[2024-01-25 17:47:20,525] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:47:20,527] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:47:20,527] [INFO] DQC Reference Directory: /var/lib/cwl/stg49a42440-02b2-4136-95e2-b9c8d9f178db/dqc_reference
[2024-01-25 17:47:21,697] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:47:21,697] [INFO] Task started: Prodigal
[2024-01-25 17:47:21,698] [INFO] Running command: gunzip -c /var/lib/cwl/stg675a17f3-f6d1-4f38-b337-95aacb3837ce/GCF_002013555.1_ASM201355v1_genomic.fna.gz | prodigal -d GCF_002013555.1_ASM201355v1_genomic.fna/cds.fna -a GCF_002013555.1_ASM201355v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:47:43,749] [INFO] Task succeeded: Prodigal
[2024-01-25 17:47:43,750] [INFO] Task started: HMMsearch
[2024-01-25 17:47:43,750] [INFO] Running command: hmmsearch --tblout GCF_002013555.1_ASM201355v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg49a42440-02b2-4136-95e2-b9c8d9f178db/dqc_reference/reference_markers.hmm GCF_002013555.1_ASM201355v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:47:43,995] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:47:43,996] [INFO] Found 6/6 markers.
[2024-01-25 17:47:44,041] [INFO] Query marker FASTA was written to GCF_002013555.1_ASM201355v1_genomic.fna/markers.fasta
[2024-01-25 17:47:44,042] [INFO] Task started: Blastn
[2024-01-25 17:47:44,042] [INFO] Running command: blastn -query GCF_002013555.1_ASM201355v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg49a42440-02b2-4136-95e2-b9c8d9f178db/dqc_reference/reference_markers.fasta -out GCF_002013555.1_ASM201355v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:47:45,069] [INFO] Task succeeded: Blastn
[2024-01-25 17:47:45,072] [INFO] Selected 10 target genomes.
[2024-01-25 17:47:45,072] [INFO] Target genome list was writen to GCF_002013555.1_ASM201355v1_genomic.fna/target_genomes.txt
[2024-01-25 17:47:45,082] [INFO] Task started: fastANI
[2024-01-25 17:47:45,082] [INFO] Running command: fastANI --query /var/lib/cwl/stg675a17f3-f6d1-4f38-b337-95aacb3837ce/GCF_002013555.1_ASM201355v1_genomic.fna.gz --refList GCF_002013555.1_ASM201355v1_genomic.fna/target_genomes.txt --output GCF_002013555.1_ASM201355v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:47:57,106] [INFO] Task succeeded: fastANI
[2024-01-25 17:47:57,107] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg49a42440-02b2-4136-95e2-b9c8d9f178db/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:47:57,107] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg49a42440-02b2-4136-95e2-b9c8d9f178db/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:47:57,115] [INFO] Found 10 fastANI hits (3 hits with ANI > threshold)
[2024-01-25 17:47:57,115] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:47:57,115] [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
Mycobacteroides immunogenum	strain=MC 779	GCA_002013555.1	83262	83262	type	True	100.0	1835	1836	95	conclusive
Mycobacteroides immunogenum	strain=ATCC 700505	GCA_002101665.1	83262	83262	type	True	99.9974	1825	1836	95	conclusive
Mycobacteroides immunogenum	strain=CCUG 47286	GCA_001605725.1	83262	83262	type	True	99.9922	1836	1836	95	conclusive
Mycobacteroides franklinii	strain=DSM 45524	GCA_002086225.1	948102	948102	type	True	86.5623	1399	1836	95	below_threshold
Mycobacteroides abscessus subsp. massiliense	strain=CCUG 48898	GCA_000239055.2	1962118	36809	type	True	86.4088	1338	1836	95	below_threshold
Mycobacteroides abscessus subsp. massiliense	strain=JCM 15300	GCA_000497265.2	1962118	36809	type	True	86.3954	1353	1836	95	below_threshold
Mycobacteroides abscessus subsp. bolletii	strain=CCUG 50184	GCA_006409125.1	319705	36809	type	True	86.3616	1359	1836	95	below_threshold
Mycobacteroides abscessus subsp. bolletii	strain=BD	GCA_000239035.2	319705	36809	type	True	86.3547	1353	1836	95	below_threshold
Mycobacteroides saopaulense	strain=CCUG 66554	GCA_002086715.1	1578165	1578165	type	True	85.3403	1289	1836	95	below_threshold
