[2024-01-24 12:06:14,620] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:06:14,629] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:06:14,630] [INFO] DQC Reference Directory: /var/lib/cwl/stg0aab126e-d4f7-42d4-ad21-7ea018d06f22/dqc_reference
[2024-01-24 12:06:16,056] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:06:16,060] [INFO] Task started: Prodigal
[2024-01-24 12:06:16,060] [INFO] Running command: gunzip -c /var/lib/cwl/stg333a16f4-273d-475f-80b7-1f1deeaca7a4/GCF_016592155.1_ASM1659215v1_genomic.fna.gz | prodigal -d GCF_016592155.1_ASM1659215v1_genomic.fna/cds.fna -a GCF_016592155.1_ASM1659215v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:06:32,793] [INFO] Task succeeded: Prodigal
[2024-01-24 12:06:32,794] [INFO] Task started: HMMsearch
[2024-01-24 12:06:32,794] [INFO] Running command: hmmsearch --tblout GCF_016592155.1_ASM1659215v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0aab126e-d4f7-42d4-ad21-7ea018d06f22/dqc_reference/reference_markers.hmm GCF_016592155.1_ASM1659215v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:06:33,142] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:06:33,143] [INFO] Found 6/6 markers.
[2024-01-24 12:06:33,205] [INFO] Query marker FASTA was written to GCF_016592155.1_ASM1659215v1_genomic.fna/markers.fasta
[2024-01-24 12:06:33,205] [INFO] Task started: Blastn
[2024-01-24 12:06:33,205] [INFO] Running command: blastn -query GCF_016592155.1_ASM1659215v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0aab126e-d4f7-42d4-ad21-7ea018d06f22/dqc_reference/reference_markers.fasta -out GCF_016592155.1_ASM1659215v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:06:34,282] [INFO] Task succeeded: Blastn
[2024-01-24 12:06:34,285] [INFO] Selected 9 target genomes.
[2024-01-24 12:06:34,286] [INFO] Target genome list was writen to GCF_016592155.1_ASM1659215v1_genomic.fna/target_genomes.txt
[2024-01-24 12:06:34,291] [INFO] Task started: fastANI
[2024-01-24 12:06:34,291] [INFO] Running command: fastANI --query /var/lib/cwl/stg333a16f4-273d-475f-80b7-1f1deeaca7a4/GCF_016592155.1_ASM1659215v1_genomic.fna.gz --refList GCF_016592155.1_ASM1659215v1_genomic.fna/target_genomes.txt --output GCF_016592155.1_ASM1659215v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:06:45,317] [INFO] Task succeeded: fastANI
[2024-01-24 12:06:45,317] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0aab126e-d4f7-42d4-ad21-7ea018d06f22/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:06:45,318] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0aab126e-d4f7-42d4-ad21-7ea018d06f22/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:06:45,326] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:06:45,326] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:06:45,326] [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 heckeshornense	strain=JCM 15655	GCA_016592155.1	110505	110505	type	True	100.0	1651	1652	95	conclusive
Mycobacterium xenopi	strain=DSM 43995	GCA_002102015.1	1789	1789	type	True	90.4978	1263	1652	95	below_threshold
Mycobacterium xenopi	strain=JCM 15661T	GCA_009936235.1	1789	1789	type	True	90.4007	1305	1652	95	below_threshold
Mycobacterium xenopi	strain=NCTC10042	GCA_900453395.1	1789	1789	type	True	90.3314	1306	1652	95	below_threshold
Mycobacterium noviomagense	strain=DSM 45145	GCA_002086415.1	459858	459858	type	True	83.9017	1115	1652	95	below_threshold
Mycobacterium noviomagense	strain=JCM 16367	GCA_010731635.1	459858	459858	type	True	83.8903	1152	1652	95	below_threshold
Mycobacterium kyorinense	strain=DSM 45166	GCA_002101735.1	487514	487514	type	True	81.3315	986	1652	95	below_threshold
Mycobacterium kubicae	strain=CIP 106428	GCA_002101745.1	120959	120959	type	True	79.0683	737	1652	95	below_threshold
Mycobacterium kubicae	strain=JCM 13573	GCA_010723135.1	120959	120959	type	True	79.048	751	1652	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:06:45,328] [INFO] DFAST Taxonomy check result was written to GCF_016592155.1_ASM1659215v1_genomic.fna/tc_result.tsv
[2024-01-24 12:06:45,329] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:06:45,329] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:06:45,329] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0aab126e-d4f7-42d4-ad21-7ea018d06f22/dqc_reference/checkm_data
[2024-01-24 12:06:45,331] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:06:45,382] [INFO] Task started: CheckM
