[2024-01-24 13:12:37,505] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:12:37,507] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:12:37,507] [INFO] DQC Reference Directory: /var/lib/cwl/stgd65a08d5-eff4-45e9-87cc-bc77da9b574a/dqc_reference
[2024-01-24 13:12:38,902] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:12:38,903] [INFO] Task started: Prodigal
[2024-01-24 13:12:38,903] [INFO] Running command: gunzip -c /var/lib/cwl/stg6bc5071a-93b9-4ef5-b1a1-07c5d775ae95/GCF_010730745.1_ASM1073074v1_genomic.fna.gz | prodigal -d GCF_010730745.1_ASM1073074v1_genomic.fna/cds.fna -a GCF_010730745.1_ASM1073074v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:12:55,841] [INFO] Task succeeded: Prodigal
[2024-01-24 13:12:55,841] [INFO] Task started: HMMsearch
[2024-01-24 13:12:55,841] [INFO] Running command: hmmsearch --tblout GCF_010730745.1_ASM1073074v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd65a08d5-eff4-45e9-87cc-bc77da9b574a/dqc_reference/reference_markers.hmm GCF_010730745.1_ASM1073074v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:12:56,135] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:12:56,136] [INFO] Found 6/6 markers.
[2024-01-24 13:12:56,177] [INFO] Query marker FASTA was written to GCF_010730745.1_ASM1073074v1_genomic.fna/markers.fasta
[2024-01-24 13:12:56,177] [INFO] Task started: Blastn
[2024-01-24 13:12:56,178] [INFO] Running command: blastn -query GCF_010730745.1_ASM1073074v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd65a08d5-eff4-45e9-87cc-bc77da9b574a/dqc_reference/reference_markers.fasta -out GCF_010730745.1_ASM1073074v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:12:57,415] [INFO] Task succeeded: Blastn
[2024-01-24 13:12:57,419] [INFO] Selected 13 target genomes.
[2024-01-24 13:12:57,419] [INFO] Target genome list was writen to GCF_010730745.1_ASM1073074v1_genomic.fna/target_genomes.txt
[2024-01-24 13:12:57,427] [INFO] Task started: fastANI
[2024-01-24 13:12:57,427] [INFO] Running command: fastANI --query /var/lib/cwl/stg6bc5071a-93b9-4ef5-b1a1-07c5d775ae95/GCF_010730745.1_ASM1073074v1_genomic.fna.gz --refList GCF_010730745.1_ASM1073074v1_genomic.fna/target_genomes.txt --output GCF_010730745.1_ASM1073074v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:13:16,486] [INFO] Task succeeded: fastANI
[2024-01-24 13:13:16,486] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd65a08d5-eff4-45e9-87cc-bc77da9b574a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:13:16,486] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd65a08d5-eff4-45e9-87cc-bc77da9b574a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:13:16,499] [INFO] Found 13 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:13:16,500] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:13:16,500] [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=JCM 14842	GCA_010730745.1	53376	53376	type	True	100.0	1683	1683	95	conclusive
Mycobacterium heidelbergense	strain=DSM 44471	GCA_002086215.1	53376	53376	type	True	99.959	1608	1683	95	conclusive
Mycobacterium paraense	strain=IEC26	GCA_002101815.1	767916	767916	type	True	86.2481	1248	1683	95	below_threshold
Mycobacterium palustre	strain=DSM 44572	GCA_002101785.1	153971	153971	type	True	85.8322	1208	1683	95	below_threshold
Mycobacterium avium subsp. avium	strain=DSM 44156	GCA_009741445.1	44454	1764	type	True	84.5594	1160	1683	95	below_threshold
Mycobacterium helveticum	strain=16-83	GCA_007714205.1	2592811	2592811	type	True	84.2601	1053	1683	95	below_threshold
Mycobacterium bohemicum	strain=DSM 44277	GCA_002102025.1	56425	56425	type	True	84.2242	1175	1683	95	below_threshold
Mycobacterium intracellulare subsp. yongonense	strain=05-1390	GCA_000418535.2	1203599	1767	type	True	84.1957	1186	1683	95	below_threshold
Mycobacterium intracellulare subsp. chimaera	strain=DSM 44623	GCA_002219285.1	222805	1767	type	True	84.1679	1167	1683	95	below_threshold
Mycobacterium bohemicum	strain=DSM 44277	GCA_001053185.1	56425	56425	type	True	84.0743	1143	1683	95	below_threshold
Mycobacterium lacus	strain=JCM 15657	GCA_010731535.1	169765	169765	type	True	83.2368	1064	1683	95	below_threshold
Mycobacterium angelicum	strain=DSM 45057	GCA_002086155.1	470074	470074	type	True	82.0814	1099	1683	95	below_threshold
Mycobacterium simiae	strain=JCM 12377	GCA_010727605.1	1784	1784	type	True	81.9268	1093	1683	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:13:16,507] [INFO] DFAST Taxonomy check result was written to GCF_010730745.1_ASM1073074v1_genomic.fna/tc_result.tsv
