[2024-01-24 13:24:12,285] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:24:12,287] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:24:12,287] [INFO] DQC Reference Directory: /var/lib/cwl/stg59c31df7-dc05-4bf1-bc25-92e282046425/dqc_reference
[2024-01-24 13:24:13,464] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:24:13,465] [INFO] Task started: Prodigal
[2024-01-24 13:24:13,465] [INFO] Running command: gunzip -c /var/lib/cwl/stg612754df-85cd-4918-a6a6-22fd410753c8/GCF_009741445.1_ASM974144v1_genomic.fna.gz | prodigal -d GCF_009741445.1_ASM974144v1_genomic.fna/cds.fna -a GCF_009741445.1_ASM974144v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:24:30,104] [INFO] Task succeeded: Prodigal
[2024-01-24 13:24:30,105] [INFO] Task started: HMMsearch
[2024-01-24 13:24:30,105] [INFO] Running command: hmmsearch --tblout GCF_009741445.1_ASM974144v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg59c31df7-dc05-4bf1-bc25-92e282046425/dqc_reference/reference_markers.hmm GCF_009741445.1_ASM974144v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:24:30,322] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:24:30,323] [INFO] Found 6/6 markers.
[2024-01-24 13:24:30,363] [INFO] Query marker FASTA was written to GCF_009741445.1_ASM974144v1_genomic.fna/markers.fasta
[2024-01-24 13:24:30,363] [INFO] Task started: Blastn
[2024-01-24 13:24:30,363] [INFO] Running command: blastn -query GCF_009741445.1_ASM974144v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg59c31df7-dc05-4bf1-bc25-92e282046425/dqc_reference/reference_markers.fasta -out GCF_009741445.1_ASM974144v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:24:31,546] [INFO] Task succeeded: Blastn
[2024-01-24 13:24:31,549] [INFO] Selected 16 target genomes.
[2024-01-24 13:24:31,550] [INFO] Target genome list was writen to GCF_009741445.1_ASM974144v1_genomic.fna/target_genomes.txt
[2024-01-24 13:24:31,565] [INFO] Task started: fastANI
[2024-01-24 13:24:31,565] [INFO] Running command: fastANI --query /var/lib/cwl/stg612754df-85cd-4918-a6a6-22fd410753c8/GCF_009741445.1_ASM974144v1_genomic.fna.gz --refList GCF_009741445.1_ASM974144v1_genomic.fna/target_genomes.txt --output GCF_009741445.1_ASM974144v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:24:51,952] [INFO] Task succeeded: fastANI
[2024-01-24 13:24:51,952] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg59c31df7-dc05-4bf1-bc25-92e282046425/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:24:51,952] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg59c31df7-dc05-4bf1-bc25-92e282046425/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:24:51,965] [INFO] Found 16 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:24:51,966] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:24:51,966] [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 avium subsp. avium	strain=DSM 44156	GCA_009741445.1	44454	1764	type	True	100.0	1649	1652	95	conclusive
Mycobacterium avium subsp. avium	strain=ATCC 25291	GCA_000174035.1	44454	1764	type	True	99.8952	1492	1652	95	conclusive
Mycobacterium intracellulare	strain=ATCC 13950	GCA_023278525.1	1767	1767	suspected-type	True	87.8572	1417	1652	95	below_threshold
Mycobacterium intracellulare	strain=ATCC 13950	GCA_000277125.1	1767	1767	suspected-type	True	87.8531	1418	1652	95	below_threshold
Mycobacterium paraintracellulare	strain=KCTC 29084	GCA_002104735.1	1138383	1138383	suspected-type	True	87.7915	1411	1652	95	below_threshold
Mycobacterium paraintracellulare	strain=JCM 30622	GCA_010731935.1	1138383	1138383	suspected-type	True	87.7765	1459	1652	95	below_threshold
Mycobacterium paraintracellulare	strain=MOTT64	GCA_000276825.1	1138383	1138383	suspected-type	True	87.7496	1444	1652	95	below_threshold
Mycobacterium intracellulare	strain=ATCC 13950	GCA_000172115.1	1767	1767	suspected-type	True	87.6967	1265	1652	95	below_threshold
Mycobacterium marseillense	strain=JCM 17324	GCA_010731675.1	701042	701042	type	True	87.1022	1425	1652	95	below_threshold
Mycobacterium marseillense	strain=DSM 45437	GCA_002086345.1	701042	701042	type	True	87.0951	1392	1652	95	below_threshold
Mycobacterium colombiense	strain=CECT 3035	GCA_000222105.4	339268	339268	suspected-type	True	86.9867	1447	1652	95	below_threshold
Mycobacterium colombiense	strain=CECT 3035	GCA_002105755.1	339268	339268	suspected-type	True	86.9866	1452	1652	95	below_threshold
Mycobacterium mantenii	strain=JCM 18113	GCA_010731775.1	560555	560555	type	True	86.5384	1411	1652	95	below_threshold
Mycobacterium arosiense	strain=DSM 45069	GCA_002086125.1	425468	425468	type	True	86.3126	1296	1652	95	below_threshold
Mycobacterium parmense	strain=DSM 44553	GCA_002102335.1	185642	185642	type	True	83.5924	1183	1652	95	below_threshold
