[2024-01-25 17:55:05,464] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:55:05,466] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:55:05,466] [INFO] DQC Reference Directory: /var/lib/cwl/stg2435c1ac-e16b-4b80-94c2-bf7763767edc/dqc_reference
[2024-01-25 17:55:06,577] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:55:06,578] [INFO] Task started: Prodigal
[2024-01-25 17:55:06,578] [INFO] Running command: gunzip -c /var/lib/cwl/stgb27d82ec-cc95-44ef-a819-8554ff50f28f/GCF_022558505.1_ASM2255850v1_genomic.fna.gz | prodigal -d GCF_022558505.1_ASM2255850v1_genomic.fna/cds.fna -a GCF_022558505.1_ASM2255850v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:55:24,331] [INFO] Task succeeded: Prodigal
[2024-01-25 17:55:24,332] [INFO] Task started: HMMsearch
[2024-01-25 17:55:24,332] [INFO] Running command: hmmsearch --tblout GCF_022558505.1_ASM2255850v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2435c1ac-e16b-4b80-94c2-bf7763767edc/dqc_reference/reference_markers.hmm GCF_022558505.1_ASM2255850v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:55:24,580] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:55:24,581] [INFO] Found 6/6 markers.
[2024-01-25 17:55:24,624] [INFO] Query marker FASTA was written to GCF_022558505.1_ASM2255850v1_genomic.fna/markers.fasta
[2024-01-25 17:55:24,624] [INFO] Task started: Blastn
[2024-01-25 17:55:24,624] [INFO] Running command: blastn -query GCF_022558505.1_ASM2255850v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2435c1ac-e16b-4b80-94c2-bf7763767edc/dqc_reference/reference_markers.fasta -out GCF_022558505.1_ASM2255850v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:55:25,689] [INFO] Task succeeded: Blastn
[2024-01-25 17:55:25,692] [INFO] Selected 17 target genomes.
[2024-01-25 17:55:25,692] [INFO] Target genome list was writen to GCF_022558505.1_ASM2255850v1_genomic.fna/target_genomes.txt
[2024-01-25 17:55:25,697] [INFO] Task started: fastANI
[2024-01-25 17:55:25,697] [INFO] Running command: fastANI --query /var/lib/cwl/stgb27d82ec-cc95-44ef-a819-8554ff50f28f/GCF_022558505.1_ASM2255850v1_genomic.fna.gz --refList GCF_022558505.1_ASM2255850v1_genomic.fna/target_genomes.txt --output GCF_022558505.1_ASM2255850v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:55:44,958] [INFO] Task succeeded: fastANI
[2024-01-25 17:55:44,958] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2435c1ac-e16b-4b80-94c2-bf7763767edc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:55:44,959] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2435c1ac-e16b-4b80-94c2-bf7763767edc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:55:44,969] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 17:55:44,969] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 17:55:44,969] [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	89.4543	1370	1773	95	below_threshold
Mycobacterium heidelbergense	strain=JCM 14842	GCA_010730745.1	53376	53376	type	True	89.4287	1417	1773	95	below_threshold
Mycobacterium paraense	strain=IEC26	GCA_002101815.1	767916	767916	type	True	85.6511	1275	1773	95	below_threshold
Mycobacterium palustre	strain=DSM 44572	GCA_002101785.1	153971	153971	type	True	85.147	1192	1773	95	below_threshold
Mycobacterium intracellulare	strain=ATCC 13950	GCA_023278525.1	1767	1767	suspected-type	True	83.8611	1199	1773	95	below_threshold
Mycobacterium intracellulare subsp. yongonense	strain=05-1390	GCA_000418535.2	1203599	1767	type	True	83.8176	1193	1773	95	below_threshold
Mycobacterium bohemicum	strain=DSM 44277	GCA_002102025.1	56425	56425	type	True	83.801	1215	1773	95	below_threshold
Mycobacterium bohemicum	strain=DSM 44277	GCA_001053185.1	56425	56425	type	True	83.6999	1171	1773	95	below_threshold
Mycobacterium colombiense	strain=CECT 3035	GCA_002105755.1	339268	339268	suspected-type	True	83.6984	1208	1773	95	below_threshold
Mycobacterium colombiense	strain=CECT 3035	GCA_000222105.4	339268	339268	suspected-type	True	83.6811	1214	1773	95	below_threshold
Mycobacterium ostraviense	strain=241/15	GCA_002705925.1	2738409	2738409	type	True	81.9625	1104	1773	95	below_threshold
Mycobacterium tuberculosis	strain=H37Rv	GCA_003266045.1	1773	1773	type	True	81.7924	904	1773	95	below_threshold
Mycobacterium tuberculosis variant microti	strain=ATCC 19422	GCA_002982215.1	1806	1773	type	True	81.7828	853	1773	95	below_threshold
