[2024-01-25 17:51:50,458] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:51:50,460] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:51:50,460] [INFO] DQC Reference Directory: /var/lib/cwl/stgd46e57c4-5aa3-4c54-9235-90adb160e525/dqc_reference
[2024-01-25 17:51:51,591] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:51:51,592] [INFO] Task started: Prodigal
[2024-01-25 17:51:51,592] [INFO] Running command: gunzip -c /var/lib/cwl/stg204e553b-d5a1-468f-8124-83d3e3cb54b6/GCF_010730575.1_ASM1073057v1_genomic.fna.gz | prodigal -d GCF_010730575.1_ASM1073057v1_genomic.fna/cds.fna -a GCF_010730575.1_ASM1073057v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:52:09,646] [INFO] Task succeeded: Prodigal
[2024-01-25 17:52:09,646] [INFO] Task started: HMMsearch
[2024-01-25 17:52:09,646] [INFO] Running command: hmmsearch --tblout GCF_010730575.1_ASM1073057v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd46e57c4-5aa3-4c54-9235-90adb160e525/dqc_reference/reference_markers.hmm GCF_010730575.1_ASM1073057v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:52:09,958] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:52:09,959] [INFO] Found 6/6 markers.
[2024-01-25 17:52:10,007] [INFO] Query marker FASTA was written to GCF_010730575.1_ASM1073057v1_genomic.fna/markers.fasta
[2024-01-25 17:52:10,007] [INFO] Task started: Blastn
[2024-01-25 17:52:10,007] [INFO] Running command: blastn -query GCF_010730575.1_ASM1073057v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd46e57c4-5aa3-4c54-9235-90adb160e525/dqc_reference/reference_markers.fasta -out GCF_010730575.1_ASM1073057v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:52:11,146] [INFO] Task succeeded: Blastn
[2024-01-25 17:52:11,148] [INFO] Selected 18 target genomes.
[2024-01-25 17:52:11,149] [INFO] Target genome list was writen to GCF_010730575.1_ASM1073057v1_genomic.fna/target_genomes.txt
[2024-01-25 17:52:11,173] [INFO] Task started: fastANI
[2024-01-25 17:52:11,173] [INFO] Running command: fastANI --query /var/lib/cwl/stg204e553b-d5a1-468f-8124-83d3e3cb54b6/GCF_010730575.1_ASM1073057v1_genomic.fna.gz --refList GCF_010730575.1_ASM1073057v1_genomic.fna/target_genomes.txt --output GCF_010730575.1_ASM1073057v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:52:35,144] [INFO] Task succeeded: fastANI
[2024-01-25 17:52:35,145] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd46e57c4-5aa3-4c54-9235-90adb160e525/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:52:35,145] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd46e57c4-5aa3-4c54-9235-90adb160e525/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:52:35,157] [INFO] Found 18 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 17:52:35,157] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:52:35,157] [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 parmense	strain=JCM 14742	GCA_010730575.1	185642	185642	type	True	100.0	1984	1984	95	conclusive
Mycobacterium parmense	strain=DSM 44553	GCA_002102335.1	185642	185642	type	True	99.9562	1917	1984	95	conclusive
Mycobacterium nebraskense	strain=DSM 44803	GCA_002102255.1	244292	244292	type	True	84.6699	1370	1984	95	below_threshold
Mycobacterium helveticum	strain=16-83	GCA_007714205.1	2592811	2592811	type	True	84.5138	1257	1984	95	below_threshold
Mycobacterium heidelbergense	strain=DSM 44471	GCA_002086215.1	53376	53376	type	True	83.7875	1163	1984	95	below_threshold
Mycobacterium heidelbergense	strain=JCM 14842	GCA_010730745.1	53376	53376	type	True	83.7854	1179	1984	95	below_threshold
Mycobacterium paraense	strain=IEC26	GCA_002101815.1	767916	767916	type	True	83.6929	1294	1984	95	below_threshold
Mycobacterium avium subsp. avium	strain=ATCC 25291	GCA_000174035.1	44454	1764	type	True	83.6509	1124	1984	95	below_threshold
Mycobacterium avium subsp. avium	strain=DSM 44156	GCA_009741445.1	44454	1764	type	True	83.6469	1210	1984	95	below_threshold
Mycobacterium seoulense	strain=JCM 16018	GCA_010731595.1	386911	386911	type	True	83.4469	1277	1984	95	below_threshold
Mycobacterium bohemicum	strain=DSM 44277	GCA_002102025.1	56425	56425	type	True	83.4026	1265	1984	95	below_threshold
Mycobacterium bohemicum	strain=DSM 44277	GCA_001053185.1	56425	56425	type	True	83.3576	1215	1984	95	below_threshold
Mycobacterium paraintracellulare	strain=MOTT64	GCA_000276825.1	1138383	1138383	suspected-type	True	83.2892	1223	1984	95	below_threshold
Mycobacterium paraintracellulare	strain=JCM 30622	GCA_010731935.1	1138383	1138383	suspected-type	True	83.1969	1256	1984	95	below_threshold
Mycobacterium colombiense	strain=CECT 3035	GCA_000222105.4	339268	339268	suspected-type	True	83.1585	1271	1984	95	below_threshold
Mycobacterium colombiense	strain=CECT 3035	GCA_002105755.1	339268	339268	suspected-type	True	83.1563	1281	1984	95	below_threshold
Mycobacterium marseillense	strain=JCM 17324	GCA_010731675.1	701042	701042	type	True	82.9332	1215	1984	95	below_threshold
Mycobacterium ahvazicum	strain=AFP003	GCA_900176255.2	1964395	1964395	type	True	82.0068	1205	1984	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:52:35,159] [INFO] DFAST Taxonomy check result was written to GCF_010730575.1_ASM1073057v1_genomic.fna/tc_result.tsv
