[2024-01-24 11:20:34,422] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:20:34,424] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:20:34,424] [INFO] DQC Reference Directory: /var/lib/cwl/stg40b735a0-5a25-4c1d-bbda-caeaa601a84f/dqc_reference
[2024-01-24 11:20:35,638] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:20:35,638] [INFO] Task started: Prodigal
[2024-01-24 11:20:35,639] [INFO] Running command: gunzip -c /var/lib/cwl/stgc8b0d62b-55bc-496d-a631-77c89a149046/GCF_010723305.1_ASM1072330v1_genomic.fna.gz | prodigal -d GCF_010723305.1_ASM1072330v1_genomic.fna/cds.fna -a GCF_010723305.1_ASM1072330v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:20:49,787] [INFO] Task succeeded: Prodigal
[2024-01-24 11:20:49,787] [INFO] Task started: HMMsearch
[2024-01-24 11:20:49,787] [INFO] Running command: hmmsearch --tblout GCF_010723305.1_ASM1072330v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg40b735a0-5a25-4c1d-bbda-caeaa601a84f/dqc_reference/reference_markers.hmm GCF_010723305.1_ASM1072330v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:20:50,062] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:20:50,063] [INFO] Found 6/6 markers.
[2024-01-24 11:20:50,101] [INFO] Query marker FASTA was written to GCF_010723305.1_ASM1072330v1_genomic.fna/markers.fasta
[2024-01-24 11:20:50,101] [INFO] Task started: Blastn
[2024-01-24 11:20:50,101] [INFO] Running command: blastn -query GCF_010723305.1_ASM1072330v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg40b735a0-5a25-4c1d-bbda-caeaa601a84f/dqc_reference/reference_markers.fasta -out GCF_010723305.1_ASM1072330v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:20:51,023] [INFO] Task succeeded: Blastn
[2024-01-24 11:20:51,027] [INFO] Selected 20 target genomes.
[2024-01-24 11:20:51,028] [INFO] Target genome list was writen to GCF_010723305.1_ASM1072330v1_genomic.fna/target_genomes.txt
[2024-01-24 11:20:51,039] [INFO] Task started: fastANI
[2024-01-24 11:20:51,040] [INFO] Running command: fastANI --query /var/lib/cwl/stgc8b0d62b-55bc-496d-a631-77c89a149046/GCF_010723305.1_ASM1072330v1_genomic.fna.gz --refList GCF_010723305.1_ASM1072330v1_genomic.fna/target_genomes.txt --output GCF_010723305.1_ASM1072330v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:21:11,181] [INFO] Task succeeded: fastANI
[2024-01-24 11:21:11,181] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg40b735a0-5a25-4c1d-bbda-caeaa601a84f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:21:11,182] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg40b735a0-5a25-4c1d-bbda-caeaa601a84f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:21:11,202] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:21:11,202] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:21:11,203] [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 botniense	strain=JCM 17322	GCA_010723305.1	84962	84962	type	True	100.0	1442	1442	95	conclusive
Mycobacterium branderi	strain=JCM 12687	GCA_010728725.1	43348	43348	type	True	79.8937	822	1442	95	below_threshold
Mycobacterium xenopi	strain=NCTC10042	GCA_900453395.1	1789	1789	type	True	79.845	814	1442	95	below_threshold
Mycobacterium xenopi	strain=JCM 15661T	GCA_009936235.1	1789	1789	type	True	79.8091	810	1442	95	below_threshold
Mycobacterium xenopi	strain=DSM 43995	GCA_002102015.1	1789	1789	type	True	79.7807	791	1442	95	below_threshold
Mycobacterium noviomagense	strain=DSM 45145	GCA_002086415.1	459858	459858	type	True	79.6854	796	1442	95	below_threshold
Mycobacterium noviomagense	strain=JCM 16367	GCA_010731635.1	459858	459858	type	True	79.6169	824	1442	95	below_threshold
Mycobacterium heidelbergense	strain=JCM 14842	GCA_010730745.1	53376	53376	type	True	79.5159	758	1442	95	below_threshold
Mycobacterium heidelbergense	strain=DSM 44471	GCA_002086215.1	53376	53376	type	True	79.5064	750	1442	95	below_threshold
Mycobacterium fragae	strain=DSM 45731	GCA_002102185.1	1260918	1260918	type	True	79.5041	763	1442	95	below_threshold
Mycobacterium palustre	strain=DSM 44572	GCA_002101785.1	153971	153971	type	True	79.3527	739	1442	95	below_threshold
Mycobacterium helveticum	strain=16-83	GCA_007714205.1	2592811	2592811	type	True	79.1495	698	1442	95	below_threshold
Mycobacterium ostraviense	strain=241/15	GCA_002705925.1	2738409	2738409	type	True	78.9502	677	1442	95	below_threshold
Mycobacterium intracellulare	strain=ATCC 13950	GCA_000277125.1	1767	1767	suspected-type	True	78.934	700	1442	95	below_threshold
Mycobacterium intracellulare	strain=ATCC 13950	GCA_023278525.1	1767	1767	suspected-type	True	78.9165	704	1442	95	below_threshold
Mycobacterium arosiense	strain=DSM 45069	GCA_002086125.1	425468	425468	type	True	78.8988	636	1442	95	below_threshold
Mycobacterium genavense	strain=ATCC 51234	GCA_000526915.1	36812	36812	type	True	78.8317	601	1442	95	below_threshold
Mycobacterium angelicum	strain=DSM 45057	GCA_002086155.1	470074	470074	type	True	78.5544	672	1442	95	below_threshold
Mycobacterium szulgai	strain=DSM 44166	GCA_002116635.1	1787	1787	type	True	78.5064	647	1442	95	below_threshold
Mycobacterium basiliense		GCA_900292015.1	2094119	2094119	type	True	77.8756	545	1442	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:21:11,204] [INFO] DFAST Taxonomy check result was written to GCF_010723305.1_ASM1072330v1_genomic.fna/tc_result.tsv
