[2024-01-24 15:19:52,571] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:19:52,573] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:19:52,573] [INFO] DQC Reference Directory: /var/lib/cwl/stgb96ec93a-b657-4da2-b40a-944f9c74c565/dqc_reference
[2024-01-24 15:19:53,870] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:19:53,871] [INFO] Task started: Prodigal
[2024-01-24 15:19:53,872] [INFO] Running command: gunzip -c /var/lib/cwl/stg60fd4087-a8b8-4331-ac38-e399bad77437/GCF_005670675.1_ASM567067v1_genomic.fna.gz | prodigal -d GCF_005670675.1_ASM567067v1_genomic.fna/cds.fna -a GCF_005670675.1_ASM567067v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:20:14,899] [INFO] Task succeeded: Prodigal
[2024-01-24 15:20:14,900] [INFO] Task started: HMMsearch
[2024-01-24 15:20:14,900] [INFO] Running command: hmmsearch --tblout GCF_005670675.1_ASM567067v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb96ec93a-b657-4da2-b40a-944f9c74c565/dqc_reference/reference_markers.hmm GCF_005670675.1_ASM567067v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:20:15,289] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:20:15,290] [INFO] Found 6/6 markers.
[2024-01-24 15:20:15,344] [INFO] Query marker FASTA was written to GCF_005670675.1_ASM567067v1_genomic.fna/markers.fasta
[2024-01-24 15:20:15,344] [INFO] Task started: Blastn
[2024-01-24 15:20:15,345] [INFO] Running command: blastn -query GCF_005670675.1_ASM567067v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb96ec93a-b657-4da2-b40a-944f9c74c565/dqc_reference/reference_markers.fasta -out GCF_005670675.1_ASM567067v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:20:16,656] [INFO] Task succeeded: Blastn
[2024-01-24 15:20:16,660] [INFO] Selected 13 target genomes.
[2024-01-24 15:20:16,661] [INFO] Target genome list was writen to GCF_005670675.1_ASM567067v1_genomic.fna/target_genomes.txt
[2024-01-24 15:20:16,666] [INFO] Task started: fastANI
[2024-01-24 15:20:16,666] [INFO] Running command: fastANI --query /var/lib/cwl/stg60fd4087-a8b8-4331-ac38-e399bad77437/GCF_005670675.1_ASM567067v1_genomic.fna.gz --refList GCF_005670675.1_ASM567067v1_genomic.fna/target_genomes.txt --output GCF_005670675.1_ASM567067v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:20:36,550] [INFO] Task succeeded: fastANI
[2024-01-24 15:20:36,551] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb96ec93a-b657-4da2-b40a-944f9c74c565/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:20:36,551] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb96ec93a-b657-4da2-b40a-944f9c74c565/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:20:36,567] [INFO] Found 13 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 15:20:36,568] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:20:36,568] [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
Mycolicibacterium cosmeticum	strain=DSM 44829	GCA_005670675.1	258533	258533	type	True	100.0	2128	2131	95	conclusive
Mycolicibacterium cosmeticum	strain=DSM 44829	GCA_000613185.1	258533	258533	type	True	99.9991	2128	2131	95	conclusive
Mycolicibacterium canariasense	strain=JCM15298	GCA_001570445.1	228230	228230	type	True	92.7954	1694	2131	95	below_threshold
Mycolicibacterium canariasense	strain=CCUG 47953	GCA_002101555.1	228230	228230	type	True	92.7791	1674	2131	95	below_threshold
Mycolicibacterium fluoranthenivorans	strain=DSM 44556	GCA_011758805.1	258505	258505	type	True	84.8913	1467	2131	95	below_threshold
Mycolicibacterium bacteremicum	strain=DSM 45578	GCA_002086115.1	564198	564198	type	True	82.0078	1191	2131	95	below_threshold
Mycolicibacterium fallax	strain=JCM 6405	GCA_010726955.1	1793	1793	type	True	80.686	805	2131	95	below_threshold
Mycolicibacterium fallax	strain=DSM 44179	GCA_002101995.1	1793	1793	type	True	80.5265	808	2131	95	below_threshold
Mycolicibacterium anyangense	strain=JCM 30275	GCA_010731855.1	1431246	1431246	type	True	80.1874	908	2131	95	below_threshold
Mycobacterium pallens	strain=JCM 16370	GCA_019456675.1	370524	370524	type	True	80.0774	944	2131	95	below_threshold
Mycobacterium crocinum	strain=JCM 16369	GCA_022370635.3	388459	388459	type	True	79.8689	952	2131	95	below_threshold
Mycolicibacterium vinylchloridicum	strain=CECT 8761	GCA_013404075.1	2736928	2736928	type	True	79.7863	915	2131	95	below_threshold
Mycolicibacterium stellerae	strain=CECT 8783	GCA_003719305.1	2358193	2358193	type	True	79.3716	925	2131	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:20:36,570] [INFO] DFAST Taxonomy check result was written to GCF_005670675.1_ASM567067v1_genomic.fna/tc_result.tsv
[2024-01-24 15:20:36,571] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:20:36,571] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:20:36,572] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb96ec93a-b657-4da2-b40a-944f9c74c565/dqc_reference/checkm_data