[2024-01-24 12:06:45,382] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016592155.1_ASM1659215v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016592155.1_ASM1659215v1_genomic.fna/checkm_input GCF_016592155.1_ASM1659215v1_genomic.fna/checkm_result
[2024-01-24 12:07:33,220] [INFO] Task succeeded: CheckM
[2024-01-24 12:07:33,221] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:07:33,246] [INFO] ===== Completeness check finished =====
[2024-01-24 12:07:33,247] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:07:33,247] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016592155.1_ASM1659215v1_genomic.fna/markers.fasta)
[2024-01-24 12:07:33,247] [INFO] Task started: Blastn
[2024-01-24 12:07:33,248] [INFO] Running command: blastn -query GCF_016592155.1_ASM1659215v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0aab126e-d4f7-42d4-ad21-7ea018d06f22/dqc_reference/reference_markers_gtdb.fasta -out GCF_016592155.1_ASM1659215v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:07:34,644] [INFO] Task succeeded: Blastn
[2024-01-24 12:07:34,649] [INFO] Selected 16 target genomes.
[2024-01-24 12:07:34,650] [INFO] Target genome list was writen to GCF_016592155.1_ASM1659215v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:07:34,666] [INFO] Task started: fastANI
[2024-01-24 12:07:34,667] [INFO] Running command: fastANI --query /var/lib/cwl/stg333a16f4-273d-475f-80b7-1f1deeaca7a4/GCF_016592155.1_ASM1659215v1_genomic.fna.gz --refList GCF_016592155.1_ASM1659215v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016592155.1_ASM1659215v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:07:52,865] [INFO] Task succeeded: fastANI
[2024-01-24 12:07:52,893] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:07:52,893] [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_016592155.1	s__Mycobacterium heckeshornense	100.0	1650	1652	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.54	99.17	0.94	0.93	4	conclusive
GCF_009936235.1	s__Mycobacterium xenopi	90.387	1306	1652	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.67	99.09	0.97	0.94	5	-
GCF_010731635.1	s__Mycobacterium noviomagense	83.8835	1151	1652	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002101595.1	s__Mycobacterium celatum	81.3643	964	1652	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.99	99.99	0.99	0.99	2	-
GCF_002101735.1	s__Mycobacterium kyorinense	81.3154	987	1652	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.84	99.84	0.96	0.94	3	-
GCF_010728725.1	s__Mycobacterium branderi	81.1254	985	1652	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	80.2057	861	1652	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.01	99.01	0.95	0.95	2	-
GCF_001668725.1	s__Mycobacterium sp001668725	80.1468	849	1652	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.46	99.46	0.97	0.97	2	-
GCF_010723305.1	s__Mycobacterium botniense	80.0347	773	1652	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003284935.1	s__Mycobacterium arosiense_A	79.89	783	1652	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001954275.1	s__Mycobacterium sp001954275	79.8382	821	1652	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.75	98.75	0.90	0.90	2	-
GCF_001053185.1	s__Mycobacterium bohemicum	79.7579	770	1652	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.81	99.81	0.97	0.97	2	-
GCA_008709575.1	s__Mycobacterium sp008709575	79.7072	700	1652	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019246375.1	s__Mycobacterium sp019246375	79.7002	561	1652	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001667945.1	s__Mycobacterium sinense_B	79.1683	653	1652	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.61	99.42	0.94	0.94	3	-
GCF_015689175.1	s__Mycobacterium kubicae	79.0914	741	1652	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.05	97.98	0.96	0.92	7	-
--------------------------------------------------------------------------------
[2024-01-24 12:07:52,896] [INFO] GTDB search result was written to GCF_016592155.1_ASM1659215v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:07:52,896] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:07:52,900] [INFO] DFAST_QC result json was written to GCF_016592155.1_ASM1659215v1_genomic.fna/dqc_result.json
[2024-01-24 12:07:52,900] [INFO] DFAST_QC completed!
[2024-01-24 12:07:52,901] [INFO] Total running time: 0h1m38s