[2024-01-25 17:40:20,526] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:40:20,528] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:40:20,529] [INFO] DQC Reference Directory: /var/lib/cwl/stg882fd675-460a-457b-9904-85666c1f34ae/dqc_reference
[2024-01-25 17:40:21,619] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:40:21,620] [INFO] Task started: Prodigal
[2024-01-25 17:40:21,620] [INFO] Running command: gunzip -c /var/lib/cwl/stg79a8d4ce-9f69-4a1b-ab1b-cf62b138689c/GCF_000583735.1_ASM58373v1_genomic.fna.gz | prodigal -d GCF_000583735.1_ASM58373v1_genomic.fna/cds.fna -a GCF_000583735.1_ASM58373v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:40:50,929] [INFO] Task succeeded: Prodigal
[2024-01-25 17:40:50,929] [INFO] Task started: HMMsearch
[2024-01-25 17:40:50,929] [INFO] Running command: hmmsearch --tblout GCF_000583735.1_ASM58373v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg882fd675-460a-457b-9904-85666c1f34ae/dqc_reference/reference_markers.hmm GCF_000583735.1_ASM58373v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:40:51,437] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:40:51,438] [INFO] Found 6/6 markers.
[2024-01-25 17:40:51,516] [INFO] Query marker FASTA was written to GCF_000583735.1_ASM58373v1_genomic.fna/markers.fasta
[2024-01-25 17:40:51,516] [INFO] Task started: Blastn
[2024-01-25 17:40:51,517] [INFO] Running command: blastn -query GCF_000583735.1_ASM58373v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg882fd675-460a-457b-9904-85666c1f34ae/dqc_reference/reference_markers.fasta -out GCF_000583735.1_ASM58373v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:40:52,697] [INFO] Task succeeded: Blastn
[2024-01-25 17:40:52,700] [INFO] Selected 9 target genomes.
[2024-01-25 17:40:52,700] [INFO] Target genome list was writen to GCF_000583735.1_ASM58373v1_genomic.fna/target_genomes.txt
[2024-01-25 17:40:52,730] [INFO] Task started: fastANI
[2024-01-25 17:40:52,730] [INFO] Running command: fastANI --query /var/lib/cwl/stg79a8d4ce-9f69-4a1b-ab1b-cf62b138689c/GCF_000583735.1_ASM58373v1_genomic.fna.gz --refList GCF_000583735.1_ASM58373v1_genomic.fna/target_genomes.txt --output GCF_000583735.1_ASM58373v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:41:13,901] [INFO] Task succeeded: fastANI
[2024-01-25 17:41:13,901] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg882fd675-460a-457b-9904-85666c1f34ae/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:41:13,902] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg882fd675-460a-457b-9904-85666c1f34ae/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:41:13,909] [INFO] Found 9 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 17:41:13,909] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:41:13,909] [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 wratislaviensis	strain=NBRC 100605	GCA_000583735.1	44752	44752	suspected-type	True	100.0	3398	3402	95	conclusive
Rhodococcus wratislaviensis	strain=NCTC13229	GCA_900455735.1	44752	44752	suspected-type	True	98.8972	2410	3402	95	conclusive
Rhodococcus opacus	strain=ATCC 51881	GCA_012396235.1	37919	37919	type	True	94.0937	2159	3402	95	below_threshold
Rhodococcus opacus	strain=DSM 43205	GCA_001646735.1	37919	37919	type	True	93.9512	2082	3402	95	below_threshold
Rhodococcus koreensis	strain=NBRC 100607	GCA_001894845.1	99653	99653	type	True	90.6958	2274	3402	95	below_threshold
Rhodococcus pseudokoreensis	strain=R79	GCA_017068395.1	2811421	2811421	type	True	90.5346	2193	3402	95	below_threshold
Rhodococcus jostii	strain=DSM 44719	GCA_900105375.1	132919	132919	type	True	90.2478	2434	3402	95	below_threshold
Rhodococcus jostii	strain=NBRC 16295	GCA_001894825.1	132919	132919	type	True	90.2358	2343	3402	95	below_threshold
Prescottella defluvii	strain=Ca11	GCA_000738775.1	1323361	1323361	type	True	80.0071	822	3402	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:41:13,911] [INFO] DFAST Taxonomy check result was written to GCF_000583735.1_ASM58373v1_genomic.fna/tc_result.tsv
