[2024-01-24 12:31:05,405] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:31:05,406] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:31:05,407] [INFO] DQC Reference Directory: /var/lib/cwl/stg48f8cc8a-d163-48fa-9efc-a58ab8dceb5c/dqc_reference
[2024-01-24 12:31:06,735] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:31:06,735] [INFO] Task started: Prodigal
[2024-01-24 12:31:06,736] [INFO] Running command: gunzip -c /var/lib/cwl/stg9d72e124-2a41-4aac-a72d-7f23b7ab74ce/GCF_022374895.2_ASM2237489v2_genomic.fna.gz | prodigal -d GCF_022374895.2_ASM2237489v2_genomic.fna/cds.fna -a GCF_022374895.2_ASM2237489v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:31:30,079] [INFO] Task succeeded: Prodigal
[2024-01-24 12:31:30,080] [INFO] Task started: HMMsearch
[2024-01-24 12:31:30,080] [INFO] Running command: hmmsearch --tblout GCF_022374895.2_ASM2237489v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg48f8cc8a-d163-48fa-9efc-a58ab8dceb5c/dqc_reference/reference_markers.hmm GCF_022374895.2_ASM2237489v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:31:30,398] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:31:30,399] [INFO] Found 6/6 markers.
[2024-01-24 12:31:30,450] [INFO] Query marker FASTA was written to GCF_022374895.2_ASM2237489v2_genomic.fna/markers.fasta
[2024-01-24 12:31:30,451] [INFO] Task started: Blastn
[2024-01-24 12:31:30,451] [INFO] Running command: blastn -query GCF_022374895.2_ASM2237489v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg48f8cc8a-d163-48fa-9efc-a58ab8dceb5c/dqc_reference/reference_markers.fasta -out GCF_022374895.2_ASM2237489v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:31:31,687] [INFO] Task succeeded: Blastn
[2024-01-24 12:31:31,689] [INFO] Selected 12 target genomes.
[2024-01-24 12:31:31,690] [INFO] Target genome list was writen to GCF_022374895.2_ASM2237489v2_genomic.fna/target_genomes.txt
[2024-01-24 12:31:31,695] [INFO] Task started: fastANI
[2024-01-24 12:31:31,695] [INFO] Running command: fastANI --query /var/lib/cwl/stg9d72e124-2a41-4aac-a72d-7f23b7ab74ce/GCF_022374895.2_ASM2237489v2_genomic.fna.gz --refList GCF_022374895.2_ASM2237489v2_genomic.fna/target_genomes.txt --output GCF_022374895.2_ASM2237489v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:31:49,410] [INFO] Task succeeded: fastANI
[2024-01-24 12:31:49,410] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg48f8cc8a-d163-48fa-9efc-a58ab8dceb5c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:31:49,411] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg48f8cc8a-d163-48fa-9efc-a58ab8dceb5c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:31:49,429] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:31:49,429] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:31:49,429] [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 lentiflavum	strain=ATCC 51985	GCA_022374895.2	141349	141349	type	True	100.0	2051	2053	95	conclusive
Mycobacterium ahvazicum	strain=AFP003	GCA_900176255.2	1964395	1964395	type	True	91.6317	1676	2053	95	below_threshold
Mycobacterium triplex	strain=DSM 44626	GCA_000689255.1	47839	47839	type	True	88.691	1592	2053	95	below_threshold
Mycobacterium triplex	strain=DSM 44626	GCA_002102415.1	47839	47839	type	True	88.6591	1579	2053	95	below_threshold
Mycobacterium florentinum	strain=DSM 44852	GCA_002101635.1	292462	292462	type	True	88.6314	1580	2053	95	below_threshold
Mycobacterium florentinum	strain=JCM 14740	GCA_010730355.1	292462	292462	type	True	88.6161	1591	2053	95	below_threshold
Mycobacterium stomatepiae	strain=JCM 17783	GCA_010731715.1	470076	470076	type	True	87.6487	1557	2053	95	below_threshold
Mycobacterium genavense	strain=ATCC 51234	GCA_000526915.1	36812	36812	type	True	87.5104	1371	2053	95	below_threshold
Mycobacterium simiae	strain=JCM 12377	GCA_010727605.1	1784	1784	type	True	83.2715	1362	2053	95	below_threshold
Mycobacterium shigaense	strain=UN-152	GCA_002983495.1	722731	722731	type	True	82.8371	1311	2053	95	below_threshold
Mycobacterium numidiamassiliense	strain=AB215	GCA_900157365.1	1841861	1841861	type	True	82.78	1379	2053	95	below_threshold