[2024-01-24 13:13:16,508] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:13:16,509] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:13:16,509] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd65a08d5-eff4-45e9-87cc-bc77da9b574a/dqc_reference/checkm_data
[2024-01-24 13:13:16,511] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:13:16,565] [INFO] Task started: CheckM
[2024-01-24 13:13:16,565] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_010730745.1_ASM1073074v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_010730745.1_ASM1073074v1_genomic.fna/checkm_input GCF_010730745.1_ASM1073074v1_genomic.fna/checkm_result
[2024-01-24 13:14:07,558] [INFO] Task succeeded: CheckM
[2024-01-24 13:14:07,560] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:14:07,585] [INFO] ===== Completeness check finished =====
[2024-01-24 13:14:07,586] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:14:07,586] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_010730745.1_ASM1073074v1_genomic.fna/markers.fasta)
[2024-01-24 13:14:07,586] [INFO] Task started: Blastn
[2024-01-24 13:14:07,587] [INFO] Running command: blastn -query GCF_010730745.1_ASM1073074v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd65a08d5-eff4-45e9-87cc-bc77da9b574a/dqc_reference/reference_markers_gtdb.fasta -out GCF_010730745.1_ASM1073074v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:14:09,135] [INFO] Task succeeded: Blastn
[2024-01-24 13:14:09,139] [INFO] Selected 17 target genomes.
[2024-01-24 13:14:09,140] [INFO] Target genome list was writen to GCF_010730745.1_ASM1073074v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:14:09,152] [INFO] Task started: fastANI
[2024-01-24 13:14:09,153] [INFO] Running command: fastANI --query /var/lib/cwl/stg6bc5071a-93b9-4ef5-b1a1-07c5d775ae95/GCF_010730745.1_ASM1073074v1_genomic.fna.gz --refList GCF_010730745.1_ASM1073074v1_genomic.fna/target_genomes_gtdb.txt --output GCF_010730745.1_ASM1073074v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:14:33,489] [INFO] Task succeeded: fastANI
[2024-01-24 13:14:33,507] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:14:33,507] [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_010730745.1	s__Mycobacterium heidelbergense	100.0	1683	1683	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_002086305.1	s__Mycobacterium malmoense_B	89.5851	1370	1683	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.01	99.01	0.95	0.95	2	-
GCF_001667035.1	s__Mycobacterium sp001667035	86.3785	1192	1683	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001673535.1	s__Mycobacterium sp001673535	86.2758	1193	1683	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900157385.1	s__Mycobacterium terramassiliense	86.1912	1278	1683	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	86.1482	1213	1683	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	86.0694	1191	1683	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	86.0256	1208	1683	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001668725.1	s__Mycobacterium sp001668725	86.014	1243	1683	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.46	99.46	0.97	0.97	2	-
GCF_900078675.2	s__Mycobacterium interjectum	85.9962	1225	1683	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	85.97	1247	1683	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000455205.1	s__Mycobacterium sp000455205	85.7094	1188	1683	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	96.16	95.96	0.85	0.84	3	-
GCF_002102155.1	s__Mycobacterium europaeum	84.4126	1175	1683	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.26	99.26	0.97	0.97	2	-
GCF_001053185.1	s__Mycobacterium bohemicum	84.0701	1144	1683	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.81	99.81	0.97	0.97	2	-
GCF_900157365.1	s__Mycobacterium numidiamassiliense	83.2793	1154	1683	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002086155.1	s__Mycobacterium angelicum	82.1077	1096	1683	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010727605.1	s__Mycobacterium simiae	81.9382	1090	1683	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.04	97.21	0.97	0.92	4	-
--------------------------------------------------------------------------------
[2024-01-24 13:14:33,509] [INFO] GTDB search result was written to GCF_010730745.1_ASM1073074v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:14:33,510] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:14:33,513] [INFO] DFAST_QC result json was written to GCF_010730745.1_ASM1073074v1_genomic.fna/dqc_result.json
[2024-01-24 13:14:33,513] [INFO] DFAST_QC completed!
[2024-01-24 13:14:33,514] [INFO] Total running time: 0h1m56s