[2024-01-25 18:46:35,684] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:46:35,686] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:46:35,686] [INFO] DQC Reference Directory: /var/lib/cwl/stg1264f6fd-eec2-446f-8ace-846c653b6bac/dqc_reference
[2024-01-25 18:46:36,845] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:46:36,845] [INFO] Task started: Prodigal
[2024-01-25 18:46:36,845] [INFO] Running command: gunzip -c /var/lib/cwl/stgb93a9f33-ffe5-4d84-85b9-b3ad6ef2900b/GCF_025822865.1_ASM2582286v1_genomic.fna.gz | prodigal -d GCF_025822865.1_ASM2582286v1_genomic.fna/cds.fna -a GCF_025822865.1_ASM2582286v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:46:54,297] [INFO] Task succeeded: Prodigal
[2024-01-25 18:46:54,297] [INFO] Task started: HMMsearch
[2024-01-25 18:46:54,297] [INFO] Running command: hmmsearch --tblout GCF_025822865.1_ASM2582286v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1264f6fd-eec2-446f-8ace-846c653b6bac/dqc_reference/reference_markers.hmm GCF_025822865.1_ASM2582286v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:46:54,638] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:46:54,639] [INFO] Found 6/6 markers.
[2024-01-25 18:46:54,700] [INFO] Query marker FASTA was written to GCF_025822865.1_ASM2582286v1_genomic.fna/markers.fasta
[2024-01-25 18:46:54,701] [INFO] Task started: Blastn
[2024-01-25 18:46:54,701] [INFO] Running command: blastn -query GCF_025822865.1_ASM2582286v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1264f6fd-eec2-446f-8ace-846c653b6bac/dqc_reference/reference_markers.fasta -out GCF_025822865.1_ASM2582286v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:46:55,816] [INFO] Task succeeded: Blastn
[2024-01-25 18:46:55,819] [INFO] Selected 11 target genomes.
[2024-01-25 18:46:55,820] [INFO] Target genome list was writen to GCF_025822865.1_ASM2582286v1_genomic.fna/target_genomes.txt
[2024-01-25 18:46:55,826] [INFO] Task started: fastANI
[2024-01-25 18:46:55,827] [INFO] Running command: fastANI --query /var/lib/cwl/stgb93a9f33-ffe5-4d84-85b9-b3ad6ef2900b/GCF_025822865.1_ASM2582286v1_genomic.fna.gz --refList GCF_025822865.1_ASM2582286v1_genomic.fna/target_genomes.txt --output GCF_025822865.1_ASM2582286v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:47:10,904] [INFO] Task succeeded: fastANI
[2024-01-25 18:47:10,905] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1264f6fd-eec2-446f-8ace-846c653b6bac/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:47:10,905] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1264f6fd-eec2-446f-8ace-846c653b6bac/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:47:10,913] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 18:47:10,913] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 18:47:10,913] [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 nebraskense	strain=DSM 44803	GCA_002102255.1	244292	244292	type	True	89.9495	1491	1778	95	below_threshold
Mycobacterium seoulense	strain=JCM 16018	GCA_010731595.1	386911	386911	type	True	89.1212	1535	1778	95	below_threshold
Mycobacterium paraseoulense	strain=JCM 16952	GCA_010731655.1	590652	590652	type	True	88.8727	1537	1778	95	below_threshold
Mycobacterium paraseoulense	strain=DSM 45000	GCA_002086475.1	590652	590652	type	True	88.8686	1487	1778	95	below_threshold
Mycobacterium heidelbergense	strain=JCM 14842	GCA_010730745.1	53376	53376	type	True	84.3478	1163	1778	95	below_threshold
Mycobacterium colombiense	strain=CECT 3035	GCA_000222105.4	339268	339268	suspected-type	True	84.3354	1335	1778	95	below_threshold
Mycobacterium colombiense	strain=CECT 3035	GCA_002105755.1	339268	339268	suspected-type	True	84.3116	1351	1778	95	below_threshold
Mycobacterium mantenii	strain=JCM 18113	GCA_010731775.1	560555	560555	type	True	84.2377	1385	1778	95	below_threshold
Mycobacterium arosiense	strain=DSM 45069	GCA_002086125.1	425468	425468	type	True	83.7278	1232	1778	95	below_threshold