Mycobacterium shigaense	strain=JCM 32072	GCA_002356315.1	722731	722731	type	True	82.7788	1313	2053	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:31:49,431] [INFO] DFAST Taxonomy check result was written to GCF_022374895.2_ASM2237489v2_genomic.fna/tc_result.tsv
[2024-01-24 12:31:49,432] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:31:49,432] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:31:49,432] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg48f8cc8a-d163-48fa-9efc-a58ab8dceb5c/dqc_reference/checkm_data
[2024-01-24 12:31:49,433] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:31:49,492] [INFO] Task started: CheckM
[2024-01-24 12:31:49,492] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_022374895.2_ASM2237489v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_022374895.2_ASM2237489v2_genomic.fna/checkm_input GCF_022374895.2_ASM2237489v2_genomic.fna/checkm_result
[2024-01-24 12:32:52,335] [INFO] Task succeeded: CheckM
[2024-01-24 12:32:52,336] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:32:52,362] [INFO] ===== Completeness check finished =====
[2024-01-24 12:32:52,362] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:32:52,362] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_022374895.2_ASM2237489v2_genomic.fna/markers.fasta)
[2024-01-24 12:32:52,363] [INFO] Task started: Blastn
[2024-01-24 12:32:52,363] [INFO] Running command: blastn -query GCF_022374895.2_ASM2237489v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg48f8cc8a-d163-48fa-9efc-a58ab8dceb5c/dqc_reference/reference_markers_gtdb.fasta -out GCF_022374895.2_ASM2237489v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:32:54,057] [INFO] Task succeeded: Blastn
[2024-01-24 12:32:54,062] [INFO] Selected 11 target genomes.
[2024-01-24 12:32:54,062] [INFO] Target genome list was writen to GCF_022374895.2_ASM2237489v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:32:54,079] [INFO] Task started: fastANI
[2024-01-24 12:32:54,080] [INFO] Running command: fastANI --query /var/lib/cwl/stg9d72e124-2a41-4aac-a72d-7f23b7ab74ce/GCF_022374895.2_ASM2237489v2_genomic.fna.gz --refList GCF_022374895.2_ASM2237489v2_genomic.fna/target_genomes_gtdb.txt --output GCF_022374895.2_ASM2237489v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:33:10,459] [INFO] Task succeeded: fastANI
[2024-01-24 12:33:10,473] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:33:10,473] [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_001373395.1	s__Mycobacterium lentiflavum	99.2216	1917	2053	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_900176255.2	s__Mycobacterium ahvazicum	91.6322	1676	2053	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000689255.1	s__Mycobacterium triplex	88.6769	1594	2053	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.99	99.99	1.00	1.00	2	-
GCF_010730355.1	s__Mycobacterium florentinum	88.6072	1592	2053	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_010731715.1	s__Mycobacterium stomatepiae	87.6461	1557	2053	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	87.5198	1370	2053	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003112775.1	s__Mycobacterium montefiorense	86.1976	1475	2053	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900157375.1	s__Mycobacterium rhizamassiliense	83.3728	1355	2053	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	83.2637	1363	2053	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.04	97.21	0.97	0.92	4	-
GCF_002356315.1	s__Mycobacterium shigaense	82.8121	1308	2053	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.91	99.82	1.00	1.00	3	-
GCF_900157365.1	s__Mycobacterium numidiamassiliense	82.7883	1377	2053	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 12:33:10,475] [INFO] GTDB search result was written to GCF_022374895.2_ASM2237489v2_genomic.fna/result_gtdb.tsv
[2024-01-24 12:33:10,476] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:33:10,480] [INFO] DFAST_QC result json was written to GCF_022374895.2_ASM2237489v2_genomic.fna/dqc_result.json
[2024-01-24 12:33:10,480] [INFO] DFAST_QC completed!
[2024-01-24 12:33:10,480] [INFO] Total running time: 0h2m5s