[2024-01-25 17:52:35,159] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:52:35,159] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:52:35,160] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd46e57c4-5aa3-4c54-9235-90adb160e525/dqc_reference/checkm_data
[2024-01-25 17:52:35,161] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:52:35,217] [INFO] Task started: CheckM
[2024-01-25 17:52:35,218] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_010730575.1_ASM1073057v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_010730575.1_ASM1073057v1_genomic.fna/checkm_input GCF_010730575.1_ASM1073057v1_genomic.fna/checkm_result
[2024-01-25 17:53:40,396] [INFO] Task succeeded: CheckM
[2024-01-25 17:53:40,397] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:53:40,415] [INFO] ===== Completeness check finished =====
[2024-01-25 17:53:40,415] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:53:40,416] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_010730575.1_ASM1073057v1_genomic.fna/markers.fasta)
[2024-01-25 17:53:40,416] [INFO] Task started: Blastn
[2024-01-25 17:53:40,416] [INFO] Running command: blastn -query GCF_010730575.1_ASM1073057v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd46e57c4-5aa3-4c54-9235-90adb160e525/dqc_reference/reference_markers_gtdb.fasta -out GCF_010730575.1_ASM1073057v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:53:42,040] [INFO] Task succeeded: Blastn
[2024-01-25 17:53:42,043] [INFO] Selected 19 target genomes.
[2024-01-25 17:53:42,043] [INFO] Target genome list was writen to GCF_010730575.1_ASM1073057v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:53:42,067] [INFO] Task started: fastANI
[2024-01-25 17:53:42,067] [INFO] Running command: fastANI --query /var/lib/cwl/stg204e553b-d5a1-468f-8124-83d3e3cb54b6/GCF_010730575.1_ASM1073057v1_genomic.fna.gz --refList GCF_010730575.1_ASM1073057v1_genomic.fna/target_genomes_gtdb.txt --output GCF_010730575.1_ASM1073057v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:54:08,615] [INFO] Task succeeded: fastANI
[2024-01-25 17:54:08,627] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:54:08,627] [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_010730575.1	s__Mycobacterium parmense	100.0	1984	1984	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_002086735.1	s__Mycobacterium scrofulaceum	84.9253	1401	1984	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002102255.1	s__Mycobacterium nebraskense	84.6692	1370	1984	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.58	99.42	0.93	0.92	4	-
GCF_010730745.1	s__Mycobacterium heidelbergense	83.7887	1178	1984	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002101815.1	s__Mycobacterium paraense	83.7201	1291	1984	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.85	98.84	0.95	0.95	4	-
GCF_009741445.1	s__Mycobacterium avium	83.61	1219	1984	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	96.9043	98.75	98.29	0.92	0.84	206	-
GCF_001673535.1	s__Mycobacterium sp001673535	83.5394	1227	1984	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002102155.1	s__Mycobacterium europaeum	83.5302	1277	1984	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.26	99.26	0.97	0.97	2	-
GCF_001667015.1	s__Mycobacterium sp001667015	83.4691	1247	1984	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001668725.1	s__Mycobacterium sp001668725	83.4165	1303	1984	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.46	99.46	0.97	0.97	2	-
GCF_900157385.1	s__Mycobacterium terramassiliense	83.3785	1319	1984	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900240975.1	s__Mycobacterium sp900240975	83.3716	1278	1984	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	97.65	95.35	0.92	0.88	4	-
GCF_001667185.1	s__Mycobacterium sp001667185	83.3508	1261	1984	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001053185.1	s__Mycobacterium bohemicum	83.3441	1216	1984	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.81	99.81	0.97	0.97	2	-
GCF_002104765.1	s__Mycobacterium vulneris	83.3064	1353	1984	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001666835.1	s__Mycobacterium sp001666835	83.1524	1211	1984	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.04	99.01	0.94	0.94	3	-
GCF_003284935.1	s__Mycobacterium arosiense_A	83.067	1172	1984	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902652685.1	s__Mycobacterium sp902652685	82.9081	1213	1984	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001666755.1	s__Mycobacterium sp001666755	82.7364	1168	1984	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.50	99.03	0.96	0.95	3	-
--------------------------------------------------------------------------------
[2024-01-25 17:54:08,629] [INFO] GTDB search result was written to GCF_010730575.1_ASM1073057v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:54:08,629] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:54:08,633] [INFO] DFAST_QC result json was written to GCF_010730575.1_ASM1073057v1_genomic.fna/dqc_result.json
[2024-01-25 17:54:08,633] [INFO] DFAST_QC completed!
[2024-01-25 17:54:08,633] [INFO] Total running time: 0h2m18s