[2024-01-24 12:39:41,738] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:39:41,741] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:39:41,741] [INFO] DQC Reference Directory: /var/lib/cwl/stg360e1e73-d2f7-4e19-9be5-6960a19d4610/dqc_reference
[2024-01-24 12:39:43,089] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:39:43,090] [INFO] Task started: Prodigal
[2024-01-24 12:39:43,090] [INFO] Running command: gunzip -c /var/lib/cwl/stg78bdf57e-bfc4-4f12-aa44-f3400472d8d7/GCF_010727945.1_ASM1072794v1_genomic.fna.gz | prodigal -d GCF_010727945.1_ASM1072794v1_genomic.fna/cds.fna -a GCF_010727945.1_ASM1072794v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:40:01,138] [INFO] Task succeeded: Prodigal
[2024-01-24 12:40:01,139] [INFO] Task started: HMMsearch
[2024-01-24 12:40:01,139] [INFO] Running command: hmmsearch --tblout GCF_010727945.1_ASM1072794v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg360e1e73-d2f7-4e19-9be5-6960a19d4610/dqc_reference/reference_markers.hmm GCF_010727945.1_ASM1072794v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:40:01,695] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:40:01,696] [INFO] Found 6/6 markers.
[2024-01-24 12:40:01,754] [INFO] Query marker FASTA was written to GCF_010727945.1_ASM1072794v1_genomic.fna/markers.fasta
[2024-01-24 12:40:01,755] [INFO] Task started: Blastn
[2024-01-24 12:40:01,755] [INFO] Running command: blastn -query GCF_010727945.1_ASM1072794v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg360e1e73-d2f7-4e19-9be5-6960a19d4610/dqc_reference/reference_markers.fasta -out GCF_010727945.1_ASM1072794v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:40:02,927] [INFO] Task succeeded: Blastn
[2024-01-24 12:40:02,931] [INFO] Selected 23 target genomes.
[2024-01-24 12:40:02,931] [INFO] Target genome list was writen to GCF_010727945.1_ASM1072794v1_genomic.fna/target_genomes.txt
[2024-01-24 12:40:02,940] [INFO] Task started: fastANI
[2024-01-24 12:40:02,940] [INFO] Running command: fastANI --query /var/lib/cwl/stg78bdf57e-bfc4-4f12-aa44-f3400472d8d7/GCF_010727945.1_ASM1072794v1_genomic.fna.gz --refList GCF_010727945.1_ASM1072794v1_genomic.fna/target_genomes.txt --output GCF_010727945.1_ASM1072794v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:40:31,235] [INFO] Task succeeded: fastANI
[2024-01-24 12:40:31,235] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg360e1e73-d2f7-4e19-9be5-6960a19d4610/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:40:31,236] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg360e1e73-d2f7-4e19-9be5-6960a19d4610/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:40:31,258] [INFO] Found 23 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:40:31,258] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:40:31,259] [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
Mycobacterium cookii	strain=JCM 12404	GCA_010727945.1	1775	1775	type	True	100.0	1772	1772	95	conclusive
Mycobacterium celatum	strain=DSM 44243	GCA_002101595.1	28045	28045	type	True	81.1208	943	1772	95	below_threshold
Mycobacterium celatum	strain=ATCC 51131	GCA_000974705.1	28045	28045	type	True	81.1094	737	1772	95	below_threshold
Mycobacterium branderi	strain=JCM 12687	GCA_010728725.1	43348	43348	type	True	80.9848	994	1772	95	below_threshold
Mycobacterium fragae	strain=DSM 45731	GCA_002102185.1	1260918	1260918	type	True	80.8433	979	1772	95	below_threshold
Mycobacterium avium subsp. avium	strain=ATCC 25291	GCA_000174035.1	44454	1764	type	True	80.8034	885	1772	95	below_threshold
Mycobacterium avium subsp. avium	strain=DSM 44156	GCA_009741445.1	44454	1764	type	True	80.6471	949	1772	95	below_threshold
Mycobacterium paraense	strain=IEC26	GCA_002101815.1	767916	767916	type	True	80.598	1001	1772	95	below_threshold
Mycobacterium intracellulare	strain=ATCC 13950	GCA_023278525.1	1767	1767	suspected-type	True	80.4163	906	1772	95	below_threshold
Mycobacterium colombiense	strain=CECT 3035	GCA_000222105.4	339268	339268	suspected-type	True	80.384	956	1772	95	below_threshold
Mycobacterium colombiense	strain=CECT 3035	GCA_002105755.1	339268	339268	suspected-type	True	80.3732	952	1772	95	below_threshold
Mycobacterium bohemicum	strain=DSM 44277	GCA_002102025.1	56425	56425	type	True	80.2477	945	1772	95	below_threshold
Mycobacterium bohemicum	strain=DSM 44277	GCA_001053185.1	56425	56425	type	True	80.196	918	1772	95	below_threshold
Mycobacterium seoulense	strain=JCM 16018	GCA_010731595.1	386911	386911	type	True	80.1815	960	1772	95	below_threshold
Mycobacterium parmense	strain=JCM 14742	GCA_010730575.1	185642	185642	type	True	80.1795	929	1772	95	below_threshold
Mycobacterium parmense	strain=DSM 44553	GCA_002102335.1	185642	185642	type	True	80.1741	930	1772	95	below_threshold
Mycobacterium mantenii	strain=JCM 18113	GCA_010731775.1	560555	560555	type	True	80.1629	935	1772	95	below_threshold
Mycobacterium numidiamassiliense	strain=AB215	GCA_900157365.1	1841861	1841861	type	True	80.1279	915	1772	95	below_threshold
Mycobacterium noviomagense	strain=JCM 16367	GCA_010731635.1	459858	459858	type	True	79.8236	842	1772	95	below_threshold
Mycobacterium noviomagense	strain=DSM 45145	GCA_002086415.1	459858	459858	type	True	79.7261	828	1772	95	below_threshold
