[2024-01-25 18:52:20,794] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:52:20,796] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:52:20,796] [INFO] DQC Reference Directory: /var/lib/cwl/stg3255fbd3-8e6e-4441-9cbf-8831e3b15260/dqc_reference
[2024-01-25 18:52:21,967] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:52:21,968] [INFO] Task started: Prodigal
[2024-01-25 18:52:21,969] [INFO] Running command: gunzip -c /var/lib/cwl/stg8646abb3-00bb-4b56-b8fc-892116fb17ab/GCF_900566085.1_LAUMK41_genomic.fna.gz | prodigal -d GCF_900566085.1_LAUMK41_genomic.fna/cds.fna -a GCF_900566085.1_LAUMK41_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:52:40,585] [INFO] Task succeeded: Prodigal
[2024-01-25 18:52:40,585] [INFO] Task started: HMMsearch
[2024-01-25 18:52:40,585] [INFO] Running command: hmmsearch --tblout GCF_900566085.1_LAUMK41_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3255fbd3-8e6e-4441-9cbf-8831e3b15260/dqc_reference/reference_markers.hmm GCF_900566085.1_LAUMK41_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:52:40,849] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:52:40,850] [INFO] Found 6/6 markers.
[2024-01-25 18:52:40,903] [INFO] Query marker FASTA was written to GCF_900566085.1_LAUMK41_genomic.fna/markers.fasta
[2024-01-25 18:52:40,903] [INFO] Task started: Blastn
[2024-01-25 18:52:40,903] [INFO] Running command: blastn -query GCF_900566085.1_LAUMK41_genomic.fna/markers.fasta -db /var/lib/cwl/stg3255fbd3-8e6e-4441-9cbf-8831e3b15260/dqc_reference/reference_markers.fasta -out GCF_900566085.1_LAUMK41_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:52:41,907] [INFO] Task succeeded: Blastn
[2024-01-25 18:52:41,910] [INFO] Selected 10 target genomes.
[2024-01-25 18:52:41,910] [INFO] Target genome list was writen to GCF_900566085.1_LAUMK41_genomic.fna/target_genomes.txt
[2024-01-25 18:52:41,915] [INFO] Task started: fastANI
[2024-01-25 18:52:41,915] [INFO] Running command: fastANI --query /var/lib/cwl/stg8646abb3-00bb-4b56-b8fc-892116fb17ab/GCF_900566085.1_LAUMK41_genomic.fna.gz --refList GCF_900566085.1_LAUMK41_genomic.fna/target_genomes.txt --output GCF_900566085.1_LAUMK41_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:52:56,906] [INFO] Task succeeded: fastANI
[2024-01-25 18:52:56,906] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3255fbd3-8e6e-4441-9cbf-8831e3b15260/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:52:56,906] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3255fbd3-8e6e-4441-9cbf-8831e3b15260/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:52:56,914] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:52:56,914] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:52:56,914] [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 attenuatum	strain=MK41	GCA_900566085.1	2341086	2341086	type	True	100.0	2045	2059	95	conclusive
Mycobacterium kansasii	strain=ATCC 12478	GCA_000157895.2	1768	1768	type	True	90.2196	1765	2059	95	below_threshold
Mycobacterium pseudokansasii	strain=MK142	GCA_900566075.1	2341080	2341080	type	True	89.7502	1706	2059	95	below_threshold
Mycobacterium innocens	strain=MK13	GCA_900566055.1	2341083	2341083	type	True	88.3265	1537	2059	95	below_threshold
Mycobacterium persicum	strain=AFPC-000227	GCA_002086675.1	1487726	1487726	type	True	87.922	1640	2059	95	below_threshold
Mycobacterium ostraviense	strain=241/15	GCA_002705925.1	2738409	2738409	type	True	87.8999	1640	2059	95	below_threshold
Mycobacterium gastri	strain=DSM 43505	GCA_002102175.1	1777	1777	type	True	87.8384	1520	2059	95	below_threshold
Mycobacterium paraense	strain=IEC26	GCA_002101815.1	767916	767916	type	True	80.9771	1071	2059	95	below_threshold
Mycobacterium avium subsp. avium	strain=ATCC 25291	GCA_000174035.1	44454	1764	type	True	80.9395	908	2059	95	below_threshold
Mycobacterium avium subsp. avium	strain=DSM 44156	GCA_009741445.1	44454	1764	type	True	80.8453	974	2059	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:52:56,916] [INFO] DFAST Taxonomy check result was written to GCF_900566085.1_LAUMK41_genomic.fna/tc_result.tsv