Mycobacteroides saopaulense	strain=EPM10906	GCA_001456355.1	1578165	1578165	type	True	85.0143	1303	1836	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:47:57,116] [INFO] DFAST Taxonomy check result was written to GCF_002013555.1_ASM201355v1_genomic.fna/tc_result.tsv
[2024-01-25 17:47:57,117] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:47:57,117] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:47:57,117] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg49a42440-02b2-4136-95e2-b9c8d9f178db/dqc_reference/checkm_data
[2024-01-25 17:47:57,122] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:47:57,174] [INFO] Task started: CheckM
[2024-01-25 17:47:57,174] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002013555.1_ASM201355v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002013555.1_ASM201355v1_genomic.fna/checkm_input GCF_002013555.1_ASM201355v1_genomic.fna/checkm_result
[2024-01-25 17:49:00,895] [INFO] Task succeeded: CheckM
[2024-01-25 17:49:00,896] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:49:00,914] [INFO] ===== Completeness check finished =====
[2024-01-25 17:49:00,914] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:49:00,915] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002013555.1_ASM201355v1_genomic.fna/markers.fasta)
[2024-01-25 17:49:00,915] [INFO] Task started: Blastn
[2024-01-25 17:49:00,915] [INFO] Running command: blastn -query GCF_002013555.1_ASM201355v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg49a42440-02b2-4136-95e2-b9c8d9f178db/dqc_reference/reference_markers_gtdb.fasta -out GCF_002013555.1_ASM201355v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:49:02,484] [INFO] Task succeeded: Blastn
[2024-01-25 17:49:02,486] [INFO] Selected 9 target genomes.
[2024-01-25 17:49:02,487] [INFO] Target genome list was writen to GCF_002013555.1_ASM201355v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:49:02,493] [INFO] Task started: fastANI
[2024-01-25 17:49:02,494] [INFO] Running command: fastANI --query /var/lib/cwl/stg675a17f3-f6d1-4f38-b337-95aacb3837ce/GCF_002013555.1_ASM201355v1_genomic.fna.gz --refList GCF_002013555.1_ASM201355v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002013555.1_ASM201355v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:49:13,941] [INFO] Task succeeded: fastANI
[2024-01-25 17:49:13,948] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:49:13,948] [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_001605725.1	s__Mycobacterium immunogenum	99.9922	1836	1836	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.78	96.59	0.98	0.90	18	conclusive
GCF_002013895.1	s__Mycobacterium franklinii	86.495	1418	1836	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.20	95.66	0.94	0.87	12	-
GCA_000069185.1	s__Mycobacterium abscessus	86.4421	1371	1836	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.55	96.83	0.93	0.86	1820	-
GCF_001456355.1	s__Mycobacterium saopaulense	85.0081	1304	1836	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.82	98.51	0.95	0.95	4	-
GCF_014204435.1	s__Mycobacterium chelonae_A	84.6002	1082	1836	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004924335.1	s__Mycobacterium salmoniphilum	84.2439	1266	1836	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	97.49	96.58	0.95	0.92	5	-
GCF_002013465.1	s__Mycobacterium sp002013465	84.1814	1255	1836	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	95.45	95.17	0.93	0.91	7	-
GCF_002356335.1	s__Mycobacterium stephanolepidis	84.1642	1273	1836	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002013415.1	s__Mycobacterium sp002013415	84.0602	1254	1836	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.14	98.85	0.92	0.91	4	-
--------------------------------------------------------------------------------
[2024-01-25 17:49:13,949] [INFO] GTDB search result was written to GCF_002013555.1_ASM201355v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:49:13,949] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:49:13,952] [INFO] DFAST_QC result json was written to GCF_002013555.1_ASM201355v1_genomic.fna/dqc_result.json
[2024-01-25 17:49:13,952] [INFO] DFAST_QC completed!
[2024-01-25 17:49:13,952] [INFO] Total running time: 0h1m53s