[2024-01-24 11:21:07,404] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:21:07,407] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:21:07,407] [INFO] DQC Reference Directory: /var/lib/cwl/stge86d3cbc-5e7c-4e34-bcd8-c6357eba6aa5/dqc_reference
[2024-01-24 11:21:11,962] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:21:11,963] [INFO] Task started: Prodigal
[2024-01-24 11:21:11,964] [INFO] Running command: gunzip -c /var/lib/cwl/stg67bbe968-72ed-4314-871c-ad06d52aee8e/GCF_002086545.1_ASM208654v1_genomic.fna.gz | prodigal -d GCF_002086545.1_ASM208654v1_genomic.fna/cds.fna -a GCF_002086545.1_ASM208654v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:21:30,884] [INFO] Task succeeded: Prodigal
[2024-01-24 11:21:30,885] [INFO] Task started: HMMsearch
[2024-01-24 11:21:30,885] [INFO] Running command: hmmsearch --tblout GCF_002086545.1_ASM208654v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge86d3cbc-5e7c-4e34-bcd8-c6357eba6aa5/dqc_reference/reference_markers.hmm GCF_002086545.1_ASM208654v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:21:31,191] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:21:31,193] [INFO] Found 6/6 markers.
[2024-01-24 11:21:31,244] [INFO] Query marker FASTA was written to GCF_002086545.1_ASM208654v1_genomic.fna/markers.fasta
[2024-01-24 11:21:31,244] [INFO] Task started: Blastn
[2024-01-24 11:21:31,244] [INFO] Running command: blastn -query GCF_002086545.1_ASM208654v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge86d3cbc-5e7c-4e34-bcd8-c6357eba6aa5/dqc_reference/reference_markers.fasta -out GCF_002086545.1_ASM208654v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:21:32,398] [INFO] Task succeeded: Blastn
[2024-01-24 11:21:32,401] [INFO] Selected 16 target genomes.
[2024-01-24 11:21:32,402] [INFO] Target genome list was writen to GCF_002086545.1_ASM208654v1_genomic.fna/target_genomes.txt
[2024-01-24 11:21:32,409] [INFO] Task started: fastANI
[2024-01-24 11:21:32,409] [INFO] Running command: fastANI --query /var/lib/cwl/stg67bbe968-72ed-4314-871c-ad06d52aee8e/GCF_002086545.1_ASM208654v1_genomic.fna.gz --refList GCF_002086545.1_ASM208654v1_genomic.fna/target_genomes.txt --output GCF_002086545.1_ASM208654v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:21:54,015] [INFO] Task succeeded: fastANI
[2024-01-24 11:21:54,016] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge86d3cbc-5e7c-4e34-bcd8-c6357eba6aa5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:21:54,016] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge86d3cbc-5e7c-4e34-bcd8-c6357eba6aa5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:21:54,031] [INFO] Found 16 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:21:54,032] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:21:54,032] [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 asiaticum	strain=DSM 44297	GCA_002086545.1	1790	1790	suspected-type	True	100.0	1937	1942	95	conclusive
Mycobacterium asiaticum	strain=DSM 44297	GCA_000613245.1	1790	1790	suspected-type	True	99.9418	1930	1942	95	conclusive
Mycobacterium paragordonae	strain=49061	GCA_003614435.1	1389713	1389713	type	True	81.9942	1395	1942	95	below_threshold
Mycobacterium paragordonae	strain=JCM 18565	GCA_010723415.1	1389713	1389713	type	True	81.9176	1422	1942	95	below_threshold
Mycobacterium gordonae	strain=DSM 44160	GCA_002101675.1	1778	1778	type	True	81.7262	1311	1942	95	below_threshold
Mycobacterium avium subsp. avium	strain=ATCC 25291	GCA_000174035.1	44454	1764	type	True	81.1812	978	1942	95	below_threshold
Mycobacterium avium subsp. avium	strain=DSM 44156	GCA_009741445.1	44454	1764	type	True	81.1637	1054	1942	95	below_threshold
Mycobacterium palustre	strain=DSM 44572	GCA_002101785.1	153971	153971	type	True	80.9055	1023	1942	95	below_threshold
Mycobacterium angelicum	strain=DSM 45057	GCA_002086155.1	470074	470074	type	True	80.872	1108	1942	95	below_threshold
Mycobacterium kubicae	strain=JCM 13573	GCA_010723135.1	120959	120959	type	True	80.7565	1107	1942	95	below_threshold
Mycobacterium kubicae	strain=JCM 13573	GCA_015689175.1	120959	120959	type	True	80.6959	1122	1942	95	below_threshold
Mycobacterium kubicae	strain=CIP 106428	GCA_002101745.1	120959	120959	type	True	80.6804	1113	1942	95	below_threshold
Mycobacterium bohemicum	strain=DSM 44277	GCA_002102025.1	56425	56425	type	True	80.6496	1033	1942	95	below_threshold
Mycobacterium szulgai	strain=DSM 44166	GCA_002116635.1	1787	1787	type	True	80.6021	1114	1942	95	below_threshold
Mycobacterium conspicuum	strain=DSM 44136	GCA_002102095.1	44010	44010	type	True	80.5964	1085	1942	95	below_threshold
