[2024-01-24 12:29:18,849] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:29:18,851] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:29:18,851] [INFO] DQC Reference Directory: /var/lib/cwl/stg85c67109-6394-4a1d-ada8-8d93efb2b947/dqc_reference
[2024-01-24 12:29:20,020] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:29:20,021] [INFO] Task started: Prodigal
[2024-01-24 12:29:20,021] [INFO] Running command: gunzip -c /var/lib/cwl/stg1c9cd1df-bc0e-45fc-acd8-5211ce6f7746/GCF_019645855.1_ASM1964585v1_genomic.fna.gz | prodigal -d GCF_019645855.1_ASM1964585v1_genomic.fna/cds.fna -a GCF_019645855.1_ASM1964585v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:29:40,823] [INFO] Task succeeded: Prodigal
[2024-01-24 12:29:40,824] [INFO] Task started: HMMsearch
[2024-01-24 12:29:40,824] [INFO] Running command: hmmsearch --tblout GCF_019645855.1_ASM1964585v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg85c67109-6394-4a1d-ada8-8d93efb2b947/dqc_reference/reference_markers.hmm GCF_019645855.1_ASM1964585v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:29:41,118] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:29:41,120] [INFO] Found 6/6 markers.
[2024-01-24 12:29:41,166] [INFO] Query marker FASTA was written to GCF_019645855.1_ASM1964585v1_genomic.fna/markers.fasta
[2024-01-24 12:29:41,167] [INFO] Task started: Blastn
[2024-01-24 12:29:41,167] [INFO] Running command: blastn -query GCF_019645855.1_ASM1964585v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg85c67109-6394-4a1d-ada8-8d93efb2b947/dqc_reference/reference_markers.fasta -out GCF_019645855.1_ASM1964585v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:29:42,261] [INFO] Task succeeded: Blastn
[2024-01-24 12:29:42,265] [INFO] Selected 17 target genomes.
[2024-01-24 12:29:42,265] [INFO] Target genome list was writen to GCF_019645855.1_ASM1964585v1_genomic.fna/target_genomes.txt
[2024-01-24 12:29:42,275] [INFO] Task started: fastANI
[2024-01-24 12:29:42,275] [INFO] Running command: fastANI --query /var/lib/cwl/stg1c9cd1df-bc0e-45fc-acd8-5211ce6f7746/GCF_019645855.1_ASM1964585v1_genomic.fna.gz --refList GCF_019645855.1_ASM1964585v1_genomic.fna/target_genomes.txt --output GCF_019645855.1_ASM1964585v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:30:02,105] [INFO] Task succeeded: fastANI
[2024-01-24 12:30:02,106] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg85c67109-6394-4a1d-ada8-8d93efb2b947/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:30:02,106] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg85c67109-6394-4a1d-ada8-8d93efb2b947/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:30:02,132] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:30:02,132] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:30:02,132] [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 heidelbergense	strain=DSM 44471	GCA_002086215.1	53376	53376	type	True	89.4302	1367	1773	95	below_threshold
Mycobacterium heidelbergense	strain=JCM 14842	GCA_010730745.1	53376	53376	type	True	89.4247	1413	1773	95	below_threshold
Mycobacterium paraense	strain=IEC26	GCA_002101815.1	767916	767916	type	True	85.6487	1276	1773	95	below_threshold
Mycobacterium palustre	strain=DSM 44572	GCA_002101785.1	153971	153971	type	True	85.1615	1186	1773	95	below_threshold
Mycobacterium intracellulare	strain=ATCC 13950	GCA_023278525.1	1767	1767	suspected-type	True	83.8556	1191	1773	95	below_threshold
Mycobacterium intracellulare subsp. yongonense	strain=05-1390	GCA_000418535.2	1203599	1767	type	True	83.8213	1188	1773	95	below_threshold
Mycobacterium bohemicum	strain=DSM 44277	GCA_002102025.1	56425	56425	type	True	83.7757	1217	1773	95	below_threshold
Mycobacterium bohemicum	strain=DSM 44277	GCA_001053185.1	56425	56425	type	True	83.7363	1167	1773	95	below_threshold
Mycobacterium colombiense	strain=CECT 3035	GCA_000222105.4	339268	339268	suspected-type	True	83.7283	1208	1773	95	below_threshold
Mycobacterium colombiense	strain=CECT 3035	GCA_002105755.1	339268	339268	suspected-type	True	83.705	1201	1773	95	below_threshold
Mycobacterium ostraviense	strain=241/15	GCA_002705925.1	2738409	2738409	type	True	81.9847	1098	1773	95	below_threshold
Mycobacterium tuberculosis	strain=H37Rv	GCA_003266045.1	1773	1773	type	True	81.7781	901	1773	95	below_threshold
Mycobacterium tuberculosis variant microti	strain=ATCC 19422	GCA_002982215.1	1806	1773	type	True	81.7393	855	1773	95	below_threshold
Mycobacterium tuberculosis	strain=H37Rv	GCA_000667805.1	1773	1773	type	True	81.6731	931	1773	95	below_threshold
Mycobacterium tuberculosis	strain=H37Rv	GCA_000195955.2	1773	1773	type	True	81.6632	928	1773	95	below_threshold
