[2024-01-25 18:43:35,556] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:43:35,557] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:43:35,557] [INFO] DQC Reference Directory: /var/lib/cwl/stg8619e46d-2311-4c4c-ac4e-12d6991aee99/dqc_reference
[2024-01-25 18:43:36,674] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:43:36,675] [INFO] Task started: Prodigal
[2024-01-25 18:43:36,675] [INFO] Running command: gunzip -c /var/lib/cwl/stg824e4b96-0f3d-4ae2-b88f-abb9419a899f/GCF_000418535.1_ASM41853v2_genomic.fna.gz | prodigal -d GCF_000418535.1_ASM41853v2_genomic.fna/cds.fna -a GCF_000418535.1_ASM41853v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:44:03,734] [INFO] Task succeeded: Prodigal
[2024-01-25 18:44:03,734] [INFO] Task started: HMMsearch
[2024-01-25 18:44:03,734] [INFO] Running command: hmmsearch --tblout GCF_000418535.1_ASM41853v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8619e46d-2311-4c4c-ac4e-12d6991aee99/dqc_reference/reference_markers.hmm GCF_000418535.1_ASM41853v2_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:44:04,004] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:44:04,005] [INFO] Found 6/6 markers.
[2024-01-25 18:44:04,050] [INFO] Query marker FASTA was written to GCF_000418535.1_ASM41853v2_genomic.fna/markers.fasta
[2024-01-25 18:44:04,050] [INFO] Task started: Blastn
[2024-01-25 18:44:04,050] [INFO] Running command: blastn -query GCF_000418535.1_ASM41853v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg8619e46d-2311-4c4c-ac4e-12d6991aee99/dqc_reference/reference_markers.fasta -out GCF_000418535.1_ASM41853v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:44:05,205] [INFO] Task succeeded: Blastn
[2024-01-25 18:44:05,208] [INFO] Selected 11 target genomes.
[2024-01-25 18:44:05,208] [INFO] Target genome list was writen to GCF_000418535.1_ASM41853v2_genomic.fna/target_genomes.txt
[2024-01-25 18:44:05,212] [INFO] Task started: fastANI
[2024-01-25 18:44:05,213] [INFO] Running command: fastANI --query /var/lib/cwl/stg824e4b96-0f3d-4ae2-b88f-abb9419a899f/GCF_000418535.1_ASM41853v2_genomic.fna.gz --refList GCF_000418535.1_ASM41853v2_genomic.fna/target_genomes.txt --output GCF_000418535.1_ASM41853v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:44:21,754] [INFO] Task succeeded: fastANI
[2024-01-25 18:44:21,755] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8619e46d-2311-4c4c-ac4e-12d6991aee99/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:44:21,755] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8619e46d-2311-4c4c-ac4e-12d6991aee99/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:44:21,764] [INFO] Found 11 fastANI hits (9 hits with ANI > threshold)
[2024-01-25 18:44:21,764] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-25 18:44:21,764] [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 intracellulare subsp. yongonense	strain=05-1390	GCA_000418535.2	1203599	1767	type	True	100.0	1885	1886	95	inconclusive
Mycobacterium intracellulare subsp. chimaera	strain=DSM 44623	GCA_002219285.1	222805	1767	type	True	97.936	1697	1886	95	inconclusive
Mycobacterium intracellulare subsp. chimaera	strain=DSM 44623	GCA_002101575.1	222805	1767	type	True	97.8967	1671	1886	95	inconclusive
Mycobacterium intracellulare subsp. chimaera	strain=JCM_14737	GCA_001938095.1	222805	1767	type	True	97.8925	1699	1886	95	inconclusive
Mycobacterium paraintracellulare	strain=MOTT64	GCA_000276825.1	1138383	1138383	suspected-type	True	97.6549	1641	1886	95	inconclusive
Mycobacterium paraintracellulare	strain=KCTC 29084	GCA_002104735.1	1138383	1138383	suspected-type	True	97.6479	1597	1886	95	inconclusive
Mycobacterium paraintracellulare	strain=JCM 30622	GCA_010731935.1	1138383	1138383	suspected-type	True	97.6425	1643	1886	95	inconclusive
Mycobacterium intracellulare	strain=ATCC 13950	GCA_023278525.1	1767	1767	suspected-type	True	97.5078	1631	1886	95	inconclusive
Mycobacterium intracellulare	strain=ATCC 13950	GCA_000172115.1	1767	1767	suspected-type	True	97.4323	1427	1886	95	inconclusive
Mycobacterium marseillense	strain=JCM 17324	GCA_010731675.1	701042	701042	type	True	92.5294	1629	1886	95	below_threshold
Mycobacterium heidelbergense	strain=JCM 14842	GCA_010730745.1	53376	53376	type	True	84.1216	1172	1886	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:44:21,766] [INFO] DFAST Taxonomy check result was written to GCF_000418535.1_ASM41853v2_genomic.fna/tc_result.tsv