Mycobacterium tuberculosis	strain=H37Rv	GCA_000667805.1	1773	1773	type	True	81.6846	921	1773	95	below_threshold
Mycobacterium tuberculosis	strain=H37Rv	GCA_000195955.2	1773	1773	type	True	81.6589	928	1773	95	below_threshold
Mycobacterium tuberculosis	strain=H37Rv	GCA_000277735.2	1773	1773	type	True	81.6331	934	1773	95	below_threshold
Mycobacterium noviomagense	strain=DSM 45145	GCA_002086415.1	459858	459858	type	True	80.6844	893	1773	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:55:44,973] [INFO] DFAST Taxonomy check result was written to GCF_022558505.1_ASM2255850v1_genomic.fna/tc_result.tsv
[2024-01-25 17:55:44,974] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:55:44,974] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:55:44,974] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2435c1ac-e16b-4b80-94c2-bf7763767edc/dqc_reference/checkm_data
[2024-01-25 17:55:44,975] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:55:45,024] [INFO] Task started: CheckM
[2024-01-25 17:55:45,024] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_022558505.1_ASM2255850v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_022558505.1_ASM2255850v1_genomic.fna/checkm_input GCF_022558505.1_ASM2255850v1_genomic.fna/checkm_result
[2024-01-25 17:56:35,825] [INFO] Task succeeded: CheckM
[2024-01-25 17:56:35,826] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:56:35,844] [INFO] ===== Completeness check finished =====
[2024-01-25 17:56:35,845] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:56:35,845] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_022558505.1_ASM2255850v1_genomic.fna/markers.fasta)
[2024-01-25 17:56:35,846] [INFO] Task started: Blastn
[2024-01-25 17:56:35,846] [INFO] Running command: blastn -query GCF_022558505.1_ASM2255850v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2435c1ac-e16b-4b80-94c2-bf7763767edc/dqc_reference/reference_markers_gtdb.fasta -out GCF_022558505.1_ASM2255850v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:56:37,418] [INFO] Task succeeded: Blastn
[2024-01-25 17:56:37,420] [INFO] Selected 15 target genomes.
[2024-01-25 17:56:37,421] [INFO] Target genome list was writen to GCF_022558505.1_ASM2255850v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:56:37,434] [INFO] Task started: fastANI
[2024-01-25 17:56:37,434] [INFO] Running command: fastANI --query /var/lib/cwl/stgb27d82ec-cc95-44ef-a819-8554ff50f28f/GCF_022558505.1_ASM2255850v1_genomic.fna.gz --refList GCF_022558505.1_ASM2255850v1_genomic.fna/target_genomes_gtdb.txt --output GCF_022558505.1_ASM2255850v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:56:56,757] [INFO] Task succeeded: fastANI
[2024-01-25 17:56:56,767] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:56:56,767] [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	99.962	1713	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	89.4234	1418	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	85.6441	1276	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	85.4328	1292	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	85.4007	1227	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_001672915.1	s__Mycobacterium sp001672915	85.3923	1217	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	85.3324	1265	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_001667015.1	s__Mycobacterium sp001667015	85.3003	1225	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	85.2652	1257	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	85.2342	1287	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	83.7095	1170	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	81.6937	924	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	81.4704	960	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	81.3811	959	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	78.79	476	1773	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:56:56,768] [INFO] GTDB search result was written to GCF_022558505.1_ASM2255850v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:56:56,769] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:56:56,775] [INFO] DFAST_QC result json was written to GCF_022558505.1_ASM2255850v1_genomic.fna/dqc_result.json
[2024-01-25 17:56:56,775] [INFO] DFAST_QC completed!
[2024-01-25 17:56:56,775] [INFO] Total running time: 0h1m51s