[2024-01-24 14:14:37,203] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:14:37,206] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:14:37,207] [INFO] DQC Reference Directory: /var/lib/cwl/stg45836cae-ee98-4755-ab53-a32e1f4552c4/dqc_reference
[2024-01-24 14:14:38,907] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:14:38,909] [INFO] Task started: Prodigal
[2024-01-24 14:14:38,909] [INFO] Running command: gunzip -c /var/lib/cwl/stg3538cb25-30cb-48f0-a6e1-527e2ee0045e/GCF_010726505.1_ASM1072650v1_genomic.fna.gz | prodigal -d GCF_010726505.1_ASM1072650v1_genomic.fna/cds.fna -a GCF_010726505.1_ASM1072650v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:14:53,638] [INFO] Task succeeded: Prodigal
[2024-01-24 14:14:53,639] [INFO] Task started: HMMsearch
[2024-01-24 14:14:53,639] [INFO] Running command: hmmsearch --tblout GCF_010726505.1_ASM1072650v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg45836cae-ee98-4755-ab53-a32e1f4552c4/dqc_reference/reference_markers.hmm GCF_010726505.1_ASM1072650v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:14:53,954] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:14:53,955] [INFO] Found 6/6 markers.
[2024-01-24 14:14:54,003] [INFO] Query marker FASTA was written to GCF_010726505.1_ASM1072650v1_genomic.fna/markers.fasta
[2024-01-24 14:14:54,004] [INFO] Task started: Blastn
[2024-01-24 14:14:54,004] [INFO] Running command: blastn -query GCF_010726505.1_ASM1072650v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg45836cae-ee98-4755-ab53-a32e1f4552c4/dqc_reference/reference_markers.fasta -out GCF_010726505.1_ASM1072650v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:14:55,299] [INFO] Task succeeded: Blastn
[2024-01-24 14:14:55,303] [INFO] Selected 14 target genomes.
[2024-01-24 14:14:55,304] [INFO] Target genome list was writen to GCF_010726505.1_ASM1072650v1_genomic.fna/target_genomes.txt
[2024-01-24 14:14:55,330] [INFO] Task started: fastANI
[2024-01-24 14:14:55,331] [INFO] Running command: fastANI --query /var/lib/cwl/stg3538cb25-30cb-48f0-a6e1-527e2ee0045e/GCF_010726505.1_ASM1072650v1_genomic.fna.gz --refList GCF_010726505.1_ASM1072650v1_genomic.fna/target_genomes.txt --output GCF_010726505.1_ASM1072650v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:15:13,823] [INFO] Task succeeded: fastANI
[2024-01-24 14:15:13,824] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg45836cae-ee98-4755-ab53-a32e1f4552c4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:15:13,824] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg45836cae-ee98-4755-ab53-a32e1f4552c4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:15:13,836] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:15:13,837] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:15:13,837] [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
Mycolicibacter senuensis	strain=JCM 16017	GCA_010723225.1	386913	386913	type	True	92.9093	1367	1486	95	below_threshold
Mycolicibacter senuensis	strain=DSM 44999	GCA_002101885.1	386913	386913	type	True	92.904	1334	1486	95	below_threshold
Mycolicibacter terrae	strain=CIP 104321	GCA_002101955.1	1788	1788	type	True	87.6632	1197	1486	95	below_threshold
Mycolicibacter terrae	strain=JCM 12143	GCA_010727125.1	1788	1788	type	True	87.638	1246	1486	95	below_threshold
Mycolicibacter kumamotonensis	strain=CST 7247	GCA_010093495.1	354243	354243	type	True	87.4962	1186	1486	95	below_threshold
Mycolicibacter kumamotonensis	strain=DSM 45093	GCA_002086285.1	354243	354243	type	True	87.3074	1226	1486	95	below_threshold
Mycolicibacter longobardus	strain=DSM 45394	GCA_002102265.1	1108812	1108812	type	True	86.0543	1162	1486	95	below_threshold
Mycolicibacter nonchromogenicus	strain=DSM 44164	GCA_002101775.1	1782	1782	type	True	84.2504	1105	1486	95	below_threshold
Mycobacterium palustre	strain=DSM 44572	GCA_002101785.1	153971	153971	type	True	80.0069	768	1486	95	below_threshold
Mycobacterium pallens	strain=JCM 16370	GCA_019456675.1	370524	370524	type	True	79.2285	718	1486	95	below_threshold
Mycobacterium crocinum	strain=JCM 16369	GCA_022370635.3	388459	388459	type	True	79.1491	699	1486	95	below_threshold
Mycolicibacterium fortuitum subsp. fortuitum	strain=JCM 6387	GCA_022179545.1	144549	1766	type	True	79.1348	690	1486	95	below_threshold
Mycolicibacterium baixiangningiae	strain=LJ126	GCA_014893035.1	2761578	2761578	type	True	79.0457	687	1486	95	below_threshold
