[2024-01-25 17:34:07,123] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:34:07,128] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:34:07,128] [INFO] DQC Reference Directory: /var/lib/cwl/stg64c86015-0086-441f-9d8d-d2b78ff8429e/dqc_reference
[2024-01-25 17:34:09,030] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:34:09,031] [INFO] Task started: Prodigal
[2024-01-25 17:34:09,031] [INFO] Running command: gunzip -c /var/lib/cwl/stgafcd4f45-72e3-438a-9b22-8d3a5b17a5f9/GCF_025821365.1_ASM2582136v1_genomic.fna.gz | prodigal -d GCF_025821365.1_ASM2582136v1_genomic.fna/cds.fna -a GCF_025821365.1_ASM2582136v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:34:26,730] [INFO] Task succeeded: Prodigal
[2024-01-25 17:34:26,730] [INFO] Task started: HMMsearch
[2024-01-25 17:34:26,730] [INFO] Running command: hmmsearch --tblout GCF_025821365.1_ASM2582136v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg64c86015-0086-441f-9d8d-d2b78ff8429e/dqc_reference/reference_markers.hmm GCF_025821365.1_ASM2582136v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:34:27,084] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:34:27,087] [INFO] Found 6/6 markers.
[2024-01-25 17:34:27,142] [INFO] Query marker FASTA was written to GCF_025821365.1_ASM2582136v1_genomic.fna/markers.fasta
[2024-01-25 17:34:27,142] [INFO] Task started: Blastn
[2024-01-25 17:34:27,142] [INFO] Running command: blastn -query GCF_025821365.1_ASM2582136v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg64c86015-0086-441f-9d8d-d2b78ff8429e/dqc_reference/reference_markers.fasta -out GCF_025821365.1_ASM2582136v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:34:28,275] [INFO] Task succeeded: Blastn
[2024-01-25 17:34:28,280] [INFO] Selected 16 target genomes.
[2024-01-25 17:34:28,280] [INFO] Target genome list was writen to GCF_025821365.1_ASM2582136v1_genomic.fna/target_genomes.txt
[2024-01-25 17:34:28,300] [INFO] Task started: fastANI
[2024-01-25 17:34:28,300] [INFO] Running command: fastANI --query /var/lib/cwl/stgafcd4f45-72e3-438a-9b22-8d3a5b17a5f9/GCF_025821365.1_ASM2582136v1_genomic.fna.gz --refList GCF_025821365.1_ASM2582136v1_genomic.fna/target_genomes.txt --output GCF_025821365.1_ASM2582136v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:34:48,978] [INFO] Task succeeded: fastANI
[2024-01-25 17:34:48,979] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg64c86015-0086-441f-9d8d-d2b78ff8429e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:34:48,979] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg64c86015-0086-441f-9d8d-d2b78ff8429e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:34:48,989] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:34:48,990] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:34:48,990] [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 gadium	strain=JCM 12688	GCA_010728925.1	1794	1794	type	True	99.993	1932	1941	95	conclusive
Mycolicibacterium tusciae	strain=DSM 44338	GCA_002086795.1	75922	75922	type	True	94.5553	1649	1941	95	below_threshold
Mycolicibacterium moriokaense	strain=JCM 6375	GCA_010726085.1	39691	39691	type	True	83.4421	1407	1941	95	below_threshold
Mycolicibacterium moriokaense	strain=CIP105393	GCA_002086395.1	39691	39691	type	True	83.4301	1407	1941	95	below_threshold
Mycolicibacterium rutilum	strain=DSM 45405	GCA_900108565.1	370526	370526	type	True	81.5964	1144	1941	95	below_threshold
Mycobacterium lehmannii	strain=CECT 8763	GCA_002245535.1	2048550	2048550	type	True	80.8796	1067	1941	95	below_threshold
Mycolicibacterium malmesburyense	strain=WCM 7299	GCA_001050015.1	1566886	1566886	type	True	80.8445	1056	1941	95	below_threshold
Mycolicibacterium phlei	strain=DSM 43239 = CCUG 21000	GCA_001582015.1	1771	1771	type	True	80.7826	1066	1941	95	below_threshold
Mycolicibacterium elephantis	strain=DSM 44368	GCA_004014805.1	81858	81858	type	True	80.6071	1035	1941	95	below_threshold
Mycolicibacterium pulveris	strain=JCM 6370	GCA_010725725.1	36813	36813	type	True	80.5739	1041	1941	95	below_threshold
Mycolicibacterium agri	strain=JCM 6377	GCA_010722915.1	36811	36811	type	True	80.0004	965	1941	95	below_threshold
Mycolicibacterium aromaticivorans	strain=JS19b1	GCA_000559085.2	318425	318425	type	True	79.4094	792	1941	95	below_threshold
Mycolicibacterium aichiense	strain=NCTC10820	GCA_900453085.1	1799	1799	type	True	79.1232	814	1941	95	below_threshold
Mycolicibacterium aichiense	strain=JCM 6376	GCA_010726245.1	1799	1799	type	True	79.0648	814	1941	95	below_threshold
Mycolicibacterium rhodesiae	strain=DSM 44223	GCA_002086695.1	36814	36814	type	True	79.0172	792	1941	95	below_threshold
Mycolicibacterium helvum	strain=JCM 30396	GCA_010731895.1	1534349	1534349	type	True	78.7714	739	1941	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:34:48,991] [INFO] DFAST Taxonomy check result was written to GCF_025821365.1_ASM2582136v1_genomic.fna/tc_result.tsv
