[2024-01-24 13:22:40,699] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:22:40,700] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:22:40,700] [INFO] DQC Reference Directory: /var/lib/cwl/stga76173af-6603-4296-ba47-3071b4324a9e/dqc_reference
[2024-01-24 13:22:42,023] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:22:42,024] [INFO] Task started: Prodigal
[2024-01-24 13:22:42,025] [INFO] Running command: gunzip -c /var/lib/cwl/stg6fd45f37-9ba5-4cc4-8382-eeb880cfde9c/GCF_003990875.1_ASM399087v1_genomic.fna.gz | prodigal -d GCF_003990875.1_ASM399087v1_genomic.fna/cds.fna -a GCF_003990875.1_ASM399087v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:23:18,350] [INFO] Task succeeded: Prodigal
[2024-01-24 13:23:18,350] [INFO] Task started: HMMsearch
[2024-01-24 13:23:18,350] [INFO] Running command: hmmsearch --tblout GCF_003990875.1_ASM399087v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga76173af-6603-4296-ba47-3071b4324a9e/dqc_reference/reference_markers.hmm GCF_003990875.1_ASM399087v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:23:18,674] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:23:18,677] [INFO] Found 6/6 markers.
[2024-01-24 13:23:18,739] [INFO] Query marker FASTA was written to GCF_003990875.1_ASM399087v1_genomic.fna/markers.fasta
[2024-01-24 13:23:18,739] [INFO] Task started: Blastn
[2024-01-24 13:23:18,740] [INFO] Running command: blastn -query GCF_003990875.1_ASM399087v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga76173af-6603-4296-ba47-3071b4324a9e/dqc_reference/reference_markers.fasta -out GCF_003990875.1_ASM399087v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:23:19,869] [INFO] Task succeeded: Blastn
[2024-01-24 13:23:19,872] [INFO] Selected 7 target genomes.
[2024-01-24 13:23:19,873] [INFO] Target genome list was writen to GCF_003990875.1_ASM399087v1_genomic.fna/target_genomes.txt
[2024-01-24 13:23:19,877] [INFO] Task started: fastANI
[2024-01-24 13:23:19,877] [INFO] Running command: fastANI --query /var/lib/cwl/stg6fd45f37-9ba5-4cc4-8382-eeb880cfde9c/GCF_003990875.1_ASM399087v1_genomic.fna.gz --refList GCF_003990875.1_ASM399087v1_genomic.fna/target_genomes.txt --output GCF_003990875.1_ASM399087v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:23:31,301] [INFO] Task succeeded: fastANI
[2024-01-24 13:23:31,301] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga76173af-6603-4296-ba47-3071b4324a9e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:23:31,302] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga76173af-6603-4296-ba47-3071b4324a9e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:23:31,312] [INFO] Found 7 fastANI hits (5 hits with ANI > threshold)
[2024-01-24 13:23:31,312] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 13:23:31,312] [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 erythropolis	strain=JCM 3201	GCA_003990875.1	1833	1833	type	True	100.0	2215	2216	95	inconclusive
Rhodococcus erythropolis	strain=NBRC 15567	GCA_001552595.1	1833	1833	type	True	99.9771	2148	2216	95	inconclusive
Rhodococcus erythropolis	strain=DSM 43066	GCA_022134675.1	1833	1833	type	True	99.9726	2157	2216	95	inconclusive
Rhodococcus qingshengii	strain=JCM 15477	GCA_001646745.1	334542	334542	type	True	95.4008	1969	2216	95	inconclusive
Rhodococcus qingshengii	strain=djl-6	GCA_023221595.1	334542	334542	type	True	95.3984	2003	2216	95	inconclusive
Rhodococcus opacus	strain=ATCC 51881	GCA_012396235.1	37919	37919	type	True	79.2399	761	2216	95	below_threshold
Rhodococcus opacus	strain=DSM 43205	GCA_001646735.1	37919	37919	type	True	79.2376	757	2216	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:23:31,314] [INFO] DFAST Taxonomy check result was written to GCF_003990875.1_ASM399087v1_genomic.fna/tc_result.tsv
[2024-01-24 13:23:31,314] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:23:31,315] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:23:31,315] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga76173af-6603-4296-ba47-3071b4324a9e/dqc_reference/checkm_data
[2024-01-24 13:23:31,316] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:23:31,379] [INFO] Task started: CheckM
[2024-01-24 13:23:31,380] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003990875.1_ASM399087v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003990875.1_ASM399087v1_genomic.fna/checkm_input GCF_003990875.1_ASM399087v1_genomic.fna/checkm_result
[2024-01-24 13:25:04,572] [INFO] Task succeeded: CheckM
[2024-01-24 13:25:04,574] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:25:04,598] [INFO] ===== Completeness check finished =====
[2024-01-24 13:25:04,598] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:25:04,599] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003990875.1_ASM399087v1_genomic.fna/markers.fasta)
[2024-01-24 13:25:04,599] [INFO] Task started: Blastn
[2024-01-24 13:25:04,599] [INFO] Running command: blastn -query GCF_003990875.1_ASM399087v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga76173af-6603-4296-ba47-3071b4324a9e/dqc_reference/reference_markers_gtdb.fasta -out GCF_003990875.1_ASM399087v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:25:06,139] [INFO] Task succeeded: Blastn
[2024-01-24 13:25:06,144] [INFO] Selected 8 target genomes.
[2024-01-24 13:25:06,144] [INFO] Target genome list was writen to GCF_003990875.1_ASM399087v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:25:06,178] [INFO] Task started: fastANI
[2024-01-24 13:25:06,179] [INFO] Running command: fastANI --query /var/lib/cwl/stg6fd45f37-9ba5-4cc4-8382-eeb880cfde9c/GCF_003990875.1_ASM399087v1_genomic.fna.gz --refList GCF_003990875.1_ASM399087v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003990875.1_ASM399087v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:25:21,680] [INFO] Task succeeded: fastANI
[2024-01-24 13:25:21,692] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:25:21,692] [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_001552595.1	s__Rhodococcus erythropolis	99.9771	2148	2216	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.5281	98.72	98.39	0.92	0.80	38	conclusive
GCF_001646745.1	s__Rhodococcus qingshengii	95.4008	1969	2216	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.5281	98.54	97.59	0.89	0.82	63	-
GCF_016598535.1	s__Rhodococcus erythropolis_D	94.2202	1940	2216	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	98.18	96.26	0.93	0.90	6	-
GCF_005938745.2	s__Rhodococcus sp005938745	83.5998	1298	2216	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001894805.1	s__Rhodococcus globerulus	83.4715	1266	2216	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	99.06	98.09	0.93	0.89	13	-
GCF_002245895.1	s__Rhodococcus sp002245895	82.2646	1174	2216	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000014565.1	s__Rhodococcus jostii_A	79.301	771	2216	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	97.76	95.96	0.81	0.77	4	-
GCF_012396235.1	s__Rhodococcus opacus	79.2213	764	2216	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	98.04	95.98	0.86	0.77	23	-
--------------------------------------------------------------------------------
[2024-01-24 13:25:21,694] [INFO] GTDB search result was written to GCF_003990875.1_ASM399087v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:25:21,695] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:25:21,697] [INFO] DFAST_QC result json was written to GCF_003990875.1_ASM399087v1_genomic.fna/dqc_result.json
[2024-01-24 13:25:21,698] [INFO] DFAST_QC completed!
[2024-01-24 13:25:21,698] [INFO] Total running time: 0h2m41s