[2024-01-24 13:25:46,153] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:25:46,156] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:25:46,157] [INFO] DQC Reference Directory: /var/lib/cwl/stgf043b4c5-201e-44d1-8896-cfd0ac015bd4/dqc_reference
[2024-01-24 13:25:47,472] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:25:47,473] [INFO] Task started: Prodigal
[2024-01-24 13:25:47,473] [INFO] Running command: gunzip -c /var/lib/cwl/stg56f9ffee-4a81-4818-a5e7-5ae8b4c8843d/GCF_005049235.1_ASM504923v1_genomic.fna.gz | prodigal -d GCF_005049235.1_ASM504923v1_genomic.fna/cds.fna -a GCF_005049235.1_ASM504923v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:26:06,939] [INFO] Task succeeded: Prodigal
[2024-01-24 13:26:06,940] [INFO] Task started: HMMsearch
[2024-01-24 13:26:06,940] [INFO] Running command: hmmsearch --tblout GCF_005049235.1_ASM504923v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf043b4c5-201e-44d1-8896-cfd0ac015bd4/dqc_reference/reference_markers.hmm GCF_005049235.1_ASM504923v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:26:07,255] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:26:07,257] [INFO] Found 6/6 markers.
[2024-01-24 13:26:07,306] [INFO] Query marker FASTA was written to GCF_005049235.1_ASM504923v1_genomic.fna/markers.fasta
[2024-01-24 13:26:07,307] [INFO] Task started: Blastn
[2024-01-24 13:26:07,307] [INFO] Running command: blastn -query GCF_005049235.1_ASM504923v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf043b4c5-201e-44d1-8896-cfd0ac015bd4/dqc_reference/reference_markers.fasta -out GCF_005049235.1_ASM504923v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:26:08,772] [INFO] Task succeeded: Blastn
[2024-01-24 13:26:08,775] [INFO] Selected 6 target genomes.
[2024-01-24 13:26:08,776] [INFO] Target genome list was writen to GCF_005049235.1_ASM504923v1_genomic.fna/target_genomes.txt
[2024-01-24 13:26:08,779] [INFO] Task started: fastANI
[2024-01-24 13:26:08,779] [INFO] Running command: fastANI --query /var/lib/cwl/stg56f9ffee-4a81-4818-a5e7-5ae8b4c8843d/GCF_005049235.1_ASM504923v1_genomic.fna.gz --refList GCF_005049235.1_ASM504923v1_genomic.fna/target_genomes.txt --output GCF_005049235.1_ASM504923v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:26:17,704] [INFO] Task succeeded: fastANI
[2024-01-24 13:26:17,705] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf043b4c5-201e-44d1-8896-cfd0ac015bd4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:26:17,705] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf043b4c5-201e-44d1-8896-cfd0ac015bd4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:26:17,712] [INFO] Found 6 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:26:17,712] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:26:17,712] [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 oryzae	strain=NEAU-CX67	GCA_005049235.1	2571143	2571143	type	True	100.0	1771	1772	95	conclusive
Rhodococcus maanshanensis	strain=NBRC 100610	GCA_001894865.1	183556	183556	type	True	92.2154	1523	1772	95	below_threshold
Rhodococcus maanshanensis	strain=DSM 44675	GCA_900109405.1	183556	183556	type	True	92.1834	1535	1772	95	below_threshold
Rhodococcus tukisamuensis	strain=JCM 11308	GCA_900101735.1	168276	168276	type	True	83.626	1192	1772	95	below_threshold
Rhodococcus tukisamuensis	strain=NBRC 100609	GCA_001894985.1	168276	168276	type	True	83.5874	1199	1772	95	below_threshold
Rhodococcus spelaei	strain=C9-5	GCA_006704125.1	2546320	2546320	type	True	83.0807	1119	1772	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:26:17,714] [INFO] DFAST Taxonomy check result was written to GCF_005049235.1_ASM504923v1_genomic.fna/tc_result.tsv
[2024-01-24 13:26:17,714] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:26:17,714] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:26:17,715] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf043b4c5-201e-44d1-8896-cfd0ac015bd4/dqc_reference/checkm_data
[2024-01-24 13:26:17,716] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:26:17,764] [INFO] Task started: CheckM
[2024-01-24 13:26:17,765] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_005049235.1_ASM504923v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_005049235.1_ASM504923v1_genomic.fna/checkm_input GCF_005049235.1_ASM504923v1_genomic.fna/checkm_result
[2024-01-24 13:27:16,086] [INFO] Task succeeded: CheckM
[2024-01-24 13:27:16,087] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:27:16,107] [INFO] ===== Completeness check finished =====
[2024-01-24 13:27:16,108] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:27:16,108] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_005049235.1_ASM504923v1_genomic.fna/markers.fasta)
[2024-01-24 13:27:16,108] [INFO] Task started: Blastn
[2024-01-24 13:27:16,109] [INFO] Running command: blastn -query GCF_005049235.1_ASM504923v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf043b4c5-201e-44d1-8896-cfd0ac015bd4/dqc_reference/reference_markers_gtdb.fasta -out GCF_005049235.1_ASM504923v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:27:18,162] [INFO] Task succeeded: Blastn
[2024-01-24 13:27:18,165] [INFO] Selected 9 target genomes.
[2024-01-24 13:27:18,166] [INFO] Target genome list was writen to GCF_005049235.1_ASM504923v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:27:18,189] [INFO] Task started: fastANI
[2024-01-24 13:27:18,190] [INFO] Running command: fastANI --query /var/lib/cwl/stg56f9ffee-4a81-4818-a5e7-5ae8b4c8843d/GCF_005049235.1_ASM504923v1_genomic.fna.gz --refList GCF_005049235.1_ASM504923v1_genomic.fna/target_genomes_gtdb.txt --output GCF_005049235.1_ASM504923v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:27:30,182] [INFO] Task succeeded: fastANI
[2024-01-24 13:27:30,194] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:27:30,194] [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_005049235.1	s__Rhodococcus oryzae	100.0	1771	1772	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	95.56	95.24	0.93	0.92	5	conclusive
GCF_001894865.1	s__Rhodococcus maanshanensis	92.1896	1525	1772	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	98.18	96.37	0.94	0.89	3	-
GCF_001894985.1	s__Rhodococcus tukisamuensis	83.6006	1197	1772	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	99.99	99.99	0.99	0.99	2	-
GCF_006704125.1	s__Rhodococcus sp006704125	83.0601	1124	1772	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013348805.1	s__Rhodococcus sp003350365	80.9476	913	1772	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	98.85	98.85	0.92	0.92	2	-
GCF_001646645.1	s__Rhodococcus hoagii	80.2341	787	1772	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	99.01	98.63	0.96	0.88	61	-
GCF_003051005.1	s__Rhodococcus sp003051005	80.1737	799	1772	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005484805.1	s__Rhodococcus sp005484805	80.1574	806	1772	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	79.7502	902	1772	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	99.00	98.46	0.87	0.80	4	-
--------------------------------------------------------------------------------
[2024-01-24 13:27:30,195] [INFO] GTDB search result was written to GCF_005049235.1_ASM504923v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:27:30,196] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:27:30,198] [INFO] DFAST_QC result json was written to GCF_005049235.1_ASM504923v1_genomic.fna/dqc_result.json
[2024-01-24 13:27:30,199] [INFO] DFAST_QC completed!
[2024-01-24 13:27:30,199] [INFO] Total running time: 0h1m44s