Mycobacterium bohemicum	strain=DSM 44277	GCA_001053185.1	56425	56425	type	True	83.2634	1181	1778	95	below_threshold
Mycobacterium bohemicum	strain=DSM 44277	GCA_002102025.1	56425	56425	type	True	83.2596	1255	1778	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:47:10,915] [INFO] DFAST Taxonomy check result was written to GCF_025822865.1_ASM2582286v1_genomic.fna/tc_result.tsv
[2024-01-25 18:47:10,915] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:47:10,915] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:47:10,915] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1264f6fd-eec2-446f-8ace-846c653b6bac/dqc_reference/checkm_data
[2024-01-25 18:47:10,916] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:47:10,970] [INFO] Task started: CheckM
[2024-01-25 18:47:10,971] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025822865.1_ASM2582286v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025822865.1_ASM2582286v1_genomic.fna/checkm_input GCF_025822865.1_ASM2582286v1_genomic.fna/checkm_result
[2024-01-25 18:48:02,967] [INFO] Task succeeded: CheckM
[2024-01-25 18:48:02,969] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:48:02,988] [INFO] ===== Completeness check finished =====
[2024-01-25 18:48:02,989] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:48:02,989] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025822865.1_ASM2582286v1_genomic.fna/markers.fasta)
[2024-01-25 18:48:02,990] [INFO] Task started: Blastn
[2024-01-25 18:48:02,990] [INFO] Running command: blastn -query GCF_025822865.1_ASM2582286v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1264f6fd-eec2-446f-8ace-846c653b6bac/dqc_reference/reference_markers_gtdb.fasta -out GCF_025822865.1_ASM2582286v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:48:04,735] [INFO] Task succeeded: Blastn
[2024-01-25 18:48:04,738] [INFO] Selected 8 target genomes.
[2024-01-25 18:48:04,738] [INFO] Target genome list was writen to GCF_025822865.1_ASM2582286v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:48:04,742] [INFO] Task started: fastANI
[2024-01-25 18:48:04,742] [INFO] Running command: fastANI --query /var/lib/cwl/stgb93a9f33-ffe5-4d84-85b9-b3ad6ef2900b/GCF_025822865.1_ASM2582286v1_genomic.fna.gz --refList GCF_025822865.1_ASM2582286v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025822865.1_ASM2582286v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:48:16,905] [INFO] Task succeeded: fastANI
[2024-01-25 18:48:16,911] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:48:16,911] [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_001665605.1	s__Mycobacterium sp001665605	95.8356	1612	1778	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.77	98.77	0.96	0.96	2	conclusive
GCF_001667075.1	s__Mycobacterium sp001667075	94.3859	1587	1778	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	92.859	1518	1778	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	91.7055	1513	1778	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002102255.1	s__Mycobacterium nebraskense	89.9553	1490	1778	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.58	99.42	0.93	0.92	4	-
GCF_010731595.1	s__Mycobacterium seoulense	89.1151	1536	1778	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	88.6587	1523	1778	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	97.18	96.53	0.89	0.85	6	-
GCF_002105755.1	s__Mycobacterium colombiense	84.307	1351	1778	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.60	97.75	0.94	0.91	4	-
--------------------------------------------------------------------------------
[2024-01-25 18:48:16,912] [INFO] GTDB search result was written to GCF_025822865.1_ASM2582286v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:48:16,913] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:48:16,915] [INFO] DFAST_QC result json was written to GCF_025822865.1_ASM2582286v1_genomic.fna/dqc_result.json
[2024-01-25 18:48:16,915] [INFO] DFAST_QC completed!
[2024-01-25 18:48:16,916] [INFO] Total running time: 0h1m41s