[2024-01-25 17:34:48,992] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:34:48,992] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:34:48,992] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg64c86015-0086-441f-9d8d-d2b78ff8429e/dqc_reference/checkm_data
[2024-01-25 17:34:48,993] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:34:49,054] [INFO] Task started: CheckM
[2024-01-25 17:34:49,054] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025821365.1_ASM2582136v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025821365.1_ASM2582136v1_genomic.fna/checkm_input GCF_025821365.1_ASM2582136v1_genomic.fna/checkm_result
[2024-01-25 17:35:42,147] [INFO] Task succeeded: CheckM
[2024-01-25 17:35:42,149] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 9.32%
Strain heterogeneity: 75.00%
--------------------------------------------------------------------------------
[2024-01-25 17:35:42,175] [INFO] ===== Completeness check finished =====
[2024-01-25 17:35:42,175] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:35:42,176] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025821365.1_ASM2582136v1_genomic.fna/markers.fasta)
[2024-01-25 17:35:42,177] [INFO] Task started: Blastn
[2024-01-25 17:35:42,177] [INFO] Running command: blastn -query GCF_025821365.1_ASM2582136v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg64c86015-0086-441f-9d8d-d2b78ff8429e/dqc_reference/reference_markers_gtdb.fasta -out GCF_025821365.1_ASM2582136v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:35:43,981] [INFO] Task succeeded: Blastn
[2024-01-25 17:35:43,984] [INFO] Selected 16 target genomes.
[2024-01-25 17:35:43,985] [INFO] Target genome list was writen to GCF_025821365.1_ASM2582136v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:35:43,995] [INFO] Task started: fastANI
[2024-01-25 17:35:43,995] [INFO] Running command: fastANI --query /var/lib/cwl/stgafcd4f45-72e3-438a-9b22-8d3a5b17a5f9/GCF_025821365.1_ASM2582136v1_genomic.fna.gz --refList GCF_025821365.1_ASM2582136v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025821365.1_ASM2582136v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:36:07,320] [INFO] Task succeeded: fastANI
[2024-01-25 17:36:07,330] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:36:07,331] [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_010728925.1	s__Mycobacterium gadium	99.993	1932	1941	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002086795.1	s__Mycobacterium tusciae	94.5553	1649	1941	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010726765.1	s__Mycobacterium gallinarum	93.0375	1712	1941	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002591975.1	s__Mycobacterium neglectum	85.5078	1507	1941	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000243415.2	s__Mycobacterium tusciae_A	84.8847	1487	1941	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000230895.2	s__Mycobacterium rhodesiae_A	84.4789	1538	1941	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010726085.1	s__Mycobacterium moriokaense	83.4553	1405	1941	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001722335.1	s__Mycobacterium flavescens_A	81.2467	1115	1941	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002245535.1	s__Mycobacterium lehmannii	80.8696	1069	1941	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.2034	97.95	97.72	0.91	0.88	6	-
GCF_001499855.1	s__Mycobacterium sp001499855	80.8213	1047	1941	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.76	99.52	0.98	0.97	3	-
GCF_001499905.1	s__Mycobacterium sp001499905	80.3611	984	1941	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000559085.1	s__Mycobacterium aromaticivorans	79.3978	793	1941	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010726245.1	s__Mycobacterium aichiense	79.093	809	1941	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002086695.1	s__Mycobacterium rhodesiae	79.0147	791	1941	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002887815.1	s__Mycobacterium sp002887815	79.0091	790	1941	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013337765.1	s__Mycobacterium sp003053865	78.8892	789	1941	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	95.43	95.41	0.83	0.83	3	-
--------------------------------------------------------------------------------
[2024-01-25 17:36:07,332] [INFO] GTDB search result was written to GCF_025821365.1_ASM2582136v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:36:07,334] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:36:07,337] [INFO] DFAST_QC result json was written to GCF_025821365.1_ASM2582136v1_genomic.fna/dqc_result.json
[2024-01-25 17:36:07,337] [INFO] DFAST_QC completed!
[2024-01-25 17:36:07,337] [INFO] Total running time: 0h2m0s