[2024-01-24 11:21:11,204] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:21:11,205] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:21:11,205] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg40b735a0-5a25-4c1d-bbda-caeaa601a84f/dqc_reference/checkm_data
[2024-01-24 11:21:11,206] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:21:11,245] [INFO] Task started: CheckM
[2024-01-24 11:21:11,245] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_010723305.1_ASM1072330v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_010723305.1_ASM1072330v1_genomic.fna/checkm_input GCF_010723305.1_ASM1072330v1_genomic.fna/checkm_result
[2024-01-24 11:21:55,056] [INFO] Task succeeded: CheckM
[2024-01-24 11:21:55,058] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:21:55,076] [INFO] ===== Completeness check finished =====
[2024-01-24 11:21:55,076] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:21:55,077] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_010723305.1_ASM1072330v1_genomic.fna/markers.fasta)
[2024-01-24 11:21:55,077] [INFO] Task started: Blastn
[2024-01-24 11:21:55,077] [INFO] Running command: blastn -query GCF_010723305.1_ASM1072330v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg40b735a0-5a25-4c1d-bbda-caeaa601a84f/dqc_reference/reference_markers_gtdb.fasta -out GCF_010723305.1_ASM1072330v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:21:56,435] [INFO] Task succeeded: Blastn
[2024-01-24 11:21:56,439] [INFO] Selected 20 target genomes.
[2024-01-24 11:21:56,440] [INFO] Target genome list was writen to GCF_010723305.1_ASM1072330v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:21:56,455] [INFO] Task started: fastANI
[2024-01-24 11:21:56,456] [INFO] Running command: fastANI --query /var/lib/cwl/stgc8b0d62b-55bc-496d-a631-77c89a149046/GCF_010723305.1_ASM1072330v1_genomic.fna.gz --refList GCF_010723305.1_ASM1072330v1_genomic.fna/target_genomes_gtdb.txt --output GCF_010723305.1_ASM1072330v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:22:16,965] [INFO] Task succeeded: fastANI
[2024-01-24 11:22:16,984] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:22:16,984] [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_010723305.1	s__Mycobacterium botniense	100.0	1441	1442	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_010728725.1	s__Mycobacterium branderi	79.8985	824	1442	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_009936235.1	s__Mycobacterium xenopi	79.7819	815	1442	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.67	99.09	0.97	0.94	5	-
GCF_002101595.1	s__Mycobacterium celatum	79.7413	817	1442	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.99	99.99	0.99	0.99	2	-
GCF_003402475.1	s__Mycobacterium sp003402475	79.7045	790	1442	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010731635.1	s__Mycobacterium noviomagense	79.6205	823	1442	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002086305.1	s__Mycobacterium malmoense_B	79.6033	746	1442	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.01	99.01	0.95	0.95	2	-
GCF_010730745.1	s__Mycobacterium heidelbergense	79.5093	759	1442	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002102185.1	s__Mycobacterium fragae	79.4989	763	1442	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001672915.1	s__Mycobacterium sp001672915	79.1989	712	1442	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002102225.1	s__Mycobacterium interjectum_B	79.0794	749	1442	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002102155.1	s__Mycobacterium europaeum	79.0677	686	1442	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.26	99.26	0.97	0.97	2	-
GCF_002705925.1	s__Mycobacterium ostraviense	78.9518	678	1442	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.87	99.87	0.99	0.99	2	-
GCF_002086735.1	s__Mycobacterium scrofulaceum	78.9496	688	1442	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000277125.1	s__Mycobacterium intracellulare	78.9273	701	1442	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.48	95.71	0.93	0.84	82	-
GCF_001667735.1	s__Mycobacterium sp001667735	78.9045	643	1442	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.41	99.16	0.95	0.92	6	-
GCF_003284935.1	s__Mycobacterium arosiense_A	78.8838	656	1442	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900566055.1	s__Mycobacterium innocens	78.8814	673	1442	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.27	98.57	0.94	0.90	3	-
GCF_002101885.1	s__Mycobacterium senuense	78.4325	527	1442	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900292015.1	s__Mycobacterium basiliense	77.8821	542	1442	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 11:22:16,986] [INFO] GTDB search result was written to GCF_010723305.1_ASM1072330v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:22:16,987] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:22:16,991] [INFO] DFAST_QC result json was written to GCF_010723305.1_ASM1072330v1_genomic.fna/dqc_result.json
[2024-01-24 11:22:16,991] [INFO] DFAST_QC completed!
[2024-01-24 11:22:16,991] [INFO] Total running time: 0h1m43s