[2024-01-24 11:59:22,959] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:59:22,961] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:59:22,961] [INFO] DQC Reference Directory: /var/lib/cwl/stg23b93438-f9b9-4688-b291-339c038bb7cd/dqc_reference
[2024-01-24 11:59:25,642] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:59:25,643] [INFO] Task started: Prodigal
[2024-01-24 11:59:25,643] [INFO] Running command: gunzip -c /var/lib/cwl/stg828fa21b-f6a9-489d-a1f1-e4877ae278c4/GCF_002086795.1_ASM208679v1_genomic.fna.gz | prodigal -d GCF_002086795.1_ASM208679v1_genomic.fna/cds.fna -a GCF_002086795.1_ASM208679v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:59:44,869] [INFO] Task succeeded: Prodigal
[2024-01-24 11:59:44,870] [INFO] Task started: HMMsearch
[2024-01-24 11:59:44,870] [INFO] Running command: hmmsearch --tblout GCF_002086795.1_ASM208679v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg23b93438-f9b9-4688-b291-339c038bb7cd/dqc_reference/reference_markers.hmm GCF_002086795.1_ASM208679v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:59:45,200] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:59:45,202] [INFO] Found 6/6 markers.
[2024-01-24 11:59:45,257] [INFO] Query marker FASTA was written to GCF_002086795.1_ASM208679v1_genomic.fna/markers.fasta
[2024-01-24 11:59:45,258] [INFO] Task started: Blastn
[2024-01-24 11:59:45,258] [INFO] Running command: blastn -query GCF_002086795.1_ASM208679v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg23b93438-f9b9-4688-b291-339c038bb7cd/dqc_reference/reference_markers.fasta -out GCF_002086795.1_ASM208679v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:59:46,451] [INFO] Task succeeded: Blastn
[2024-01-24 11:59:46,455] [INFO] Selected 10 target genomes.
[2024-01-24 11:59:46,456] [INFO] Target genome list was writen to GCF_002086795.1_ASM208679v1_genomic.fna/target_genomes.txt
[2024-01-24 11:59:46,463] [INFO] Task started: fastANI
[2024-01-24 11:59:46,463] [INFO] Running command: fastANI --query /var/lib/cwl/stg828fa21b-f6a9-489d-a1f1-e4877ae278c4/GCF_002086795.1_ASM208679v1_genomic.fna.gz --refList GCF_002086795.1_ASM208679v1_genomic.fna/target_genomes.txt --output GCF_002086795.1_ASM208679v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:59:59,673] [INFO] Task succeeded: fastANI
[2024-01-24 11:59:59,673] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg23b93438-f9b9-4688-b291-339c038bb7cd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:59:59,674] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg23b93438-f9b9-4688-b291-339c038bb7cd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:59:59,685] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:59:59,685] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:59:59,685] [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 tusciae	strain=DSM 44338	GCA_002086795.1	75922	75922	type	True	100.0	2023	2023	95	conclusive
Mycolicibacterium gadium	strain=JCM 12688	GCA_010728925.1	1794	1794	type	True	94.5841	1665	2023	95	below_threshold
Mycolicibacterium moriokaense	strain=JCM 6375	GCA_010726085.1	39691	39691	type	True	83.7373	1381	2023	95	below_threshold
Mycolicibacterium moriokaense	strain=CIP105393	GCA_002086395.1	39691	39691	type	True	83.7015	1371	2023	95	below_threshold
Mycolicibacterium rutilum	strain=DSM 45405	GCA_900108565.1	370526	370526	type	True	81.4146	1147	2023	95	below_threshold
Mycolicibacterium phlei	strain=DSM 43239 = CCUG 21000	GCA_001582015.1	1771	1771	type	True	80.9423	1035	2023	95	below_threshold
Mycobacterium lehmannii	strain=CECT 8763	GCA_002245535.1	2048550	2048550	type	True	80.8354	1065	2023	95	below_threshold
Mycolicibacterium pulveris	strain=JCM 6370	GCA_010725725.1	36813	36813	type	True	80.7237	1021	2023	95	below_threshold
Mycolicibacterium elephantis	strain=DSM 44368	GCA_004014805.1	81858	81858	type	True	80.6986	1028	2023	95	below_threshold
Mycolicibacterium agri	strain=JCM 6377	GCA_010722915.1	36811	36811	type	True	79.9767	985	2023	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:59:59,687] [INFO] DFAST Taxonomy check result was written to GCF_002086795.1_ASM208679v1_genomic.fna/tc_result.tsv
[2024-01-24 11:59:59,687] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:59:59,687] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:59:59,687] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg23b93438-f9b9-4688-b291-339c038bb7cd/dqc_reference/checkm_data
[2024-01-24 11:59:59,689] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:59:59,756] [INFO] Task started: CheckM
[2024-01-24 11:59:59,757] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002086795.1_ASM208679v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002086795.1_ASM208679v1_genomic.fna/checkm_input GCF_002086795.1_ASM208679v1_genomic.fna/checkm_result
[2024-01-24 12:00:57,100] [INFO] Task succeeded: CheckM
[2024-01-24 12:00:57,101] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:00:57,123] [INFO] ===== Completeness check finished =====
[2024-01-24 12:00:57,124] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:00:57,124] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002086795.1_ASM208679v1_genomic.fna/markers.fasta)
[2024-01-24 12:00:57,124] [INFO] Task started: Blastn
[2024-01-24 12:00:57,125] [INFO] Running command: blastn -query GCF_002086795.1_ASM208679v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg23b93438-f9b9-4688-b291-339c038bb7cd/dqc_reference/reference_markers_gtdb.fasta -out GCF_002086795.1_ASM208679v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:00:58,901] [INFO] Task succeeded: Blastn
[2024-01-24 12:00:58,905] [INFO] Selected 7 target genomes.
[2024-01-24 12:00:58,905] [INFO] Target genome list was writen to GCF_002086795.1_ASM208679v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:00:58,910] [INFO] Task started: fastANI
[2024-01-24 12:00:58,911] [INFO] Running command: fastANI --query /var/lib/cwl/stg828fa21b-f6a9-489d-a1f1-e4877ae278c4/GCF_002086795.1_ASM208679v1_genomic.fna.gz --refList GCF_002086795.1_ASM208679v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002086795.1_ASM208679v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:01:09,685] [INFO] Task succeeded: fastANI
[2024-01-24 12:01:09,694] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:01:09,695] [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_002086795.1	s__Mycobacterium tusciae	100.0	2023	2023	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_010728925.1	s__Mycobacterium gadium	94.6046	1663	2023	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	93.6998	1693	2023	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	85.7706	1553	2023	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	85.1824	1527	2023	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	84.7081	1501	2023	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	83.7371	1381	2023	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:01:09,696] [INFO] GTDB search result was written to GCF_002086795.1_ASM208679v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:01:09,696] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:01:09,700] [INFO] DFAST_QC result json was written to GCF_002086795.1_ASM208679v1_genomic.fna/dqc_result.json
[2024-01-24 12:01:09,700] [INFO] DFAST_QC completed!
[2024-01-24 12:01:09,700] [INFO] Total running time: 0h1m47s