[2024-01-25 17:37:50,710] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:37:50,711] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:37:50,711] [INFO] DQC Reference Directory: /var/lib/cwl/stge34a590a-87ba-49ee-acf2-d77642aed3a8/dqc_reference
[2024-01-25 17:37:51,878] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:37:51,879] [INFO] Task started: Prodigal
[2024-01-25 17:37:51,879] [INFO] Running command: gunzip -c /var/lib/cwl/stg992f1641-f4db-478c-ba6e-8941b7a2ffb9/GCF_030509825.1_ASM3050982v1_genomic.fna.gz | prodigal -d GCF_030509825.1_ASM3050982v1_genomic.fna/cds.fna -a GCF_030509825.1_ASM3050982v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:38:06,020] [INFO] Task succeeded: Prodigal
[2024-01-25 17:38:06,020] [INFO] Task started: HMMsearch
[2024-01-25 17:38:06,020] [INFO] Running command: hmmsearch --tblout GCF_030509825.1_ASM3050982v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge34a590a-87ba-49ee-acf2-d77642aed3a8/dqc_reference/reference_markers.hmm GCF_030509825.1_ASM3050982v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:38:06,310] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:38:06,311] [INFO] Found 6/6 markers.
[2024-01-25 17:38:06,356] [INFO] Query marker FASTA was written to GCF_030509825.1_ASM3050982v1_genomic.fna/markers.fasta
[2024-01-25 17:38:06,357] [INFO] Task started: Blastn
[2024-01-25 17:38:06,357] [INFO] Running command: blastn -query GCF_030509825.1_ASM3050982v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge34a590a-87ba-49ee-acf2-d77642aed3a8/dqc_reference/reference_markers.fasta -out GCF_030509825.1_ASM3050982v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:38:07,509] [INFO] Task succeeded: Blastn
[2024-01-25 17:38:07,512] [INFO] Selected 10 target genomes.
[2024-01-25 17:38:07,513] [INFO] Target genome list was writen to GCF_030509825.1_ASM3050982v1_genomic.fna/target_genomes.txt
[2024-01-25 17:38:07,515] [INFO] Task started: fastANI
[2024-01-25 17:38:07,515] [INFO] Running command: fastANI --query /var/lib/cwl/stg992f1641-f4db-478c-ba6e-8941b7a2ffb9/GCF_030509825.1_ASM3050982v1_genomic.fna.gz --refList GCF_030509825.1_ASM3050982v1_genomic.fna/target_genomes.txt --output GCF_030509825.1_ASM3050982v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:38:20,493] [INFO] Task succeeded: fastANI
[2024-01-25 17:38:20,494] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge34a590a-87ba-49ee-acf2-d77642aed3a8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:38:20,494] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge34a590a-87ba-49ee-acf2-d77642aed3a8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:38:20,503] [INFO] Found 10 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 17:38:20,503] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:38:20,503] [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 ruber	strain=DSM 43338	GCA_001646835.1	1830	1830	type	True	99.2969	1517	1728	95	conclusive
Rhodococcus ruber	strain=NBRC 15591	GCA_001894945.1	1830	1830	type	True	99.2709	1574	1728	95	conclusive
Rhodococcus aetherivorans	strain=DSM 44752	GCA_011058165.1	191292	191292	type	True	91.9933	1449	1728	95	below_threshold
Rhodococcus aetherivorans	strain=JCM 14343	GCA_009176285.1	191292	191292	type	True	91.9753	1483	1728	95	below_threshold
Rhodococcus zopfii	strain=NBRC 100606	GCA_001895025.1	43772	43772	type	True	82.1467	1030	1728	95	below_threshold
Rhodococcus phenolicus	strain=DSM 44812	GCA_001646785.1	263849	263849	type	True	81.6367	974	1728	95	below_threshold
Rhodococcus rhodochrous	strain=DSM 43241	GCA_001646825.1	1829	1829	suspected-type	True	81.2039	878	1728	95	below_threshold
Rhodococcus yananensis	strain=FBM22-1	GCA_020515525.1	2879464	2879464	type	True	80.8615	755	1728	95	below_threshold
Nocardia amamiensis	strain=NBRC 102102	GCA_001612745.1	404578	404578	type	True	78.2958	543	1728	95	below_threshold
Mycolicibacterium insubricum	strain=JCM 16366	GCA_010731615.1	444597	444597	type	True	78.0657	420	1728	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:38:20,504] [INFO] DFAST Taxonomy check result was written to GCF_030509825.1_ASM3050982v1_genomic.fna/tc_result.tsv
