[2024-01-24 14:38:45,777] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:38:45,780] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:38:45,780] [INFO] DQC Reference Directory: /var/lib/cwl/stg1a7d737f-7848-4725-865a-9be9888f8142/dqc_reference
[2024-01-24 14:38:47,245] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:38:47,248] [INFO] Task started: Prodigal
[2024-01-24 14:38:47,249] [INFO] Running command: gunzip -c /var/lib/cwl/stgbe2a4c68-7f0c-4b08-9194-21aa26af544d/GCF_026012615.1_ASM2601261v1_genomic.fna.gz | prodigal -d GCF_026012615.1_ASM2601261v1_genomic.fna/cds.fna -a GCF_026012615.1_ASM2601261v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:39:02,085] [INFO] Task succeeded: Prodigal
[2024-01-24 14:39:02,086] [INFO] Task started: HMMsearch
[2024-01-24 14:39:02,086] [INFO] Running command: hmmsearch --tblout GCF_026012615.1_ASM2601261v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1a7d737f-7848-4725-865a-9be9888f8142/dqc_reference/reference_markers.hmm GCF_026012615.1_ASM2601261v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:39:02,397] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:39:02,399] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgbe2a4c68-7f0c-4b08-9194-21aa26af544d/GCF_026012615.1_ASM2601261v1_genomic.fna.gz]
[2024-01-24 14:39:02,452] [INFO] Query marker FASTA was written to GCF_026012615.1_ASM2601261v1_genomic.fna/markers.fasta
[2024-01-24 14:39:02,453] [INFO] Task started: Blastn
[2024-01-24 14:39:02,453] [INFO] Running command: blastn -query GCF_026012615.1_ASM2601261v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1a7d737f-7848-4725-865a-9be9888f8142/dqc_reference/reference_markers.fasta -out GCF_026012615.1_ASM2601261v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:39:03,357] [INFO] Task succeeded: Blastn
[2024-01-24 14:39:03,362] [INFO] Selected 12 target genomes.
[2024-01-24 14:39:03,362] [INFO] Target genome list was writen to GCF_026012615.1_ASM2601261v1_genomic.fna/target_genomes.txt
[2024-01-24 14:39:03,369] [INFO] Task started: fastANI
[2024-01-24 14:39:03,369] [INFO] Running command: fastANI --query /var/lib/cwl/stgbe2a4c68-7f0c-4b08-9194-21aa26af544d/GCF_026012615.1_ASM2601261v1_genomic.fna.gz --refList GCF_026012615.1_ASM2601261v1_genomic.fna/target_genomes.txt --output GCF_026012615.1_ASM2601261v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:39:18,523] [INFO] Task succeeded: fastANI
[2024-01-24 14:39:18,524] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1a7d737f-7848-4725-865a-9be9888f8142/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:39:18,524] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1a7d737f-7848-4725-865a-9be9888f8142/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:39:18,539] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:39:18,540] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:39:18,540] [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 florentinum	strain=JCM 14740	GCA_010730355.1	292462	292462	type	True	86.7255	1257	1447	95	below_threshold
Mycobacterium florentinum	strain=DSM 44852	GCA_002101635.1	292462	292462	type	True	86.6513	1259	1447	95	below_threshold
Mycobacterium triplex	strain=DSM 44626	GCA_002102415.1	47839	47839	type	True	86.4225	1210	1447	95	below_threshold
Mycobacterium triplex	strain=DSM 44626	GCA_000689255.1	47839	47839	type	True	86.4007	1212	1447	95	below_threshold
Mycobacterium stomatepiae	strain=JCM 17783	GCA_010731715.1	470076	470076	type	True	85.8572	1222	1447	95	below_threshold
Mycobacterium ahvazicum	strain=AFP003	GCA_900176255.2	1964395	1964395	type	True	85.7525	1204	1447	95	below_threshold
Mycobacterium genavense	strain=ATCC 51234	GCA_000526915.1	36812	36812	type	True	85.5322	1062	1447	95	below_threshold
Mycobacterium sherrisii	strain=ATCC BAA-832	GCA_002102355.1	243061	243061	type	True	83.1031	1084	1447	95	below_threshold
Mycobacterium simiae	strain=JCM 12377	GCA_010727605.1	1784	1784	type	True	82.8962	1095	1447	95	below_threshold
Mycobacterium numidiamassiliense	strain=AB215	GCA_900157365.1	1841861	1841861	type	True	82.291	1058	1447	95	below_threshold
Mycobacterium nebraskense	strain=DSM 44803	GCA_002102255.1	244292	244292	type	True	81.8836	962	1447	95	below_threshold
Mycobacterium mantenii	strain=JCM 18113	GCA_010731775.1	560555	560555	type	True	81.878	974	1447	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:39:18,542] [INFO] DFAST Taxonomy check result was written to GCF_026012615.1_ASM2601261v1_genomic.fna/tc_result.tsv