[2024-01-25 18:44:21,766] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:44:21,766] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:44:21,766] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8619e46d-2311-4c4c-ac4e-12d6991aee99/dqc_reference/checkm_data
[2024-01-25 18:44:21,767] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:44:21,825] [INFO] Task started: CheckM
[2024-01-25 18:44:21,825] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000418535.1_ASM41853v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000418535.1_ASM41853v2_genomic.fna/checkm_input GCF_000418535.1_ASM41853v2_genomic.fna/checkm_result
[2024-01-25 18:45:48,220] [INFO] Task succeeded: CheckM
[2024-01-25 18:45:48,221] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:45:48,249] [INFO] ===== Completeness check finished =====
[2024-01-25 18:45:48,249] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:45:48,250] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000418535.1_ASM41853v2_genomic.fna/markers.fasta)
[2024-01-25 18:45:48,250] [INFO] Task started: Blastn
[2024-01-25 18:45:48,250] [INFO] Running command: blastn -query GCF_000418535.1_ASM41853v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg8619e46d-2311-4c4c-ac4e-12d6991aee99/dqc_reference/reference_markers_gtdb.fasta -out GCF_000418535.1_ASM41853v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:45:50,068] [INFO] Task succeeded: Blastn
[2024-01-25 18:45:50,073] [INFO] Selected 17 target genomes.
[2024-01-25 18:45:50,074] [INFO] Target genome list was writen to GCF_000418535.1_ASM41853v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:45:50,105] [INFO] Task started: fastANI
[2024-01-25 18:45:50,105] [INFO] Running command: fastANI --query /var/lib/cwl/stg824e4b96-0f3d-4ae2-b88f-abb9419a899f/GCF_000418535.1_ASM41853v2_genomic.fna.gz --refList GCF_000418535.1_ASM41853v2_genomic.fna/target_genomes_gtdb.txt --output GCF_000418535.1_ASM41853v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:46:15,638] [INFO] Task succeeded: fastANI
[2024-01-25 18:46:15,649] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:46:15,649] [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_000277125.1	s__Mycobacterium intracellulare	97.5115	1633	1886	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.48	95.71	0.93	0.84	82	conclusive
GCF_010731675.1	s__Mycobacterium marseillense	92.5294	1629	1886	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.64	95.51	0.95	0.90	6	-
GCF_001667315.1	s__Mycobacterium sp001667315	90.5833	1505	1886	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004298145.1	s__Mycobacterium sp004298145	89.8544	1443	1886	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	87.333	1407	1886	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002105755.1	s__Mycobacterium colombiense	87.2896	1492	1886	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.60	97.75	0.94	0.91	4	-
GCF_002104765.1	s__Mycobacterium vulneris	87.0782	1415	1886	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003284975.1	s__Mycobacterium europaeum_A	86.9706	1370	1886	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	95.84	95.70	0.84	0.79	6	-
GCF_001665875.1	s__Mycobacterium sp001665875	86.9299	1388	1886	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001667275.1	s__Mycobacterium sp001667275	84.4888	1308	1886	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	96.42	96.39	0.93	0.93	5	-
GCF_900240975.1	s__Mycobacterium sp900240975	84.2236	1298	1886	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	97.65	95.35	0.92	0.88	4	-
GCF_001907675.1	s__Mycobacterium paraffinicum	84.0489	1325	1886	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002101815.1	s__Mycobacterium paraense	83.8989	1305	1886	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.85	98.84	0.95	0.95	4	-
GCF_001667015.1	s__Mycobacterium sp001667015	83.7649	1219	1886	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001667185.1	s__Mycobacterium sp001667185	83.7583	1241	1886	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002101785.1	s__Mycobacterium palustre	83.6347	1184	1886	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	83.5315	1264	1886	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 18:46:15,651] [INFO] GTDB search result was written to GCF_000418535.1_ASM41853v2_genomic.fna/result_gtdb.tsv
[2024-01-25 18:46:15,652] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:46:15,655] [INFO] DFAST_QC result json was written to GCF_000418535.1_ASM41853v2_genomic.fna/dqc_result.json
[2024-01-25 18:46:15,655] [INFO] DFAST_QC completed!
[2024-01-25 18:46:15,655] [INFO] Total running time: 0h2m40s