[2024-01-24 14:11:46,734] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:11:46,735] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:11:46,735] [INFO] DQC Reference Directory: /var/lib/cwl/stg7ef59a73-b168-40a3-a443-7ee72330ef0a/dqc_reference
[2024-01-24 14:11:47,918] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:11:47,919] [INFO] Task started: Prodigal
[2024-01-24 14:11:47,919] [INFO] Running command: gunzip -c /var/lib/cwl/stgb7e5d4ba-9232-4029-bfe2-29f71bb31781/GCF_008297975.1_ASM829797v1_genomic.fna.gz | prodigal -d GCF_008297975.1_ASM829797v1_genomic.fna/cds.fna -a GCF_008297975.1_ASM829797v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:12:13,579] [INFO] Task succeeded: Prodigal
[2024-01-24 14:12:13,579] [INFO] Task started: HMMsearch
[2024-01-24 14:12:13,579] [INFO] Running command: hmmsearch --tblout GCF_008297975.1_ASM829797v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7ef59a73-b168-40a3-a443-7ee72330ef0a/dqc_reference/reference_markers.hmm GCF_008297975.1_ASM829797v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:12:13,943] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:12:13,948] [INFO] Found 6/6 markers.
[2024-01-24 14:12:14,025] [INFO] Query marker FASTA was written to GCF_008297975.1_ASM829797v1_genomic.fna/markers.fasta
[2024-01-24 14:12:14,025] [INFO] Task started: Blastn
[2024-01-24 14:12:14,025] [INFO] Running command: blastn -query GCF_008297975.1_ASM829797v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7ef59a73-b168-40a3-a443-7ee72330ef0a/dqc_reference/reference_markers.fasta -out GCF_008297975.1_ASM829797v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:12:15,222] [INFO] Task succeeded: Blastn
[2024-01-24 14:12:15,225] [INFO] Selected 22 target genomes.
[2024-01-24 14:12:15,225] [INFO] Target genome list was writen to GCF_008297975.1_ASM829797v1_genomic.fna/target_genomes.txt
[2024-01-24 14:12:15,253] [INFO] Task started: fastANI
[2024-01-24 14:12:15,253] [INFO] Running command: fastANI --query /var/lib/cwl/stgb7e5d4ba-9232-4029-bfe2-29f71bb31781/GCF_008297975.1_ASM829797v1_genomic.fna.gz --refList GCF_008297975.1_ASM829797v1_genomic.fna/target_genomes.txt --output GCF_008297975.1_ASM829797v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:12:43,004] [INFO] Task succeeded: fastANI
[2024-01-24 14:12:43,005] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7ef59a73-b168-40a3-a443-7ee72330ef0a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:12:43,005] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7ef59a73-b168-40a3-a443-7ee72330ef0a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:12:43,028] [INFO] Found 22 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:12:43,028] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:12:43,028] [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
Rhodococcus cavernicola	strain=C1-24	GCA_008297975.1	2495913	2495913	type	True	100.0	1860	1864	95	conclusive
Rhodococcus spelaei	strain=C9-5	GCA_006704125.1	2546320	2546320	type	True	78.6828	541	1864	95	below_threshold
Rhodococcus tukisamuensis	strain=JCM 11308	GCA_900101735.1	168276	168276	type	True	78.6771	561	1864	95	below_threshold
Rhodococcus oryzae	strain=NEAU-CX67	GCA_005049235.1	2571143	2571143	type	True	78.6434	578	1864	95	below_threshold
Rhodococcus tukisamuensis	strain=NBRC 100609	GCA_001894985.1	168276	168276	type	True	78.6424	560	1864	95	below_threshold
Rhodococcus maanshanensis	strain=NBRC 100610	GCA_001894865.1	183556	183556	type	True	78.641	582	1864	95	below_threshold
Rhodococcus maanshanensis	strain=DSM 44675	GCA_900109405.1	183556	183556	type	True	78.5825	589	1864	95	below_threshold
Prescottella defluvii	strain=Ca11	GCA_000738775.1	1323361	1323361	type	True	78.5445	488	1864	95	below_threshold
Rhodococcus wratislaviensis	strain=NCTC13229	GCA_900455735.1	44752	44752	suspected-type	True	78.3855	577	1864	95	below_threshold
Rhodococcus jostii	strain=NBRC 16295	GCA_001894825.1	132919	132919	type	True	78.3622	587	1864	95	below_threshold
Rhodococcus pseudokoreensis	strain=R79	GCA_017068395.1	2811421	2811421	type	True	78.3472	594	1864	95	below_threshold
Nocardia farcinica	strain=NCTC11134	GCA_001182745.2	37329	37329	type	True	78.3366	561	1864	95	below_threshold
Rhodococcus fascians	strain=LMG 3623	GCA_000761055.1	1828	1828	type	True	78.3364	405	1864	95	below_threshold
Rhodococcus fascians	strain=NBRC 12155	GCA_001894785.1	1828	1828	type	True	78.3105	410	1864	95	below_threshold
Nocardia farcinica	strain=DSM 43257	GCA_900156775.1	37329	37329	type	True	78.2993	560	1864	95	below_threshold
Rhodococcus jostii	strain=DSM 44719	GCA_900105375.1	132919	132919	type	True	78.2907	606	1864	95	below_threshold
Rhodococcus aetherivorans	strain=JCM 14343	GCA_009176285.1	191292	191292	type	True	78.1821	502	1864	95	below_threshold
Rhodococcus oxybenzonivorans	strain=S2-17	GCA_003130705.1	1990687	1990687	type	True	78.1539	444	1864	95	below_threshold
Nocardia brasiliensis	strain=NBRC 14402	GCA_000308475.2	37326	37326	suspected-type	True	78.0904	590	1864	95	below_threshold
Nocardia brasiliensis	strain=NCTC11294	GCA_900454265.1	37326	37326	suspected-type	True	78.0784	596	1864	95	below_threshold
Nocardia albiluteola	strain=NEAU-G5	GCA_018860155.1	2842303	2842303	type	True	77.8339	492	1864	95	below_threshold
Nocardia crassostreae	strain=NBRC 100342	GCA_001613405.1	53428	53428	type	True	77.7069	427	1864	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:12:43,031] [INFO] DFAST Taxonomy check result was written to GCF_008297975.1_ASM829797v1_genomic.fna/tc_result.tsv