[2024-01-24 14:39:18,542] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:39:18,542] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:39:18,543] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1a7d737f-7848-4725-865a-9be9888f8142/dqc_reference/checkm_data
[2024-01-24 14:39:18,544] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:39:18,601] [INFO] Task started: CheckM
[2024-01-24 14:39:18,601] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_026012615.1_ASM2601261v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_026012615.1_ASM2601261v1_genomic.fna/checkm_input GCF_026012615.1_ASM2601261v1_genomic.fna/checkm_result
[2024-01-24 14:40:01,995] [INFO] Task succeeded: CheckM
[2024-01-24 14:40:01,997] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 90.91%
Contamintation: 7.29%
Strain heterogeneity: 66.67%
--------------------------------------------------------------------------------
[2024-01-24 14:40:02,024] [INFO] ===== Completeness check finished =====
[2024-01-24 14:40:02,024] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:40:02,025] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_026012615.1_ASM2601261v1_genomic.fna/markers.fasta)
[2024-01-24 14:40:02,025] [INFO] Task started: Blastn
[2024-01-24 14:40:02,025] [INFO] Running command: blastn -query GCF_026012615.1_ASM2601261v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1a7d737f-7848-4725-865a-9be9888f8142/dqc_reference/reference_markers_gtdb.fasta -out GCF_026012615.1_ASM2601261v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:40:03,317] [INFO] Task succeeded: Blastn
[2024-01-24 14:40:03,320] [INFO] Selected 14 target genomes.
[2024-01-24 14:40:03,321] [INFO] Target genome list was writen to GCF_026012615.1_ASM2601261v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:40:03,330] [INFO] Task started: fastANI
[2024-01-24 14:40:03,331] [INFO] Running command: fastANI --query /var/lib/cwl/stgbe2a4c68-7f0c-4b08-9194-21aa26af544d/GCF_026012615.1_ASM2601261v1_genomic.fna.gz --refList GCF_026012615.1_ASM2601261v1_genomic.fna/target_genomes_gtdb.txt --output GCF_026012615.1_ASM2601261v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:40:24,988] [INFO] Task succeeded: fastANI
[2024-01-24 14:40:25,006] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:40:25,006] [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_003112775.1	s__Mycobacterium montefiorense	97.5822	1402	1447	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_010730355.1	s__Mycobacterium florentinum	86.7255	1257	1447	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000689255.1	s__Mycobacterium triplex	86.3927	1213	1447	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.99	99.99	1.00	1.00	2	-
GCF_010731715.1	s__Mycobacterium stomatepiae	85.86	1221	1447	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900176255.2	s__Mycobacterium ahvazicum	85.748	1203	1447	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000526915.1	s__Mycobacterium genavense	85.5127	1064	1447	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001665235.1	s__Mycobacterium sp001665235	84.4011	1169	1447	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002102355.1	s__Mycobacterium sherrisii	83.1025	1084	1447	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.78	99.78	0.96	0.96	2	-
GCF_010727605.1	s__Mycobacterium simiae	82.8947	1095	1447	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.04	97.21	0.97	0.92	4	-
GCF_900157365.1	s__Mycobacterium numidiamassiliense	82.2911	1058	1447	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	82.0811	951	1447	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	81.959	926	1447	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	81.8833	963	1447	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.58	99.42	0.93	0.92	4	-
GCA_002102225.1	s__Mycobacterium interjectum_B	81.8121	970	1447	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:40:25,008] [INFO] GTDB search result was written to GCF_026012615.1_ASM2601261v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:40:25,009] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:40:25,013] [INFO] DFAST_QC result json was written to GCF_026012615.1_ASM2601261v1_genomic.fna/dqc_result.json
[2024-01-24 14:40:25,013] [INFO] DFAST_QC completed!
[2024-01-24 14:40:25,013] [INFO] Total running time: 0h1m39s