[2024-01-25 18:49:35,628] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:49:35,630] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:49:35,630] [INFO] DQC Reference Directory: /var/lib/cwl/stg5201e3eb-0fa1-4e9e-8d0e-dd741f3eca78/dqc_reference
[2024-01-25 18:49:36,842] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:49:36,843] [INFO] Task started: Prodigal
[2024-01-25 18:49:36,843] [INFO] Running command: gunzip -c /var/lib/cwl/stga0b5bc39-85e6-4292-9a86-836ea2b556ec/GCF_025821465.1_ASM2582146v1_genomic.fna.gz | prodigal -d GCF_025821465.1_ASM2582146v1_genomic.fna/cds.fna -a GCF_025821465.1_ASM2582146v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:49:47,224] [INFO] Task succeeded: Prodigal
[2024-01-25 18:49:47,224] [INFO] Task started: HMMsearch
[2024-01-25 18:49:47,224] [INFO] Running command: hmmsearch --tblout GCF_025821465.1_ASM2582146v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5201e3eb-0fa1-4e9e-8d0e-dd741f3eca78/dqc_reference/reference_markers.hmm GCF_025821465.1_ASM2582146v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:49:47,435] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:49:47,436] [INFO] Found 6/6 markers.
[2024-01-25 18:49:47,477] [INFO] Query marker FASTA was written to GCF_025821465.1_ASM2582146v1_genomic.fna/markers.fasta
[2024-01-25 18:49:47,478] [INFO] Task started: Blastn
[2024-01-25 18:49:47,478] [INFO] Running command: blastn -query GCF_025821465.1_ASM2582146v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5201e3eb-0fa1-4e9e-8d0e-dd741f3eca78/dqc_reference/reference_markers.fasta -out GCF_025821465.1_ASM2582146v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:49:48,676] [INFO] Task succeeded: Blastn
[2024-01-25 18:49:48,679] [INFO] Selected 12 target genomes.
[2024-01-25 18:49:48,679] [INFO] Target genome list was writen to GCF_025821465.1_ASM2582146v1_genomic.fna/target_genomes.txt
[2024-01-25 18:49:48,693] [INFO] Task started: fastANI
[2024-01-25 18:49:48,693] [INFO] Running command: fastANI --query /var/lib/cwl/stga0b5bc39-85e6-4292-9a86-836ea2b556ec/GCF_025821465.1_ASM2582146v1_genomic.fna.gz --refList GCF_025821465.1_ASM2582146v1_genomic.fna/target_genomes.txt --output GCF_025821465.1_ASM2582146v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:50:01,863] [INFO] Task succeeded: fastANI
[2024-01-25 18:50:01,864] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5201e3eb-0fa1-4e9e-8d0e-dd741f3eca78/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:50:01,864] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5201e3eb-0fa1-4e9e-8d0e-dd741f3eca78/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:50:01,872] [INFO] Found 12 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 18:50:01,873] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:50:01,873] [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
Mycolicibacterium fallax	strain=JCM 6405	GCA_010726955.1	1793	1793	type	True	99.9828	1254	1292	95	conclusive
Mycolicibacterium fallax	strain=DSM 44179	GCA_002101995.1	1793	1793	type	True	99.96	1265	1292	95	conclusive
Mycolicibacterium insubricum	strain=JCM 16366	GCA_010731615.1	444597	444597	type	True	84.2897	959	1292	95	below_threshold
Mycolicibacterium brumae	strain=ATCC 51384	GCA_025215495.1	85968	85968	type	True	83.9824	811	1292	95	below_threshold
Mycolicibacterium brumae	strain=DSM 44177	GCA_004014795.1	85968	85968	type	True	83.9345	806	1292	95	below_threshold
Mycolicibacterium chitae	strain=NCTC10485	GCA_900637205.1	1792	1792	type	True	81.9909	817	1292	95	below_threshold
Mycolicibacterium chitae	strain=JCM 12403	GCA_010727725.1	1792	1792	type	True	81.9772	823	1292	95	below_threshold
Mycolicibacterium phlei	strain=CCUG 21000	GCA_009192875.1	1771	1771	type	True	81.3899	775	1292	95	below_threshold
Mycolicibacterium phlei	strain=DSM 43239 = CCUG 21000	GCA_001582015.1	1771	1771	type	True	81.3429	777	1292	95	below_threshold
Mycolicibacterium phlei	strain=CCUG 21000	GCA_001583415.1	1771	1771	type	True	81.3214	789	1292	95	below_threshold
Mycolicibacterium chlorophenolicum	strain=NBRC 15527	GCA_001552315.1	37916	37916	type	True	80.5683	748	1292	95	below_threshold
Mycolicibacterium chubuense	strain=DSM 44219	GCA_002086595.1	1800	1800	type	True	80.479	728	1292	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:50:01,874] [INFO] DFAST Taxonomy check result was written to GCF_025821465.1_ASM2582146v1_genomic.fna/tc_result.tsv
[2024-01-25 18:50:01,875] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:50:01,875] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:50:01,875] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5201e3eb-0fa1-4e9e-8d0e-dd741f3eca78/dqc_reference/checkm_data