[2024-01-25 17:41:13,911] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:41:13,912] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:41:13,912] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg882fd675-460a-457b-9904-85666c1f34ae/dqc_reference/checkm_data
[2024-01-25 17:41:13,912] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:41:14,005] [INFO] Task started: CheckM
[2024-01-25 17:41:14,005] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000583735.1_ASM58373v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000583735.1_ASM58373v1_genomic.fna/checkm_input GCF_000583735.1_ASM58373v1_genomic.fna/checkm_result
[2024-01-25 17:43:28,819] [INFO] Task succeeded: CheckM
[2024-01-25 17:43:28,820] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:43:28,843] [INFO] ===== Completeness check finished =====
[2024-01-25 17:43:28,844] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:43:28,845] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000583735.1_ASM58373v1_genomic.fna/markers.fasta)
[2024-01-25 17:43:28,845] [INFO] Task started: Blastn
[2024-01-25 17:43:28,845] [INFO] Running command: blastn -query GCF_000583735.1_ASM58373v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg882fd675-460a-457b-9904-85666c1f34ae/dqc_reference/reference_markers_gtdb.fasta -out GCF_000583735.1_ASM58373v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:43:30,686] [INFO] Task succeeded: Blastn
[2024-01-25 17:43:30,688] [INFO] Selected 10 target genomes.
[2024-01-25 17:43:30,689] [INFO] Target genome list was writen to GCF_000583735.1_ASM58373v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:43:30,708] [INFO] Task started: fastANI
[2024-01-25 17:43:30,708] [INFO] Running command: fastANI --query /var/lib/cwl/stg79a8d4ce-9f69-4a1b-ab1b-cf62b138689c/GCF_000583735.1_ASM58373v1_genomic.fna.gz --refList GCF_000583735.1_ASM58373v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000583735.1_ASM58373v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:43:51,805] [INFO] Task succeeded: fastANI
[2024-01-25 17:43:51,813] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:43:51,813] [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_900455735.1	s__Rhodococcus wratislaviensis	98.8972	2410	3402	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	99.31	98.94	0.95	0.93	4	conclusive
GCF_012396235.1	s__Rhodococcus opacus	94.0915	2160	3402	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	98.04	95.98	0.86	0.77	23	-
GCF_000014565.1	s__Rhodococcus jostii_A	93.7407	2290	3402	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	97.76	95.96	0.81	0.77	4	-
GCF_000010805.1	s__Rhodococcus opacus_C	90.8754	2162	3402	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900105905.1	s__Rhodococcus koreensis	90.6743	2311	3402	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	99.00	98.46	0.87	0.80	4	-
GCF_017068395.1	s__Rhodococcus sp002165735	90.5229	2195	3402	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	96.37	95.32	0.78	0.69	5	-
GCF_001894825.1	s__Rhodococcus jostii	90.2528	2341	3402	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000738775.1	s__Rhodococcus defluvii	80.0373	819	3402	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004011865.1	s__Rhodococcus agglutinans	79.9627	918	3402	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006704125.1	s__Rhodococcus sp006704125	79.6312	845	3402	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:43:51,815] [INFO] GTDB search result was written to GCF_000583735.1_ASM58373v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:43:51,815] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:43:51,817] [INFO] DFAST_QC result json was written to GCF_000583735.1_ASM58373v1_genomic.fna/dqc_result.json
[2024-01-25 17:43:51,818] [INFO] DFAST_QC completed!
[2024-01-25 17:43:51,818] [INFO] Total running time: 0h3m31s