strain=DSM 24484	GCA_013409305.1	931535	931535	type	True	76.5762	65	1619	95	below_threshold
Mycolicibacterium canariasense	strain=JCM15298	GCA_001570445.1	228230	228230	type	True	76.5026	131	1619	95	below_threshold
Mycolicibacterium canariasense	strain=CCUG 47953	GCA_002101555.1	228230	228230	type	True	76.4414	132	1619	95	below_threshold
Nocardia mexicana	strain=DSM 44952	GCA_003350525.1	279262	279262	type	True	76.3948	163	1619	95	below_threshold
Nocardia mexicana	strain=NBRC 108244	GCA_001613165.1	279262	279262	type	True	76.3738	157	1619	95	below_threshold
Actinopolyspora xinjiangensis	strain=DSM 46732	GCA_900104475.1	405564	405564	type	True	75.5232	62	1619	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:19:43,813] [INFO] DFAST Taxonomy check result was written to GCF_000214175.1_ASM21417v1_genomic.fna/tc_result.tsv
[2024-01-24 14:19:43,814] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:19:43,814] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:19:43,814] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg45e03f40-3a14-4aad-bbc7-b7ee833ceca7/dqc_reference/checkm_data
[2024-01-24 14:19:43,815] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:19:43,862] [INFO] Task started: CheckM
[2024-01-24 14:19:43,862] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000214175.1_ASM21417v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000214175.1_ASM21417v1_genomic.fna/checkm_input GCF_000214175.1_ASM21417v1_genomic.fna/checkm_result
[2024-01-24 14:20:49,124] [INFO] Task succeeded: CheckM
[2024-01-24 14:20:49,125] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:20:49,146] [INFO] ===== Completeness check finished =====
[2024-01-24 14:20:49,146] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:20:49,147] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000214175.1_ASM21417v1_genomic.fna/markers.fasta)
[2024-01-24 14:20:49,147] [INFO] Task started: Blastn
[2024-01-24 14:20:49,147] [INFO] Running command: blastn -query GCF_000214175.1_ASM21417v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg45e03f40-3a14-4aad-bbc7-b7ee833ceca7/dqc_reference/reference_markers_gtdb.fasta -out GCF_000214175.1_ASM21417v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:20:50,377] [INFO] Task succeeded: Blastn
[2024-01-24 14:20:50,381] [INFO] Selected 20 target genomes.
[2024-01-24 14:20:50,381] [INFO] Target genome list was writen to GCF_000214175.1_ASM21417v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:20:50,430] [INFO] Task started: fastANI
[2024-01-24 14:20:50,430] [INFO] Running command: fastANI --query /var/lib/cwl/stg2515ca9b-6c44-4656-8752-2d85572ac017/GCF_000214175.1_ASM21417v1_genomic.fna.gz --refList GCF_000214175.1_ASM21417v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000214175.1_ASM21417v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:21:09,117] [INFO] Task succeeded: fastANI
[2024-01-24 14:21:09,137] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:21:09,138] [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_000214175.1	s__Hoyosella subflava	100.0	1619	1619	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Hoyosella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014191505.1	s__Hoyosella altamirensis	92.5527	1370	1619	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Hoyosella	95.0	99.98	99.98	0.97	0.97	2	-
GCF_014841105.1	s__Hoyosella sp014841105	77.6809	271	1619	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Hoyosella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008312885.1	s__Hoyosella sp008312885	77.596	278	1619	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Hoyosella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001182745.1	s__Nocardia farcinica	77.0855	182	1619	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	99.16	98.59	0.93	0.88	42	-
GCF_001646645.1	s__Rhodococcus hoagii	77.0257	160	1619	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	99.01	98.63	0.96	0.88	61	-
GCF_000014565.1	s__Rhodococcus jostii_A	77.0065	219	1619	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	97.76	95.96	0.81	0.77	4	-
GCF_001457595.1	s__Mycobacterium smegmatis	76.9683	160	1619	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.88	98.06	0.95	0.91	32	-
GCF_013409305.1	s__Cellulomonas soli	76.7454	66	1619	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_006704125.1	s__Rhodococcus sp006704125	76.7082	173	1619	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004362315.1	s__Mycobacterium sp004362315	76.6727	120	1619	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.02	98.99	0.96	0.96	6	-
GCF_000298235.1	s__Gordonia namibiensis	76.658	133	1619	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	97.13	97.13	0.90	0.90	2	-
GCF_003696265.1	s__Nocardia stercoris	76.6532	142	1619	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001894985.1	s__Rhodococcus tukisamuensis	76.626	188	1619	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	99.99	99.99	0.99	0.99	2	-
GCF_003051005.1	s__Rhodococcus sp003051005	76.617	162	1619	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001552715.1	s__Mycobacterium vaccae	76.5418	126	1619	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.99	99.97	1.00	1.00	3	-
GCF_002101555.1	s__Mycobacterium canariasense	76.4414	132	1619	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	100.00	100.00	0.99	0.99	2	-
GCF_001613165.1	s__Nocardia mexicana	76.384	156	1619	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_016526145.1	s__Saccharopolyspora_C sp016526145	75.8579	102	1619	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharopolyspora_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900104475.1	s__Actinopolyspora xinjiangensis	75.5232	62	1619	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinopolyspora	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:21:09,139] [INFO] GTDB search result was written to GCF_000214175.1_ASM21417v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:21:09,140] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:21:09,144] [INFO] DFAST_QC result json was written to GCF_000214175.1_ASM21417v1_genomic.fna/dqc_result.json
[2024-01-24 14:21:09,145] [INFO] DFAST_QC completed!
[2024-01-24 14:21:09,145] [INFO] Total running time: 0h2m8s