[2024-01-25 17:38:35,814] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:38:35,815] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:38:35,816] [INFO] DQC Reference Directory: /var/lib/cwl/stg69b112b6-b240-4aab-beb8-c9d544100bfc/dqc_reference
[2024-01-25 17:38:36,970] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:38:36,971] [INFO] Task started: Prodigal
[2024-01-25 17:38:36,971] [INFO] Running command: gunzip -c /var/lib/cwl/stgf6c3b29c-7789-4ffc-8c1d-443d69c81a16/GCF_025823355.1_ASM2582335v1_genomic.fna.gz | prodigal -d GCF_025823355.1_ASM2582335v1_genomic.fna/cds.fna -a GCF_025823355.1_ASM2582335v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:38:52,798] [INFO] Task succeeded: Prodigal
[2024-01-25 17:38:52,798] [INFO] Task started: HMMsearch
[2024-01-25 17:38:52,798] [INFO] Running command: hmmsearch --tblout GCF_025823355.1_ASM2582335v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg69b112b6-b240-4aab-beb8-c9d544100bfc/dqc_reference/reference_markers.hmm GCF_025823355.1_ASM2582335v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:38:53,042] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:38:53,043] [INFO] Found 6/6 markers.
[2024-01-25 17:38:53,090] [INFO] Query marker FASTA was written to GCF_025823355.1_ASM2582335v1_genomic.fna/markers.fasta
[2024-01-25 17:38:53,090] [INFO] Task started: Blastn
[2024-01-25 17:38:53,090] [INFO] Running command: blastn -query GCF_025823355.1_ASM2582335v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg69b112b6-b240-4aab-beb8-c9d544100bfc/dqc_reference/reference_markers.fasta -out GCF_025823355.1_ASM2582335v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:38:54,231] [INFO] Task succeeded: Blastn
[2024-01-25 17:38:54,234] [INFO] Selected 12 target genomes.
[2024-01-25 17:38:54,234] [INFO] Target genome list was writen to GCF_025823355.1_ASM2582335v1_genomic.fna/target_genomes.txt
[2024-01-25 17:38:54,249] [INFO] Task started: fastANI
[2024-01-25 17:38:54,249] [INFO] Running command: fastANI --query /var/lib/cwl/stgf6c3b29c-7789-4ffc-8c1d-443d69c81a16/GCF_025823355.1_ASM2582335v1_genomic.fna.gz --refList GCF_025823355.1_ASM2582335v1_genomic.fna/target_genomes.txt --output GCF_025823355.1_ASM2582335v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:39:10,665] [INFO] Task succeeded: fastANI
[2024-01-25 17:39:10,666] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg69b112b6-b240-4aab-beb8-c9d544100bfc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:39:10,666] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg69b112b6-b240-4aab-beb8-c9d544100bfc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:39:10,675] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:39:10,675] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:39:10,675] [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 seoulense	strain=JCM 16018	GCA_010731595.1	386911	386911	type	True	99.9937	1831	1833	95	conclusive
Mycobacterium paraseoulense	strain=DSM 45000	GCA_002086475.1	590652	590652	type	True	94.7732	1633	1833	95	below_threshold
Mycobacterium paraseoulense	strain=JCM 16952	GCA_010731655.1	590652	590652	type	True	94.7658	1699	1833	95	below_threshold
Mycobacterium nebraskense	strain=DSM 44803	GCA_002102255.1	244292	244292	type	True	89.9697	1529	1833	95	below_threshold
Mycobacterium avium subsp. avium	strain=ATCC 25291	GCA_000174035.1	44454	1764	type	True	84.6402	1200	1833	95	below_threshold
Mycobacterium avium subsp. avium	strain=DSM 44156	GCA_009741445.1	44454	1764	type	True	84.531	1312	1833	95	below_threshold
Mycobacterium intracellulare	strain=ATCC 13950	GCA_023278525.1	1767	1767	suspected-type	True	84.4288	1321	1833	95	below_threshold
Mycobacterium heidelbergense	strain=JCM 14842	GCA_010730745.1	53376	53376	type	True	84.417	1188	1833	95	below_threshold
Mycobacterium colombiense	strain=CECT 3035	GCA_002105755.1	339268	339268	suspected-type	True	84.3864	1367	1833	95	below_threshold
Mycobacterium bohemicum	strain=DSM 44277	GCA_002102025.1	56425	56425	type	True	83.5899	1286	1833	95	below_threshold
Mycobacterium shigaense	strain=JCM 32072	GCA_002356315.1	722731	722731	type	True	82.4339	1184	1833	95	below_threshold
