[2024-01-25 17:36:35,544] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:36:35,545] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:36:35,545] [INFO] DQC Reference Directory: /var/lib/cwl/stg89dcdd43-01e9-4ea6-bf1a-7e35763e77ba/dqc_reference
[2024-01-25 17:36:36,665] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:36:36,666] [INFO] Task started: Prodigal
[2024-01-25 17:36:36,666] [INFO] Running command: gunzip -c /var/lib/cwl/stg7fa5ec08-558b-48c4-959d-8296bf0498f5/GCF_000277735.2_ASM27773v2_genomic.fna.gz | prodigal -d GCF_000277735.2_ASM27773v2_genomic.fna/cds.fna -a GCF_000277735.2_ASM27773v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:36:55,621] [INFO] Task succeeded: Prodigal
[2024-01-25 17:36:55,622] [INFO] Task started: HMMsearch
[2024-01-25 17:36:55,622] [INFO] Running command: hmmsearch --tblout GCF_000277735.2_ASM27773v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg89dcdd43-01e9-4ea6-bf1a-7e35763e77ba/dqc_reference/reference_markers.hmm GCF_000277735.2_ASM27773v2_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:36:55,833] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:36:55,834] [INFO] Found 6/6 markers.
[2024-01-25 17:36:55,873] [INFO] Query marker FASTA was written to GCF_000277735.2_ASM27773v2_genomic.fna/markers.fasta
[2024-01-25 17:36:55,874] [INFO] Task started: Blastn
[2024-01-25 17:36:55,874] [INFO] Running command: blastn -query GCF_000277735.2_ASM27773v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg89dcdd43-01e9-4ea6-bf1a-7e35763e77ba/dqc_reference/reference_markers.fasta -out GCF_000277735.2_ASM27773v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:36:56,786] [INFO] Task succeeded: Blastn
[2024-01-25 17:36:56,789] [INFO] Selected 6 target genomes.
[2024-01-25 17:36:56,789] [INFO] Target genome list was writen to GCF_000277735.2_ASM27773v2_genomic.fna/target_genomes.txt
[2024-01-25 17:36:56,792] [INFO] Task started: fastANI
[2024-01-25 17:36:56,792] [INFO] Running command: fastANI --query /var/lib/cwl/stg7fa5ec08-558b-48c4-959d-8296bf0498f5/GCF_000277735.2_ASM27773v2_genomic.fna.gz --refList GCF_000277735.2_ASM27773v2_genomic.fna/target_genomes.txt --output GCF_000277735.2_ASM27773v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:37:06,530] [INFO] Task succeeded: fastANI
[2024-01-25 17:37:06,530] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg89dcdd43-01e9-4ea6-bf1a-7e35763e77ba/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:37:06,531] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg89dcdd43-01e9-4ea6-bf1a-7e35763e77ba/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:37:06,537] [WARNING] Following organisms are indistinguishable with ANI. [Mycobacterium tuberculosis(1773), Mycobacterium tuberculosis variant bovis(1765), Mycobacterium tuberculosis variant microti(1806), Mycobacterium tuberculosis variant africanum(33894), Mycobacterium tuberculosis variant caprae(115862), Mycobacterium tuberculosis variant pinnipedii(194542)]
[2024-01-25 17:37:06,537] [INFO] Found 6 fastANI hits (6 hits with ANI > threshold)
[2024-01-25 17:37:06,537] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:37:06,537] [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 tuberculosis	strain=H37Rv	GCA_000277735.2	1773	1773	type	True	100.0	1470	1470	95	conclusive
Mycobacterium tuberculosis	strain=H37Rv	GCA_000195955.2	1773	1773	type	True	99.9974	1470	1470	95	conclusive
Mycobacterium tuberculosis	strain=H37Rv	GCA_000667805.1	1773	1773	type	True	99.9579	1461	1470	95	conclusive
Mycobacterium tuberculosis	strain=H37Rv	GCA_003266045.1	1773	1773	type	True	99.9256	1377	1470	95	conclusive
Mycobacterium tuberculosis variant africanum	strain=ATCC 25420	GCA_002982335.1	33894	1773	type	True	99.8129	1391	1470	95	conclusive
Mycobacterium tuberculosis variant microti	strain=ATCC 19422	GCA_002982215.1	1806	1773	type	True	99.7305	1266	1470	95	conclusive
--------------------------------------------------------------------------------
[2024-01-25 17:37:06,538] [INFO] DFAST Taxonomy check result was written to GCF_000277735.2_ASM27773v2_genomic.fna/tc_result.tsv
[2024-01-25 17:37:06,539] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:37:06,539] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:37:06,539] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg89dcdd43-01e9-4ea6-bf1a-7e35763e77ba/dqc_reference/checkm_data
[2024-01-25 17:37:06,540] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:37:06,583] [INFO] Task started: CheckM
[2024-01-25 17:37:06,583] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000277735.2_ASM27773v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000277735.2_ASM27773v2_genomic.fna/checkm_input GCF_000277735.2_ASM27773v2_genomic.fna/checkm_result
[2024-01-25 17:38:00,542] [INFO] Task succeeded: CheckM
[2024-01-25 17:38:00,543] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:38:00,561] [INFO] ===== Completeness check finished =====
[2024-01-25 17:38:00,562] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:38:00,563] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000277735.2_ASM27773v2_genomic.fna/markers.fasta)
[2024-01-25 17:38:00,563] [INFO] Task started: Blastn
[2024-01-25 17:38:00,563] [INFO] Running command: blastn -query GCF_000277735.2_ASM27773v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg89dcdd43-01e9-4ea6-bf1a-7e35763e77ba/dqc_reference/reference_markers_gtdb.fasta -out GCF_000277735.2_ASM27773v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:38:01,968] [INFO] Task succeeded: Blastn
[2024-01-25 17:38:01,971] [INFO] Selected 21 target genomes.