Mycobacterium tuberculosis	strain=H37Rv	GCA_000277735.2	1773	1773	type	True	81.6283	936	1773	95	below_threshold
Mycobacterium noviomagense	strain=DSM 45145	GCA_002086415.1	459858	459858	type	True	80.7043	893	1773	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:30:02,134] [INFO] DFAST Taxonomy check result was written to GCF_019645855.1_ASM1964585v1_genomic.fna/tc_result.tsv
[2024-01-24 12:30:02,135] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:30:02,136] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:30:02,136] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg85c67109-6394-4a1d-ada8-8d93efb2b947/dqc_reference/checkm_data
[2024-01-24 12:30:02,138] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:30:02,191] [INFO] Task started: CheckM
[2024-01-24 12:30:02,192] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019645855.1_ASM1964585v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019645855.1_ASM1964585v1_genomic.fna/checkm_input GCF_019645855.1_ASM1964585v1_genomic.fna/checkm_result
[2024-01-24 12:30:57,338] [INFO] Task succeeded: CheckM
[2024-01-24 12:30:57,340] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:30:57,364] [INFO] ===== Completeness check finished =====
[2024-01-24 12:30:57,364] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:30:57,365] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019645855.1_ASM1964585v1_genomic.fna/markers.fasta)
[2024-01-24 12:30:57,365] [INFO] Task started: Blastn
[2024-01-24 12:30:57,365] [INFO] Running command: blastn -query GCF_019645855.1_ASM1964585v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg85c67109-6394-4a1d-ada8-8d93efb2b947/dqc_reference/reference_markers_gtdb.fasta -out GCF_019645855.1_ASM1964585v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:30:58,965] [INFO] Task succeeded: Blastn
[2024-01-24 12:30:58,969] [INFO] Selected 15 target genomes.
[2024-01-24 12:30:58,970] [INFO] Target genome list was writen to GCF_019645855.1_ASM1964585v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:30:58,999] [INFO] Task started: fastANI
[2024-01-24 12:30:59,000] [INFO] Running command: fastANI --query /var/lib/cwl/stg1c9cd1df-bc0e-45fc-acd8-5211ce6f7746/GCF_019645855.1_ASM1964585v1_genomic.fna.gz --refList GCF_019645855.1_ASM1964585v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019645855.1_ASM1964585v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:31:18,162] [INFO] Task succeeded: fastANI
[2024-01-24 12:31:18,188] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:31:18,188] [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_002086305.1	s__Mycobacterium malmoense_B	99.9668	1712	1773	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.01	99.01	0.95	0.95	2	conclusive
GCF_010730745.1	s__Mycobacterium heidelbergense	89.4178	1415	1773	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002101815.1	s__Mycobacterium paraense	85.6346	1278	1773	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.85	98.84	0.95	0.95	4	-
GCF_900157385.1	s__Mycobacterium terramassiliense	85.394	1303	1773	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	85.3827	1214	1773	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	85.3778	1225	1773	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	96.76	96.71	0.91	0.90	3	-
GCF_001667015.1	s__Mycobacterium sp001667015	85.3393	1221	1773	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	85.3289	1269	1773	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001665295.1	s__Mycobacterium sp001665295	85.2871	1256	1773	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900078675.2	s__Mycobacterium interjectum	85.2484	1277	1773	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	83.7363	1166	1773	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.81	99.81	0.97	0.97	2	-
GCF_000195955.2	s__Mycobacterium tuberculosis	81.6483	930	1773	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.92	97.88	0.99	0.91	6836	-
GCF_002101735.1	s__Mycobacterium kyorinense	81.4465	956	1773	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	81.3024	969	1773	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.99	99.99	0.99	0.99	2	-
GCF_003408705.1	s__Mycobacterium uberis	78.8102	475	1773	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 12:31:18,190] [INFO] GTDB search result was written to GCF_019645855.1_ASM1964585v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:31:18,191] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:31:18,198] [INFO] DFAST_QC result json was written to GCF_019645855.1_ASM1964585v1_genomic.fna/dqc_result.json
[2024-01-24 12:31:18,199] [INFO] DFAST_QC completed!
[2024-01-24 12:31:18,199] [INFO] Total running time: 0h1m59s