[2024-01-25 18:50:01,876] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:50:01,918] [INFO] Task started: CheckM
[2024-01-25 18:50:01,919] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025821465.1_ASM2582146v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025821465.1_ASM2582146v1_genomic.fna/checkm_input GCF_025821465.1_ASM2582146v1_genomic.fna/checkm_result
[2024-01-25 18:50:39,736] [INFO] Task succeeded: CheckM
[2024-01-25 18:50:39,737] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.38%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2024-01-25 18:50:39,756] [INFO] ===== Completeness check finished =====
[2024-01-25 18:50:39,756] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:50:39,757] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025821465.1_ASM2582146v1_genomic.fna/markers.fasta)
[2024-01-25 18:50:39,757] [INFO] Task started: Blastn
[2024-01-25 18:50:39,757] [INFO] Running command: blastn -query GCF_025821465.1_ASM2582146v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5201e3eb-0fa1-4e9e-8d0e-dd741f3eca78/dqc_reference/reference_markers_gtdb.fasta -out GCF_025821465.1_ASM2582146v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:50:41,643] [INFO] Task succeeded: Blastn
[2024-01-25 18:50:41,646] [INFO] Selected 17 target genomes.
[2024-01-25 18:50:41,647] [INFO] Target genome list was writen to GCF_025821465.1_ASM2582146v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:50:41,666] [INFO] Task started: fastANI
[2024-01-25 18:50:41,667] [INFO] Running command: fastANI --query /var/lib/cwl/stga0b5bc39-85e6-4292-9a86-836ea2b556ec/GCF_025821465.1_ASM2582146v1_genomic.fna.gz --refList GCF_025821465.1_ASM2582146v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025821465.1_ASM2582146v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:51:00,538] [INFO] Task succeeded: fastANI
[2024-01-25 18:51:00,548] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:51:00,549] [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_010726955.1	s__Mycobacterium fallax	99.9828	1254	1292	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.99	99.99	0.97	0.97	2	conclusive
GCF_010731615.1	s__Mycobacterium insubricum	84.2801	960	1292	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.99	99.99	1.00	1.00	2	-
GCF_004014795.1	s__Mycobacterium brumae	83.9375	806	1292	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.99	99.98	0.98	0.98	3	-
GCF_002592005.1	s__Mycobacterium palauense	81.436	782	1292	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001583415.1	s__Mycobacterium phlei	81.3274	788	1292	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.86	99.38	0.98	0.91	10	-
GCF_001668625.1	s__Mycobacterium sp001668625	81.2848	664	1292	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002102395.1	s__Mycobacterium triviale	81.0994	633	1292	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018455725.1	s__Mycobacterium sp018455725	80.9131	669	1292	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000613185.1	s__Mycobacterium cosmeticum	80.8134	741	1292	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.89	98.33	0.93	0.89	4	-
GCF_010727125.1	s__Mycobacterium terrae	80.7552	694	1292	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	100.00	99.99	1.00	1.00	3	-
GCF_011758805.1	s__Mycobacterium fluoranthenivorans	80.5341	707	1292	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	96.15	95.95	0.85	0.84	4	-
GCF_002086455.1	s__Mycobacterium algericum	80.4145	679	1292	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.66	97.92	0.93	0.90	4	-
GCF_001457595.1	s__Mycobacterium smegmatis	80.3356	709	1292	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.88	98.06	0.95	0.91	32	-
GCF_001667945.1	s__Mycobacterium sinense_B	80.3273	683	1292	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.61	99.42	0.94	0.94	3	-
GCF_001666755.1	s__Mycobacterium sp001666755	80.0354	640	1292	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.50	99.03	0.96	0.95	3	-
GCF_002798385.1	s__Mycobacterium goodii	79.8462	678	1292	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.16	99.12	0.92	0.89	7	-
GCF_002086735.1	s__Mycobacterium scrofulaceum	79.8062	666	1292	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:51:00,550] [INFO] GTDB search result was written to GCF_025821465.1_ASM2582146v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:51:00,550] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:51:00,553] [INFO] DFAST_QC result json was written to GCF_025821465.1_ASM2582146v1_genomic.fna/dqc_result.json
[2024-01-25 18:51:00,553] [INFO] DFAST_QC completed!
[2024-01-25 18:51:00,553] [INFO] Total running time: 0h1m25s