[2024-01-25 18:52:56,916] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:52:56,916] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:52:56,916] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3255fbd3-8e6e-4441-9cbf-8831e3b15260/dqc_reference/checkm_data
[2024-01-25 18:52:56,917] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:52:56,979] [INFO] Task started: CheckM
[2024-01-25 18:52:56,979] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900566085.1_LAUMK41_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900566085.1_LAUMK41_genomic.fna/checkm_input GCF_900566085.1_LAUMK41_genomic.fna/checkm_result
[2024-01-25 18:53:51,654] [INFO] Task succeeded: CheckM
[2024-01-25 18:53:51,655] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:53:51,689] [INFO] ===== Completeness check finished =====
[2024-01-25 18:53:51,689] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:53:51,689] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900566085.1_LAUMK41_genomic.fna/markers.fasta)
[2024-01-25 18:53:51,689] [INFO] Task started: Blastn
[2024-01-25 18:53:51,690] [INFO] Running command: blastn -query GCF_900566085.1_LAUMK41_genomic.fna/markers.fasta -db /var/lib/cwl/stg3255fbd3-8e6e-4441-9cbf-8831e3b15260/dqc_reference/reference_markers_gtdb.fasta -out GCF_900566085.1_LAUMK41_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:53:53,232] [INFO] Task succeeded: Blastn
[2024-01-25 18:53:53,240] [INFO] Selected 10 target genomes.
[2024-01-25 18:53:53,240] [INFO] Target genome list was writen to GCF_900566085.1_LAUMK41_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:53:53,252] [INFO] Task started: fastANI
[2024-01-25 18:53:53,252] [INFO] Running command: fastANI --query /var/lib/cwl/stg8646abb3-00bb-4b56-b8fc-892116fb17ab/GCF_900566085.1_LAUMK41_genomic.fna.gz --refList GCF_900566085.1_LAUMK41_genomic.fna/target_genomes_gtdb.txt --output GCF_900566085.1_LAUMK41_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:54:09,165] [INFO] Task succeeded: fastANI
[2024-01-25 18:54:09,172] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:54:09,172] [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_900566085.1	s__Mycobacterium attenuatum	100.0	2045	2059	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.59	99.54	0.94	0.93	4	conclusive
GCF_000157895.3	s__Mycobacterium kansasii	90.2217	1765	2059	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.70	99.15	0.98	0.95	35	-
GCF_900566075.1	s__Mycobacterium pseudokansasii	89.7521	1705	2059	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.70	99.48	0.96	0.94	7	-
GCF_900566055.1	s__Mycobacterium innocens	88.3312	1536	2059	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.27	98.57	0.94	0.90	3	-
GCF_002086675.1	s__Mycobacterium persicum	87.9278	1639	2059	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.71	99.58	0.97	0.95	12	-
GCF_002705925.1	s__Mycobacterium ostraviense	87.8859	1642	2059	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.87	99.87	0.99	0.99	2	-
GCF_002102175.1	s__Mycobacterium gastri	87.8401	1520	2059	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.95	99.95	0.95	0.95	2	-
GCF_009741445.1	s__Mycobacterium avium	80.8497	973	2059	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	96.9043	98.75	98.29	0.92	0.84	206	-
GCF_900157385.1	s__Mycobacterium terramassiliense	80.6088	1060	2059	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001053185.1	s__Mycobacterium bohemicum	80.2331	966	2059	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.81	99.81	0.97	0.97	2	-
--------------------------------------------------------------------------------
[2024-01-25 18:54:09,173] [INFO] GTDB search result was written to GCF_900566085.1_LAUMK41_genomic.fna/result_gtdb.tsv
[2024-01-25 18:54:09,174] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:54:09,177] [INFO] DFAST_QC result json was written to GCF_900566085.1_LAUMK41_genomic.fna/dqc_result.json
[2024-01-25 18:54:09,177] [INFO] DFAST_QC completed!
[2024-01-25 18:54:09,177] [INFO] Total running time: 0h1m48s