[2024-01-24 14:12:43,032] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:12:43,032] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:12:43,033] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7ef59a73-b168-40a3-a443-7ee72330ef0a/dqc_reference/checkm_data
[2024-01-24 14:12:43,035] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:12:43,092] [INFO] Task started: CheckM
[2024-01-24 14:12:43,093] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008297975.1_ASM829797v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008297975.1_ASM829797v1_genomic.fna/checkm_input GCF_008297975.1_ASM829797v1_genomic.fna/checkm_result
[2024-01-24 14:13:50,985] [INFO] Task succeeded: CheckM
[2024-01-24 14:13:50,987] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.14%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2024-01-24 14:13:51,012] [INFO] ===== Completeness check finished =====
[2024-01-24 14:13:51,013] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:13:51,013] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008297975.1_ASM829797v1_genomic.fna/markers.fasta)
[2024-01-24 14:13:51,014] [INFO] Task started: Blastn
[2024-01-24 14:13:51,014] [INFO] Running command: blastn -query GCF_008297975.1_ASM829797v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7ef59a73-b168-40a3-a443-7ee72330ef0a/dqc_reference/reference_markers_gtdb.fasta -out GCF_008297975.1_ASM829797v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:13:52,544] [INFO] Task succeeded: Blastn
[2024-01-24 14:13:52,548] [INFO] Selected 23 target genomes.
[2024-01-24 14:13:52,548] [INFO] Target genome list was writen to GCF_008297975.1_ASM829797v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:13:52,616] [INFO] Task started: fastANI
[2024-01-24 14:13:52,616] [INFO] Running command: fastANI --query /var/lib/cwl/stgb7e5d4ba-9232-4029-bfe2-29f71bb31781/GCF_008297975.1_ASM829797v1_genomic.fna.gz --refList GCF_008297975.1_ASM829797v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008297975.1_ASM829797v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:14:21,935] [INFO] Task succeeded: fastANI
[2024-01-24 14:14:21,953] [INFO] Found 23 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:14:21,954] [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_008297975.1	s__C1-24 sp008297975	100.0	1860	1864	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__C1-24	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_006704125.1	s__Rhodococcus sp006704125	78.6817	540	1864	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001894985.1	s__Rhodococcus tukisamuensis	78.6662	555	1864	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	99.99	99.99	0.99	0.99	2	-
GCF_005049235.1	s__Rhodococcus oryzae	78.6231	582	1864	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	95.56	95.24	0.93	0.92	5	-
GCF_000738775.1	s__Rhodococcus defluvii	78.5614	486	1864	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001646645.1	s__Rhodococcus hoagii	78.4783	475	1864	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	99.01	98.63	0.96	0.88	61	-
GCF_003688915.1	s__Rhodococcus_B sp000813105	78.4232	427	1864	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus_B	95.0	98.08	98.08	0.88	0.88	2	-
GCF_000010805.1	s__Rhodococcus opacus_C	78.3956	599	1864	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001894825.1	s__Rhodococcus jostii	78.3514	588	1864	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001182745.1	s__Nocardia farcinica	78.3484	560	1864	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	99.16	98.59	0.93	0.88	42	-
GCF_017068395.1	s__Rhodococcus sp002165735	78.3423	596	1864	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	96.37	95.32	0.78	0.69	5	-
GCF_002258315.1	s__Rhodococcus_B sp002258315	78.3279	456	1864	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus_B	95.0	99.99	99.99	1.00	1.00	2	-
GCF_001426085.1	s__Rhodococcus_B sp001426085	78.3243	407	1864	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002258785.1	s__Rhodococcus_B sp002258785	78.2538	433	1864	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003130705.1	s__Rhodococcus sp003130705	78.1392	446	1864	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	96.82	95.95	0.80	0.77	4	-
GCF_015355755.1	s__Nocardia sp015355755	78.0967	539	1864	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000308475.2	s__Nocardia brasiliensis	78.0866	591	1864	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.8238	100.00	99.99	1.00	1.00	3	-
GCF_000760935.2	s__Rhodococcus_B sp002259335	78.0203	437	1864	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus_B	95.0	96.52	96.34	0.85	0.83	9	-
GCF_000308415.1	s__Nocardia asiatica	78.0118	502	1864	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018860155.1	s__Nocardia sp018860155	77.8308	490	1864	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000381925.1	s__Nocardia sp000381925	77.7427	501	1864	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001613405.1	s__Nocardia crassostreae	77.7182	425	1864	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001613325.1	s__Nocardia yamanashiensis	77.6188	486	1864	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:14:21,955] [INFO] GTDB search result was written to GCF_008297975.1_ASM829797v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:14:21,956] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:14:21,961] [INFO] DFAST_QC result json was written to GCF_008297975.1_ASM829797v1_genomic.fna/dqc_result.json
[2024-01-24 14:14:21,961] [INFO] DFAST_QC completed!
[2024-01-24 14:14:21,961] [INFO] Total running time: 0h2m35s