[2024-01-24 13:59:42,833] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:59:42,835] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:59:42,836] [INFO] DQC Reference Directory: /var/lib/cwl/stg4865332d-76dd-4fd6-85c5-ef17e8379c6d/dqc_reference
[2024-01-24 13:59:44,064] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:59:44,065] [INFO] Task started: Prodigal
[2024-01-24 13:59:44,065] [INFO] Running command: gunzip -c /var/lib/cwl/stg2420992c-e7a8-449f-afb3-fe1e64c6e562/GCF_010728925.1_ASM1072892v1_genomic.fna.gz | prodigal -d GCF_010728925.1_ASM1072892v1_genomic.fna/cds.fna -a GCF_010728925.1_ASM1072892v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:00:04,462] [INFO] Task succeeded: Prodigal
[2024-01-24 14:00:04,463] [INFO] Task started: HMMsearch
[2024-01-24 14:00:04,463] [INFO] Running command: hmmsearch --tblout GCF_010728925.1_ASM1072892v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4865332d-76dd-4fd6-85c5-ef17e8379c6d/dqc_reference/reference_markers.hmm GCF_010728925.1_ASM1072892v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:00:04,768] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:00:04,770] [INFO] Found 6/6 markers.
[2024-01-24 14:00:04,822] [INFO] Query marker FASTA was written to GCF_010728925.1_ASM1072892v1_genomic.fna/markers.fasta
[2024-01-24 14:00:04,823] [INFO] Task started: Blastn
[2024-01-24 14:00:04,823] [INFO] Running command: blastn -query GCF_010728925.1_ASM1072892v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4865332d-76dd-4fd6-85c5-ef17e8379c6d/dqc_reference/reference_markers.fasta -out GCF_010728925.1_ASM1072892v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:00:05,963] [INFO] Task succeeded: Blastn
[2024-01-24 14:00:05,967] [INFO] Selected 11 target genomes.
[2024-01-24 14:00:05,967] [INFO] Target genome list was writen to GCF_010728925.1_ASM1072892v1_genomic.fna/target_genomes.txt
[2024-01-24 14:00:05,973] [INFO] Task started: fastANI
[2024-01-24 14:00:05,973] [INFO] Running command: fastANI --query /var/lib/cwl/stg2420992c-e7a8-449f-afb3-fe1e64c6e562/GCF_010728925.1_ASM1072892v1_genomic.fna.gz --refList GCF_010728925.1_ASM1072892v1_genomic.fna/target_genomes.txt --output GCF_010728925.1_ASM1072892v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:00:20,421] [INFO] Task succeeded: fastANI
[2024-01-24 14:00:20,422] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4865332d-76dd-4fd6-85c5-ef17e8379c6d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:00:20,423] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4865332d-76dd-4fd6-85c5-ef17e8379c6d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:00:20,437] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:00:20,438] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:00:20,438] [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	100.0	1988	1988	95	conclusive
Mycolicibacterium tusciae	strain=DSM 44338	GCA_002086795.1	75922	75922	type	True	94.5273	1667	1988	95	below_threshold
Mycolicibacterium moriokaense	strain=CIP105393	GCA_002086395.1	39691	39691	type	True	83.4663	1400	1988	95	below_threshold
Mycolicibacterium moriokaense	strain=JCM 6375	GCA_010726085.1	39691	39691	type	True	83.4487	1429	1988	95	below_threshold
Mycolicibacterium rutilum	strain=DSM 45405	GCA_900108565.1	370526	370526	type	True	81.6012	1153	1988	95	below_threshold
Mycolicibacterium phlei	strain=DSM 43239 = CCUG 21000	GCA_001582015.1	1771	1771	type	True	80.9284	1041	1988	95	below_threshold
Mycobacterium lehmannii	strain=CECT 8763	GCA_002245535.1	2048550	2048550	type	True	80.8525	1084	1988	95	below_threshold
Mycolicibacterium malmesburyense	strain=WCM 7299	GCA_001050015.1	1566886	1566886	type	True	80.8031	1055	1988	95	below_threshold
Mycolicibacterium elephantis	strain=DSM 44368	GCA_004014805.1	81858	81858	type	True	80.5955	1055	1988	95	below_threshold
Mycolicibacterium pulveris	strain=JCM 6370	GCA_010725725.1	36813	36813	type	True	80.5764	1079	1988	95	below_threshold
Mycolicibacterium agri	strain=JCM 6377	GCA_010722915.1	36811	36811	type	True	79.975	974	1988	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:00:20,440] [INFO] DFAST Taxonomy check result was written to GCF_010728925.1_ASM1072892v1_genomic.fna/tc_result.tsv
[2024-01-24 14:00:20,440] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:00:20,440] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:00:20,440] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4865332d-76dd-4fd6-85c5-ef17e8379c6d/dqc_reference/checkm_data
[2024-01-24 14:00:20,441] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:00:20,496] [INFO] Task started: CheckM
[2024-01-24 14:00:20,497] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_010728925.1_ASM1072892v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_010728925.1_ASM1072892v1_genomic.fna/checkm_input GCF_010728925.1_ASM1072892v1_genomic.fna/checkm_result
[2024-01-24 14:01:26,662] [INFO] Task succeeded: CheckM
[2024-01-24 14:01:26,664] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:01:26,688] [INFO] ===== Completeness check finished =====
[2024-01-24 14:01:26,688] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:01:26,689] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_010728925.1_ASM1072892v1_genomic.fna/markers.fasta)
[2024-01-24 14:01:26,689] [INFO] Task started: Blastn
[2024-01-24 14:01:26,689] [INFO] Running command: blastn -query GCF_010728925.1_ASM1072892v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4865332d-76dd-4fd6-85c5-ef17e8379c6d/dqc_reference/reference_markers_gtdb.fasta -out GCF_010728925.1_ASM1072892v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:01:28,324] [INFO] Task succeeded: Blastn
[2024-01-24 14:01:28,329] [INFO] Selected 11 target genomes.
[2024-01-24 14:01:28,329] [INFO] Target genome list was writen to GCF_010728925.1_ASM1072892v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:01:28,354] [INFO] Task started: fastANI
[2024-01-24 14:01:28,354] [INFO] Running command: fastANI --query /var/lib/cwl/stg2420992c-e7a8-449f-afb3-fe1e64c6e562/GCF_010728925.1_ASM1072892v1_genomic.fna.gz --refList GCF_010728925.1_ASM1072892v1_genomic.fna/target_genomes_gtdb.txt --output GCF_010728925.1_ASM1072892v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:01:44,712] [INFO] Task succeeded: fastANI
[2024-01-24 14:01:44,721] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:01:44,722] [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	100.0	1988	1988	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	94.5361	1666	1988	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	92.9785	1734	1988	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	85.4635	1521	1988	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	84.9452	1500	1988	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	84.4511	1542	1988	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	83.4712	1426	1988	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	81.2362	1130	1988	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	80.8467	1085	1988	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	80.799	1062	1988	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	80.4118	996	1988	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 14:01:44,723] [INFO] GTDB search result was written to GCF_010728925.1_ASM1072892v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:01:44,724] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:01:44,727] [INFO] DFAST_QC result json was written to GCF_010728925.1_ASM1072892v1_genomic.fna/dqc_result.json
[2024-01-24 14:01:44,727] [INFO] DFAST_QC completed!
[2024-01-24 14:01:44,727] [INFO] Total running time: 0h2m2s