[2024-01-24 15:27:12,775] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:27:12,779] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:27:12,780] [INFO] DQC Reference Directory: /var/lib/cwl/stga7cde65d-8931-4c4f-9302-3c496b95bf68/dqc_reference
[2024-01-24 15:27:14,211] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:27:14,212] [INFO] Task started: Prodigal
[2024-01-24 15:27:14,213] [INFO] Running command: gunzip -c /var/lib/cwl/stgca876d0e-372a-4e6d-a0c6-82f2c484c58f/GCF_012396235.1_ASM1239623v1_genomic.fna.gz | prodigal -d GCF_012396235.1_ASM1239623v1_genomic.fna/cds.fna -a GCF_012396235.1_ASM1239623v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:27:52,482] [INFO] Task succeeded: Prodigal
[2024-01-24 15:27:52,483] [INFO] Task started: HMMsearch
[2024-01-24 15:27:52,483] [INFO] Running command: hmmsearch --tblout GCF_012396235.1_ASM1239623v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga7cde65d-8931-4c4f-9302-3c496b95bf68/dqc_reference/reference_markers.hmm GCF_012396235.1_ASM1239623v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:27:53,020] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:27:53,021] [INFO] Found 6/6 markers.
[2024-01-24 15:27:53,090] [INFO] Query marker FASTA was written to GCF_012396235.1_ASM1239623v1_genomic.fna/markers.fasta
[2024-01-24 15:27:53,090] [INFO] Task started: Blastn
[2024-01-24 15:27:53,090] [INFO] Running command: blastn -query GCF_012396235.1_ASM1239623v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga7cde65d-8931-4c4f-9302-3c496b95bf68/dqc_reference/reference_markers.fasta -out GCF_012396235.1_ASM1239623v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:27:54,428] [INFO] Task succeeded: Blastn
[2024-01-24 15:27:54,432] [INFO] Selected 9 target genomes.
[2024-01-24 15:27:54,432] [INFO] Target genome list was writen to GCF_012396235.1_ASM1239623v1_genomic.fna/target_genomes.txt
[2024-01-24 15:27:54,439] [INFO] Task started: fastANI
[2024-01-24 15:27:54,440] [INFO] Running command: fastANI --query /var/lib/cwl/stgca876d0e-372a-4e6d-a0c6-82f2c484c58f/GCF_012396235.1_ASM1239623v1_genomic.fna.gz --refList GCF_012396235.1_ASM1239623v1_genomic.fna/target_genomes.txt --output GCF_012396235.1_ASM1239623v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:28:14,362] [INFO] Task succeeded: fastANI
[2024-01-24 15:28:14,362] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga7cde65d-8931-4c4f-9302-3c496b95bf68/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:28:14,362] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga7cde65d-8931-4c4f-9302-3c496b95bf68/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:28:14,371] [INFO] Found 9 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 15:28:14,371] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:28:14,372] [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 opacus	strain=ATCC 51881	GCA_012396235.1	37919	37919	type	True	100.0	2640	2646	95	conclusive
Rhodococcus opacus	strain=DSM 43205	GCA_001646735.1	37919	37919	type	True	99.9257	2475	2646	95	conclusive
Rhodococcus wratislaviensis	strain=NCTC13229	GCA_900455735.1	44752	44752	suspected-type	True	94.3553	2031	2646	95	below_threshold
Rhodococcus wratislaviensis	strain=NBRC 100605	GCA_000583735.1	44752	44752	suspected-type	True	94.1113	2150	2646	95	below_threshold
Rhodococcus koreensis	strain=NBRC 100607	GCA_001894845.1	99653	99653	type	True	90.9441	2079	2646	95	below_threshold
Rhodococcus pseudokoreensis	strain=R79	GCA_017068395.1	2811421	2811421	type	True	90.8898	2047	2646	95	below_threshold
Rhodococcus oxybenzonivorans	strain=S2-17	GCA_003130705.1	1990687	1990687	type	True	84.0984	1537	2646	95	below_threshold
Rhodococcus erythropolis	strain=JCM 3201	GCA_003990875.1	1833	1833	type	True	79.3176	756	2646	95	below_threshold
Rhodococcus erythropolis	strain=DSM 43066	GCA_022134675.1	1833	1833	type	True	79.2994	749	2646	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:28:14,373] [INFO] DFAST Taxonomy check result was written to GCF_012396235.1_ASM1239623v1_genomic.fna/tc_result.tsv