Mycolicibacterium vinylchloridicum	strain=CECT 8761	GCA_013404075.1	2736928	2736928	type	True	78.9599	700	1486	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:15:13,839] [INFO] DFAST Taxonomy check result was written to GCF_010726505.1_ASM1072650v1_genomic.fna/tc_result.tsv
[2024-01-24 14:15:13,839] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:15:13,840] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:15:13,840] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg45836cae-ee98-4755-ab53-a32e1f4552c4/dqc_reference/checkm_data
[2024-01-24 14:15:13,841] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:15:13,885] [INFO] Task started: CheckM
[2024-01-24 14:15:13,885] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_010726505.1_ASM1072650v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_010726505.1_ASM1072650v1_genomic.fna/checkm_input GCF_010726505.1_ASM1072650v1_genomic.fna/checkm_result
[2024-01-24 14:16:05,029] [INFO] Task succeeded: CheckM
[2024-01-24 14:16:05,030] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:16:05,054] [INFO] ===== Completeness check finished =====
[2024-01-24 14:16:05,054] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:16:05,055] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_010726505.1_ASM1072650v1_genomic.fna/markers.fasta)
[2024-01-24 14:16:05,055] [INFO] Task started: Blastn
[2024-01-24 14:16:05,056] [INFO] Running command: blastn -query GCF_010726505.1_ASM1072650v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg45836cae-ee98-4755-ab53-a32e1f4552c4/dqc_reference/reference_markers_gtdb.fasta -out GCF_010726505.1_ASM1072650v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:16:07,929] [INFO] Task succeeded: Blastn
[2024-01-24 14:16:07,934] [INFO] Selected 12 target genomes.
[2024-01-24 14:16:07,934] [INFO] Target genome list was writen to GCF_010726505.1_ASM1072650v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:16:07,950] [INFO] Task started: fastANI
[2024-01-24 14:16:07,950] [INFO] Running command: fastANI --query /var/lib/cwl/stg3538cb25-30cb-48f0-a6e1-527e2ee0045e/GCF_010726505.1_ASM1072650v1_genomic.fna.gz --refList GCF_010726505.1_ASM1072650v1_genomic.fna/target_genomes_gtdb.txt --output GCF_010726505.1_ASM1072650v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:16:26,293] [INFO] Task succeeded: fastANI
[2024-01-24 14:16:26,372] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:16:26,372] [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_002086455.1	s__Mycobacterium algericum	98.0471	1338	1486	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.66	97.92	0.93	0.90	4	conclusive
GCF_003284925.1	s__Mycobacterium algericum_A	94.2944	1133	1486	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002101885.1	s__Mycobacterium senuense	92.904	1334	1486	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_010727125.1	s__Mycobacterium terrae	87.6405	1245	1486	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	100.00	99.99	1.00	1.00	3	-
GCF_001667375.1	s__Mycobacterium sinense_A	87.5175	1212	1486	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	97.51	95.04	0.94	0.89	3	-
GCF_001667945.1	s__Mycobacterium sinense_B	87.3034	1167	1486	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.61	99.42	0.94	0.94	3	-
GCF_002086285.1	s__Mycobacterium kumamotonense	87.3026	1227	1486	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.55	98.48	0.89	0.87	4	-
GCF_002102265.1	s__Mycobacterium longobardum	86.0492	1162	1486	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001021505.1	s__Mycobacterium heraklionense_B	85.2228	1207	1486	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900078685.2	s__Mycobacterium icosiumassiliensis	84.7151	1092	1486	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001545925.1	s__Mycobacterium sp001545925	79.5842	645	1486	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000612725.1	s__Mycobacterium austroafricanum	79.478	690	1486	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.53	98.42	0.88	0.88	3	-
--------------------------------------------------------------------------------
[2024-01-24 14:16:26,374] [INFO] GTDB search result was written to GCF_010726505.1_ASM1072650v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:16:26,375] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:16:26,378] [INFO] DFAST_QC result json was written to GCF_010726505.1_ASM1072650v1_genomic.fna/dqc_result.json
[2024-01-24 14:16:26,378] [INFO] DFAST_QC completed!
[2024-01-24 14:16:26,378] [INFO] Total running time: 0h1m49s