Mycobacterium conspicuum	strain=JCM 14738	GCA_010730195.1	44010	44010	type	True	80.503	1118	1942	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:21:54,034] [INFO] DFAST Taxonomy check result was written to GCF_002086545.1_ASM208654v1_genomic.fna/tc_result.tsv
[2024-01-24 11:21:54,035] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:21:54,035] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:21:54,036] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge86d3cbc-5e7c-4e34-bcd8-c6357eba6aa5/dqc_reference/checkm_data
[2024-01-24 11:21:54,037] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:21:54,092] [INFO] Task started: CheckM
[2024-01-24 11:21:54,093] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002086545.1_ASM208654v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002086545.1_ASM208654v1_genomic.fna/checkm_input GCF_002086545.1_ASM208654v1_genomic.fna/checkm_result
[2024-01-24 11:22:47,549] [INFO] Task succeeded: CheckM
[2024-01-24 11:22:47,551] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:22:47,572] [INFO] ===== Completeness check finished =====
[2024-01-24 11:22:47,572] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:22:47,573] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002086545.1_ASM208654v1_genomic.fna/markers.fasta)
[2024-01-24 11:22:47,573] [INFO] Task started: Blastn
[2024-01-24 11:22:47,573] [INFO] Running command: blastn -query GCF_002086545.1_ASM208654v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge86d3cbc-5e7c-4e34-bcd8-c6357eba6aa5/dqc_reference/reference_markers_gtdb.fasta -out GCF_002086545.1_ASM208654v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:22:49,357] [INFO] Task succeeded: Blastn
[2024-01-24 11:22:49,360] [INFO] Selected 13 target genomes.
[2024-01-24 11:22:49,360] [INFO] Target genome list was writen to GCF_002086545.1_ASM208654v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:22:49,397] [INFO] Task started: fastANI
[2024-01-24 11:22:49,398] [INFO] Running command: fastANI --query /var/lib/cwl/stg67bbe968-72ed-4314-871c-ad06d52aee8e/GCF_002086545.1_ASM208654v1_genomic.fna.gz --refList GCF_002086545.1_ASM208654v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002086545.1_ASM208654v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:23:09,563] [INFO] Task succeeded: fastANI
[2024-01-24 11:23:09,574] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:23:09,574] [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_000613245.1	s__Mycobacterium asiaticum	99.9414	1930	1942	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.95	98.52	0.95	0.93	5	conclusive
GCF_001673635.1	s__Mycobacterium asiaticum_C	92.0729	1750	1942	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.07	99.07	0.94	0.94	2	-
GCF_001668675.1	s__Mycobacterium asiaticum_D	91.9559	1623	1942	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001673315.1	s__Mycobacterium asiaticum_B	84.285	1415	1942	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003614435.1	s__Mycobacterium paragordonae	82.0068	1392	1942	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.23	97.83	0.93	0.88	9	-
GCF_001417955.2	s__Mycobacterium gordonae_B	81.9764	1360	1942	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001673365.1	s__Mycobacterium asiaticum_A	81.6753	1275	1942	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017086405.1	s__Mycobacterium gordonae_D	81.4664	1302	1942	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001672915.1	s__Mycobacterium sp001672915	80.8631	1085	1942	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002086155.1	s__Mycobacterium angelicum	80.8514	1113	1942	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015689175.1	s__Mycobacterium kubicae	80.6947	1122	1942	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.05	97.98	0.96	0.92	7	-
GCF_002116635.1	s__Mycobacterium szulgai	80.5664	1119	1942	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002086275.1	s__Mycobacterium intermedium	80.4131	1161	1942	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.91	99.88	0.97	0.95	3	-
--------------------------------------------------------------------------------
[2024-01-24 11:23:09,575] [INFO] GTDB search result was written to GCF_002086545.1_ASM208654v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:23:09,576] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:23:09,581] [INFO] DFAST_QC result json was written to GCF_002086545.1_ASM208654v1_genomic.fna/dqc_result.json
[2024-01-24 11:23:09,581] [INFO] DFAST_QC completed!
[2024-01-24 11:23:09,582] [INFO] Total running time: 0h2m2s