[2024-01-24 15:20:36,573] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:20:36,631] [INFO] Task started: CheckM
[2024-01-24 15:20:36,631] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_005670675.1_ASM567067v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_005670675.1_ASM567067v1_genomic.fna/checkm_input GCF_005670675.1_ASM567067v1_genomic.fna/checkm_result
[2024-01-24 15:21:49,625] [INFO] Task succeeded: CheckM
[2024-01-24 15:21:49,626] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:21:49,655] [INFO] ===== Completeness check finished =====
[2024-01-24 15:21:49,656] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:21:49,656] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_005670675.1_ASM567067v1_genomic.fna/markers.fasta)
[2024-01-24 15:21:49,657] [INFO] Task started: Blastn
[2024-01-24 15:21:49,657] [INFO] Running command: blastn -query GCF_005670675.1_ASM567067v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb96ec93a-b657-4da2-b40a-944f9c74c565/dqc_reference/reference_markers_gtdb.fasta -out GCF_005670675.1_ASM567067v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:21:51,784] [INFO] Task succeeded: Blastn
[2024-01-24 15:21:51,788] [INFO] Selected 18 target genomes.
[2024-01-24 15:21:51,789] [INFO] Target genome list was writen to GCF_005670675.1_ASM567067v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:21:51,808] [INFO] Task started: fastANI
[2024-01-24 15:21:51,808] [INFO] Running command: fastANI --query /var/lib/cwl/stg60fd4087-a8b8-4331-ac38-e399bad77437/GCF_005670675.1_ASM567067v1_genomic.fna.gz --refList GCF_005670675.1_ASM567067v1_genomic.fna/target_genomes_gtdb.txt --output GCF_005670675.1_ASM567067v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:22:15,932] [INFO] Task succeeded: fastANI
[2024-01-24 15:22:15,950] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:22:15,951] [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_000613185.1	s__Mycobacterium cosmeticum	99.9991	2128	2131	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.89	98.33	0.93	0.89	4	conclusive
GCF_002101555.1	s__Mycobacterium canariasense	92.7901	1673	2131	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	100.00	100.00	0.99	0.99	2	-
GCF_011758805.1	s__Mycobacterium fluoranthenivorans	84.906	1465	2131	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	96.15	95.95	0.85	0.84	4	-
GCA_016197365.1	s__Mycobacterium cosmeticum_A	84.7962	1336	2131	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900078775.1	s__Mycobacterium aurum_A	82.4112	1149	2131	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001907655.1	s__Mycobacterium diernhoferi	82.0961	1129	2131	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.97	99.94	1.00	1.00	3	-
GCF_002086115.1	s__Mycobacterium bacteremicum	82.011	1190	2131	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012223425.1	s__Mycobacterium frederiksbergense	81.7199	1205	2131	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	95.39	95.39	0.91	0.91	2	-
GCA_011620645.1	s__Mycobacterium sp011620645	81.5713	798	2131	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000317305.3	s__Mycobacterium neoaurum_A	81.3046	1060	2131	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.30	95.79	0.98	0.90	7	-
GCF_001245615.1	s__Mycobacterium neworleansense	80.796	1058	2131	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004570325.1	s__Mycobacterium sp004570325	80.725	1009	2131	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010726955.1	s__Mycobacterium fallax	80.6743	806	2131	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.99	99.99	0.97	0.97	2	-
GCF_001545925.1	s__Mycobacterium sp001545925	80.5862	864	2131	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000382405.1	s__Mycobacterium sp000382405	80.3213	739	2131	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002798385.1	s__Mycobacterium goodii	80.2061	1039	2131	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.16	99.12	0.92	0.89	7	-
GCF_010729895.1	s__Mycobacterium confluentis	79.9188	915	2131	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002591975.1	s__Mycobacterium neglectum	79.1157	827	2131	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:22:15,952] [INFO] GTDB search result was written to GCF_005670675.1_ASM567067v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:22:15,953] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:22:15,956] [INFO] DFAST_QC result json was written to GCF_005670675.1_ASM567067v1_genomic.fna/dqc_result.json
[2024-01-24 15:22:15,956] [INFO] DFAST_QC completed!
[2024-01-24 15:22:15,956] [INFO] Total running time: 0h2m23s