[2024-01-24 13:25:58,054] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:25:58,055] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:25:58,055] [INFO] DQC Reference Directory: /var/lib/cwl/stgd85cbaa4-3456-4d2d-bd8b-54d9e956775c/dqc_reference
[2024-01-24 13:26:00,376] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:26:00,378] [INFO] Task started: Prodigal
[2024-01-24 13:26:00,378] [INFO] Running command: gunzip -c /var/lib/cwl/stgcdbc032b-fc30-4d43-a655-7aeac6637fec/GCF_000157895.3_ASM15789v2_genomic.fna.gz | prodigal -d GCF_000157895.3_ASM15789v2_genomic.fna/cds.fna -a GCF_000157895.3_ASM15789v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:26:23,278] [INFO] Task succeeded: Prodigal
[2024-01-24 13:26:23,279] [INFO] Task started: HMMsearch
[2024-01-24 13:26:23,279] [INFO] Running command: hmmsearch --tblout GCF_000157895.3_ASM15789v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd85cbaa4-3456-4d2d-bd8b-54d9e956775c/dqc_reference/reference_markers.hmm GCF_000157895.3_ASM15789v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:26:23,654] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:26:23,656] [INFO] Found 6/6 markers.
[2024-01-24 13:26:23,711] [INFO] Query marker FASTA was written to GCF_000157895.3_ASM15789v2_genomic.fna/markers.fasta
[2024-01-24 13:26:23,711] [INFO] Task started: Blastn
[2024-01-24 13:26:23,711] [INFO] Running command: blastn -query GCF_000157895.3_ASM15789v2_genomic.fna/markers.fasta -db /var/lib/cwl/stgd85cbaa4-3456-4d2d-bd8b-54d9e956775c/dqc_reference/reference_markers.fasta -out GCF_000157895.3_ASM15789v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:26:24,852] [INFO] Task succeeded: Blastn
[2024-01-24 13:26:24,857] [INFO] Selected 8 target genomes.
[2024-01-24 13:26:24,858] [INFO] Target genome list was writen to GCF_000157895.3_ASM15789v2_genomic.fna/target_genomes.txt
[2024-01-24 13:26:24,861] [INFO] Task started: fastANI
[2024-01-24 13:26:24,862] [INFO] Running command: fastANI --query /var/lib/cwl/stgcdbc032b-fc30-4d43-a655-7aeac6637fec/GCF_000157895.3_ASM15789v2_genomic.fna.gz --refList GCF_000157895.3_ASM15789v2_genomic.fna/target_genomes.txt --output GCF_000157895.3_ASM15789v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:26:40,445] [INFO] Task succeeded: fastANI
[2024-01-24 13:26:40,446] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd85cbaa4-3456-4d2d-bd8b-54d9e956775c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:26:40,446] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd85cbaa4-3456-4d2d-bd8b-54d9e956775c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:26:40,458] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:26:40,459] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:26:40,459] [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 kansasii	strain=ATCC 12478	GCA_000157895.2	1768	1768	type	True	100.0	2190	2192	95	conclusive
Mycobacterium innocens	strain=MK13	GCA_900566055.1	2341083	2341083	type	True	93.3785	1626	2192	95	below_threshold
Mycobacterium pseudokansasii	strain=MK142	GCA_900566075.1	2341080	2341080	type	True	92.8608	1828	2192	95	below_threshold
Mycobacterium persicum	strain=AFPC-000227	GCA_002086675.1	1487726	1487726	type	True	92.6279	1749	2192	95	below_threshold
Mycobacterium ostraviense	strain=241/15	GCA_002705925.1	2738409	2738409	type	True	92.3	1736	2192	95	below_threshold
Mycobacterium gastri	strain=DSM 43505	GCA_002102175.1	1777	1777	type	True	91.5036	1616	2192	95	below_threshold
Mycobacterium attenuatum	strain=MK41	GCA_900566085.1	2341086	2341086	type	True	90.3025	1750	2192	95	below_threshold
Mycobacterium angelicum	strain=DSM 45057	GCA_002086155.1	470074	470074	type	True	81.1674	1263	2192	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:26:40,460] [INFO] DFAST Taxonomy check result was written to GCF_000157895.3_ASM15789v2_genomic.fna/tc_result.tsv