Mycolicibacterium rutilum	strain=DSM 45405	GCA_900108565.1	370526	370526	type	True	79.7175	781	1772	95	below_threshold
Mycobacterium paragordonae	strain=JCM 18565	GCA_010723415.1	1389713	1389713	type	True	79.5709	900	1772	95	below_threshold
Mycobacterium heckeshornense	strain=JCM 15655	GCA_016592155.1	110505	110505	type	True	79.3597	781	1772	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:40:31,260] [INFO] DFAST Taxonomy check result was written to GCF_010727945.1_ASM1072794v1_genomic.fna/tc_result.tsv
[2024-01-24 12:40:31,261] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:40:31,261] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:40:31,261] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg360e1e73-d2f7-4e19-9be5-6960a19d4610/dqc_reference/checkm_data
[2024-01-24 12:40:31,262] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:40:31,316] [INFO] Task started: CheckM
[2024-01-24 12:40:31,317] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_010727945.1_ASM1072794v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_010727945.1_ASM1072794v1_genomic.fna/checkm_input GCF_010727945.1_ASM1072794v1_genomic.fna/checkm_result
[2024-01-24 12:41:25,653] [INFO] Task succeeded: CheckM
[2024-01-24 12:41:25,654] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2024-01-24 12:41:25,676] [INFO] ===== Completeness check finished =====
[2024-01-24 12:41:25,677] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:41:25,677] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_010727945.1_ASM1072794v1_genomic.fna/markers.fasta)
[2024-01-24 12:41:25,677] [INFO] Task started: Blastn
[2024-01-24 12:41:25,677] [INFO] Running command: blastn -query GCF_010727945.1_ASM1072794v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg360e1e73-d2f7-4e19-9be5-6960a19d4610/dqc_reference/reference_markers_gtdb.fasta -out GCF_010727945.1_ASM1072794v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:41:27,347] [INFO] Task succeeded: Blastn
[2024-01-24 12:41:27,352] [INFO] Selected 17 target genomes.
[2024-01-24 12:41:27,352] [INFO] Target genome list was writen to GCF_010727945.1_ASM1072794v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:41:27,376] [INFO] Task started: fastANI
[2024-01-24 12:41:27,376] [INFO] Running command: fastANI --query /var/lib/cwl/stg78bdf57e-bfc4-4f12-aa44-f3400472d8d7/GCF_010727945.1_ASM1072794v1_genomic.fna.gz --refList GCF_010727945.1_ASM1072794v1_genomic.fna/target_genomes_gtdb.txt --output GCF_010727945.1_ASM1072794v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:41:47,573] [INFO] Task succeeded: fastANI
[2024-01-24 12:41:47,595] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:41:47,595] [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_010727945.1	s__Mycobacterium cookii	100.0	1772	1772	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_001673405.1	s__Mycobacterium sp001673405	82.784	1210	1772	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002863225.1	s__Mycobacterium sp002863225	82.4524	1163	1772	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019236925.1	s__Mycobacterium sp019236925	81.6675	987	1772	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002101735.1	s__Mycobacterium kyorinense	81.2404	943	1772	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.84	99.84	0.96	0.94	3	-
GCF_003402475.1	s__Mycobacterium sp003402475	81.207	973	1772	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002101595.1	s__Mycobacterium celatum	81.1195	945	1772	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.99	99.99	0.99	0.99	2	-
GCF_002102185.1	s__Mycobacterium fragae	80.8263	983	1772	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009741445.1	s__Mycobacterium avium	80.6374	951	1772	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	96.9043	98.75	98.29	0.92	0.84	206	-
GCA_002102225.1	s__Mycobacterium interjectum_B	80.4324	995	1772	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900157365.1	s__Mycobacterium numidiamassiliense	80.1462	913	1772	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001667075.1	s__Mycobacterium sp001667075	80.1419	906	1772	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.41	99.38	0.97	0.97	3	-
GCF_010731635.1	s__Mycobacterium noviomagense	79.8305	845	1772	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900108565.1	s__Mycobacterium rutilum	79.7034	780	1772	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019243155.1	s__Mycobacterium sp019243155	79.6785	804	1772	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001665395.1	s__Mycobacterium sp001665395	79.6485	853	1772	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001417955.2	s__Mycobacterium gordonae_B	79.5725	886	1772	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 12:41:47,597] [INFO] GTDB search result was written to GCF_010727945.1_ASM1072794v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:41:47,597] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:41:47,602] [INFO] DFAST_QC result json was written to GCF_010727945.1_ASM1072794v1_genomic.fna/dqc_result.json
[2024-01-24 12:41:47,602] [INFO] DFAST_QC completed!
[2024-01-24 12:41:47,602] [INFO] Total running time: 0h2m6s