[2024-01-25 17:38:20,507] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:38:20,507] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:38:20,507] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge34a590a-87ba-49ee-acf2-d77642aed3a8/dqc_reference/checkm_data
[2024-01-25 17:38:20,508] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:38:20,581] [INFO] Task started: CheckM
[2024-01-25 17:38:20,581] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030509825.1_ASM3050982v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030509825.1_ASM3050982v1_genomic.fna/checkm_input GCF_030509825.1_ASM3050982v1_genomic.fna/checkm_result
[2024-01-25 17:39:19,905] [INFO] Task succeeded: CheckM
[2024-01-25 17:39:19,906] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:39:19,923] [INFO] ===== Completeness check finished =====
[2024-01-25 17:39:19,923] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:39:19,924] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030509825.1_ASM3050982v1_genomic.fna/markers.fasta)
[2024-01-25 17:39:19,924] [INFO] Task started: Blastn
[2024-01-25 17:39:19,924] [INFO] Running command: blastn -query GCF_030509825.1_ASM3050982v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge34a590a-87ba-49ee-acf2-d77642aed3a8/dqc_reference/reference_markers_gtdb.fasta -out GCF_030509825.1_ASM3050982v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:39:21,714] [INFO] Task succeeded: Blastn
[2024-01-25 17:39:21,719] [INFO] Selected 13 target genomes.
[2024-01-25 17:39:21,719] [INFO] Target genome list was writen to GCF_030509825.1_ASM3050982v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:39:21,724] [INFO] Task started: fastANI
[2024-01-25 17:39:21,724] [INFO] Running command: fastANI --query /var/lib/cwl/stg992f1641-f4db-478c-ba6e-8941b7a2ffb9/GCF_030509825.1_ASM3050982v1_genomic.fna.gz --refList GCF_030509825.1_ASM3050982v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030509825.1_ASM3050982v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:39:39,516] [INFO] Task succeeded: fastANI
[2024-01-25 17:39:39,525] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:39:39,525] [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_001894945.1	s__Rhodococcus ruber	99.2699	1574	1728	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	98.84	95.07	0.94	0.85	19	conclusive
GCF_011058165.1	s__Rhodococcus aetherivorans	91.9608	1451	1728	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	98.92	95.74	0.88	0.78	18	-
GCF_001895025.1	s__Rhodococcus zopfii	82.1092	1035	1728	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	97.81	97.81	0.87	0.87	2	-
GCF_015865005.1	s__Rhodococcus sp015865005	81.9984	976	1728	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001646785.1	s__Rhodococcus phenolicus	81.6377	976	1728	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900105195.1	s__Rhodococcus pyridinivorans	81.181	935	1728	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	98.16	95.17	0.90	0.84	21	-
GCF_900187265.1	s__Rhodococcus rhodochrous	81.1459	901	1728	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	97.52	95.51	0.91	0.84	11	-
GCF_001646655.1	s__Rhodococcus gordoniae	81.1161	873	1728	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	98.98	98.16	0.95	0.93	4	-
GCF_013602415.1	s__Rhodococcus sp013602415	80.9523	939	1728	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012726195.1	s__Rhodococcus sp012726195	79.8043	743	1728	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010731615.1	s__Mycobacterium insubricum	78.0988	416	1728	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.99	99.99	1.00	1.00	2	-
GCF_000526215.1	s__Nocardia sp000526215	78.0047	634	1728	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000230935.1	s__Mycobacterium rhodesiae_B	77.4538	427	1728	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:39:39,526] [INFO] GTDB search result was written to GCF_030509825.1_ASM3050982v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:39:39,527] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:39:39,530] [INFO] DFAST_QC result json was written to GCF_030509825.1_ASM3050982v1_genomic.fna/dqc_result.json
[2024-01-25 17:39:39,530] [INFO] DFAST_QC completed!
[2024-01-25 17:39:39,530] [INFO] Total running time: 0h1m49s