Mycobacterium shigaense	strain=UN-152	GCA_002983495.1	722731	722731	type	True	82.4275	1188	1833	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:39:10,677] [INFO] DFAST Taxonomy check result was written to GCF_025823355.1_ASM2582335v1_genomic.fna/tc_result.tsv
[2024-01-25 17:39:10,678] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:39:10,678] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:39:10,678] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg69b112b6-b240-4aab-beb8-c9d544100bfc/dqc_reference/checkm_data
[2024-01-25 17:39:10,679] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:39:10,731] [INFO] Task started: CheckM
[2024-01-25 17:39:10,731] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025823355.1_ASM2582335v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025823355.1_ASM2582335v1_genomic.fna/checkm_input GCF_025823355.1_ASM2582335v1_genomic.fna/checkm_result
[2024-01-25 17:40:05,508] [INFO] Task succeeded: CheckM
[2024-01-25 17:40:05,509] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:40:05,531] [INFO] ===== Completeness check finished =====
[2024-01-25 17:40:05,531] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:40:05,532] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025823355.1_ASM2582335v1_genomic.fna/markers.fasta)
[2024-01-25 17:40:05,533] [INFO] Task started: Blastn
[2024-01-25 17:40:05,533] [INFO] Running command: blastn -query GCF_025823355.1_ASM2582335v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg69b112b6-b240-4aab-beb8-c9d544100bfc/dqc_reference/reference_markers_gtdb.fasta -out GCF_025823355.1_ASM2582335v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:40:07,356] [INFO] Task succeeded: Blastn
[2024-01-25 17:40:07,360] [INFO] Selected 11 target genomes.
[2024-01-25 17:40:07,360] [INFO] Target genome list was writen to GCF_025823355.1_ASM2582335v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:40:07,372] [INFO] Task started: fastANI
[2024-01-25 17:40:07,372] [INFO] Running command: fastANI --query /var/lib/cwl/stgf6c3b29c-7789-4ffc-8c1d-443d69c81a16/GCF_025823355.1_ASM2582335v1_genomic.fna.gz --refList GCF_025823355.1_ASM2582335v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025823355.1_ASM2582335v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:40:24,179] [INFO] Task succeeded: fastANI
[2024-01-25 17:40:24,186] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:40:24,187] [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_010731595.1	s__Mycobacterium seoulense	99.9937	1831	1833	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_010731655.1	s__Mycobacterium paraseoulense	94.7658	1699	1833	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900240975.1	s__Mycobacterium sp900240975	90.3081	1554	1833	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	97.65	95.35	0.92	0.88	4	-
GCF_002102255.1	s__Mycobacterium nebraskense	89.9788	1528	1833	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.58	99.42	0.93	0.92	4	-
GCF_002102155.1	s__Mycobacterium europaeum	89.766	1527	1833	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.26	99.26	0.97	0.97	2	-
GCF_001665605.1	s__Mycobacterium sp001665605	89.287	1534	1833	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.77	98.77	0.96	0.96	2	-
GCF_001667075.1	s__Mycobacterium sp001667075	89.012	1537	1833	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.41	99.38	0.97	0.97	3	-
GCF_001666835.1	s__Mycobacterium sp001666835	88.8167	1471	1833	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.04	99.01	0.94	0.94	3	-
GCF_001667585.1	s__Mycobacterium sp001667585	88.812	1501	1833	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000164135.1	s__Mycobacterium parascrofulaceum	88.679	1505	1833	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	97.18	96.53	0.89	0.85	6	-
GCF_001907675.1	s__Mycobacterium paraffinicum	88.2146	1478	1833	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 17:40:24,188] [INFO] GTDB search result was written to GCF_025823355.1_ASM2582335v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:40:24,189] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:40:24,191] [INFO] DFAST_QC result json was written to GCF_025823355.1_ASM2582335v1_genomic.fna/dqc_result.json
[2024-01-25 17:40:24,192] [INFO] DFAST_QC completed!
[2024-01-25 17:40:24,192] [INFO] Total running time: 0h1m48s