[2024-01-25 17:38:01,971] [INFO] Target genome list was writen to GCF_000277735.2_ASM27773v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:38:01,980] [INFO] Task started: fastANI
[2024-01-25 17:38:01,980] [INFO] Running command: fastANI --query /var/lib/cwl/stg7fa5ec08-558b-48c4-959d-8296bf0498f5/GCF_000277735.2_ASM27773v2_genomic.fna.gz --refList GCF_000277735.2_ASM27773v2_genomic.fna/target_genomes_gtdb.txt --output GCF_000277735.2_ASM27773v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:38:29,324] [INFO] Task succeeded: fastANI
[2024-01-25 17:38:29,336] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:38:29,337] [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_000195955.2	s__Mycobacterium tuberculosis	99.9974	1470	1470	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.92	97.88	0.99	0.91	6836	conclusive
GCF_002104675.1	s__Mycobacterium decipiens	85.8466	1131	1470	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010730055.1	s__Mycobacterium shinjukuense	83.5688	1068	1470	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.98	99.98	1.00	1.00	2	-
GCF_010731535.1	s__Mycobacterium lacus	82.5571	1071	1470	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.99	99.99	0.99	0.99	2	-
GCF_002086305.1	s__Mycobacterium malmoense_B	81.7149	901	1470	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.01	99.01	0.95	0.95	2	-
GCF_002101845.1	s__Mycobacterium riyadhense	81.6449	1033	1470	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.42	99.30	0.97	0.96	10	-
GCF_900566055.1	s__Mycobacterium innocens	81.3328	950	1470	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.27	98.57	0.94	0.90	3	-
GCF_002705925.1	s__Mycobacterium ostraviense	81.2992	995	1470	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.87	99.87	0.99	0.99	2	-
GCF_001954195.1	s__Mycobacterium sp001954195	81.1399	836	1470	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.85	98.85	0.97	0.97	2	-
GCF_002086675.1	s__Mycobacterium persicum	81.0266	952	1470	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.71	99.58	0.97	0.95	12	-
GCF_001667015.1	s__Mycobacterium sp001667015	81.0079	845	1470	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900566075.1	s__Mycobacterium pseudokansasii	81.0046	985	1470	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.70	99.48	0.96	0.94	7	-
GCF_002101815.1	s__Mycobacterium paraense	80.9865	871	1470	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.85	98.84	0.95	0.95	4	-
GCF_001665295.1	s__Mycobacterium sp001665295	80.8901	858	1470	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002086635.1	s__Mycobacterium alsense	80.8583	874	1470	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	96.76	96.71	0.91	0.90	3	-
GCF_900157385.1	s__Mycobacterium terramassiliense	80.7413	891	1470	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007714205.1	s__Mycobacterium helveticum	80.5995	798	1470	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.98	99.98	0.99	0.99	2	-
GCF_003614435.1	s__Mycobacterium paragordonae	80.055	875	1470	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.23	97.83	0.93	0.88	9	-
GCF_002101735.1	s__Mycobacterium kyorinense	79.7815	715	1470	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.84	99.84	0.96	0.94	3	-
GCF_002101595.1	s__Mycobacterium celatum	79.7755	727	1470	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.99	99.99	0.99	0.99	2	-
GCF_001499905.1	s__Mycobacterium sp001499905	78.0697	444	1470	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:38:29,340] [INFO] GTDB search result was written to GCF_000277735.2_ASM27773v2_genomic.fna/result_gtdb.tsv
[2024-01-25 17:38:29,340] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:38:29,345] [INFO] DFAST_QC result json was written to GCF_000277735.2_ASM27773v2_genomic.fna/dqc_result.json
[2024-01-25 17:38:29,346] [INFO] DFAST_QC completed!
[2024-01-25 17:38:29,346] [INFO] Total running time: 0h1m54s