[2024-01-24 15:28:14,374] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:28:14,374] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:28:14,374] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga7cde65d-8931-4c4f-9302-3c496b95bf68/dqc_reference/checkm_data
[2024-01-24 15:28:14,375] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:28:14,451] [INFO] Task started: CheckM
[2024-01-24 15:28:14,451] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_012396235.1_ASM1239623v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_012396235.1_ASM1239623v1_genomic.fna/checkm_input GCF_012396235.1_ASM1239623v1_genomic.fna/checkm_result
[2024-01-24 15:30:01,842] [INFO] Task succeeded: CheckM
[2024-01-24 15:30:01,844] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:30:01,869] [INFO] ===== Completeness check finished =====
[2024-01-24 15:30:01,870] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:30:01,870] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_012396235.1_ASM1239623v1_genomic.fna/markers.fasta)
[2024-01-24 15:30:01,871] [INFO] Task started: Blastn
[2024-01-24 15:30:01,871] [INFO] Running command: blastn -query GCF_012396235.1_ASM1239623v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga7cde65d-8931-4c4f-9302-3c496b95bf68/dqc_reference/reference_markers_gtdb.fasta -out GCF_012396235.1_ASM1239623v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:30:03,755] [INFO] Task succeeded: Blastn
[2024-01-24 15:30:03,760] [INFO] Selected 9 target genomes.
[2024-01-24 15:30:03,760] [INFO] Target genome list was writen to GCF_012396235.1_ASM1239623v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:30:03,769] [INFO] Task started: fastANI
[2024-01-24 15:30:03,769] [INFO] Running command: fastANI --query /var/lib/cwl/stgca876d0e-372a-4e6d-a0c6-82f2c484c58f/GCF_012396235.1_ASM1239623v1_genomic.fna.gz --refList GCF_012396235.1_ASM1239623v1_genomic.fna/target_genomes_gtdb.txt --output GCF_012396235.1_ASM1239623v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:30:23,450] [INFO] Task succeeded: fastANI
[2024-01-24 15:30:23,464] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:30:23,465] [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_012396235.1	s__Rhodococcus opacus	100.0	2640	2646	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	98.04	95.98	0.86	0.77	23	conclusive
GCF_000014565.1	s__Rhodococcus jostii_A	94.4118	2175	2646	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	97.76	95.96	0.81	0.77	4	-
GCF_900455735.1	s__Rhodococcus wratislaviensis	94.3747	2029	2646	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	99.31	98.94	0.95	0.93	4	-
GCF_900105905.1	s__Rhodococcus koreensis	90.9265	2130	2646	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	90.8638	2051	2646	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	96.37	95.32	0.78	0.69	5	-
GCF_000010805.1	s__Rhodococcus opacus_C	90.7063	2048	2646	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014256275.1	s__Rhodococcus wratislaviensis_A	89.3346	1950	2646	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	99.99	99.99	0.99	0.99	2	-
GCF_003130705.1	s__Rhodococcus sp003130705	84.0912	1539	2646	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	96.82	95.95	0.80	0.77	4	-
GCF_001552595.1	s__Rhodococcus erythropolis	79.2811	750	2646	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.5281	98.72	98.39	0.92	0.80	38	-
--------------------------------------------------------------------------------
[2024-01-24 15:30:23,466] [INFO] GTDB search result was written to GCF_012396235.1_ASM1239623v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:30:23,467] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:30:23,470] [INFO] DFAST_QC result json was written to GCF_012396235.1_ASM1239623v1_genomic.fna/dqc_result.json
[2024-01-24 15:30:23,470] [INFO] DFAST_QC completed!
[2024-01-24 15:30:23,470] [INFO] Total running time: 0h3m11s