[2024-01-24 13:26:40,461] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:26:40,461] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:26:40,461] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd85cbaa4-3456-4d2d-bd8b-54d9e956775c/dqc_reference/checkm_data
[2024-01-24 13:26:40,462] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:26:40,527] [INFO] Task started: CheckM
[2024-01-24 13:26:40,527] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000157895.3_ASM15789v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000157895.3_ASM15789v2_genomic.fna/checkm_input GCF_000157895.3_ASM15789v2_genomic.fna/checkm_result
[2024-01-24 13:27:46,724] [INFO] Task succeeded: CheckM
[2024-01-24 13:27:46,725] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:27:46,747] [INFO] ===== Completeness check finished =====
[2024-01-24 13:27:46,748] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:27:46,748] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000157895.3_ASM15789v2_genomic.fna/markers.fasta)
[2024-01-24 13:27:46,749] [INFO] Task started: Blastn
[2024-01-24 13:27:46,749] [INFO] Running command: blastn -query GCF_000157895.3_ASM15789v2_genomic.fna/markers.fasta -db /var/lib/cwl/stgd85cbaa4-3456-4d2d-bd8b-54d9e956775c/dqc_reference/reference_markers_gtdb.fasta -out GCF_000157895.3_ASM15789v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:27:48,278] [INFO] Task succeeded: Blastn
[2024-01-24 13:27:48,281] [INFO] Selected 8 target genomes.
[2024-01-24 13:27:48,282] [INFO] Target genome list was writen to GCF_000157895.3_ASM15789v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:27:48,288] [INFO] Task started: fastANI
[2024-01-24 13:27:48,288] [INFO] Running command: fastANI --query /var/lib/cwl/stgcdbc032b-fc30-4d43-a655-7aeac6637fec/GCF_000157895.3_ASM15789v2_genomic.fna.gz --refList GCF_000157895.3_ASM15789v2_genomic.fna/target_genomes_gtdb.txt --output GCF_000157895.3_ASM15789v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:28:02,720] [INFO] Task succeeded: fastANI
[2024-01-24 13:28:02,728] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:28:02,728] [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_000157895.3	s__Mycobacterium kansasii	100.0	2190	2192	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.70	99.15	0.98	0.95	35	conclusive
GCF_900566055.1	s__Mycobacterium innocens	93.3902	1625	2192	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.27	98.57	0.94	0.90	3	-
GCF_900566075.1	s__Mycobacterium pseudokansasii	92.8741	1826	2192	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.70	99.48	0.96	0.94	7	-
GCF_002086675.1	s__Mycobacterium persicum	92.6279	1749	2192	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.71	99.58	0.97	0.95	12	-
GCF_002705925.1	s__Mycobacterium ostraviense	92.3211	1734	2192	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.87	99.87	0.99	0.99	2	-
GCF_002102175.1	s__Mycobacterium gastri	91.504	1616	2192	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.95	99.95	0.95	0.95	2	-
GCF_900566085.1	s__Mycobacterium attenuatum	90.3377	1744	2192	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.59	99.54	0.94	0.93	4	-
GCF_001672915.1	s__Mycobacterium sp001672915	81.1003	1100	2192	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 13:28:02,730] [INFO] GTDB search result was written to GCF_000157895.3_ASM15789v2_genomic.fna/result_gtdb.tsv
[2024-01-24 13:28:02,730] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:28:02,734] [INFO] DFAST_QC result json was written to GCF_000157895.3_ASM15789v2_genomic.fna/dqc_result.json
[2024-01-24 13:28:02,734] [INFO] DFAST_QC completed!
[2024-01-24 13:28:02,734] [INFO] Total running time: 0h2m5s