Mycobacterium parmense	strain=JCM 14742	GCA_010730575.1	185642	185642	type	True	83.5643	1215	1652	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:24:51,967] [INFO] DFAST Taxonomy check result was written to GCF_009741445.1_ASM974144v1_genomic.fna/tc_result.tsv
[2024-01-24 13:24:51,968] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:24:51,968] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:24:51,968] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg59c31df7-dc05-4bf1-bc25-92e282046425/dqc_reference/checkm_data
[2024-01-24 13:24:51,969] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:24:52,014] [INFO] Task started: CheckM
[2024-01-24 13:24:52,014] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009741445.1_ASM974144v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009741445.1_ASM974144v1_genomic.fna/checkm_input GCF_009741445.1_ASM974144v1_genomic.fna/checkm_result
[2024-01-24 13:25:47,974] [INFO] Task succeeded: CheckM
[2024-01-24 13:25:47,975] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:25:47,992] [INFO] ===== Completeness check finished =====
[2024-01-24 13:25:47,992] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:25:47,992] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009741445.1_ASM974144v1_genomic.fna/markers.fasta)
[2024-01-24 13:25:47,992] [INFO] Task started: Blastn
[2024-01-24 13:25:47,993] [INFO] Running command: blastn -query GCF_009741445.1_ASM974144v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg59c31df7-dc05-4bf1-bc25-92e282046425/dqc_reference/reference_markers_gtdb.fasta -out GCF_009741445.1_ASM974144v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:25:49,737] [INFO] Task succeeded: Blastn
[2024-01-24 13:25:49,740] [INFO] Selected 17 target genomes.
[2024-01-24 13:25:49,740] [INFO] Target genome list was writen to GCF_009741445.1_ASM974144v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:25:49,762] [INFO] Task started: fastANI
[2024-01-24 13:25:49,762] [INFO] Running command: fastANI --query /var/lib/cwl/stg612754df-85cd-4918-a6a6-22fd410753c8/GCF_009741445.1_ASM974144v1_genomic.fna.gz --refList GCF_009741445.1_ASM974144v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009741445.1_ASM974144v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:26:12,624] [INFO] Task succeeded: fastANI
[2024-01-24 13:26:12,638] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:26:12,638] [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_009741445.1	s__Mycobacterium avium	100.0	1651	1652	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	96.9043	98.75	98.29	0.92	0.84	206	conclusive
GCA_002291465.1	s__Mycobacterium lepraemurium	96.8054	1309	1652	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	96.9043	N/A	N/A	N/A	N/A	1	-
GCF_000277125.1	s__Mycobacterium intracellulare	87.8504	1419	1652	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.48	95.71	0.93	0.84	82	-
GCF_010731675.1	s__Mycobacterium marseillense	87.124	1422	1652	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.64	95.51	0.95	0.90	6	-
GCF_002105755.1	s__Mycobacterium colombiense	86.9624	1454	1652	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.60	97.75	0.94	0.91	4	-
GCF_001672755.1	s__Mycobacterium colombiense_C	86.8875	1370	1652	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004298145.1	s__Mycobacterium sp004298145	86.8327	1336	1652	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001667315.1	s__Mycobacterium sp001667315	86.8316	1377	1652	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003284935.1	s__Mycobacterium arosiense_A	86.8132	1314	1652	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001665835.1	s__Mycobacterium colombiense_A	86.7069	1407	1652	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001667275.1	s__Mycobacterium sp001667275	84.8635	1295	1652	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	96.42	96.39	0.93	0.93	5	-
GCF_002102155.1	s__Mycobacterium europaeum	84.781	1267	1652	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.26	99.26	0.97	0.97	2	-
GCF_000164135.1	s__Mycobacterium parascrofulaceum	84.7736	1296	1652	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	97.18	96.53	0.89	0.85	6	-
GCF_002086735.1	s__Mycobacterium scrofulaceum	84.7021	1264	1652	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	84.1691	1276	1652	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.04	99.01	0.94	0.94	3	-
GCA_002102225.1	s__Mycobacterium interjectum_B	83.923	1230	1652	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010730575.1	s__Mycobacterium parmense	83.5634	1217	1652	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:26:12,640] [INFO] GTDB search result was written to GCF_009741445.1_ASM974144v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:26:12,640] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:26:12,644] [INFO] DFAST_QC result json was written to GCF_009741445.1_ASM974144v1_genomic.fna/dqc_result.json
[2024-01-24 13:26:12,644] [INFO] DFAST_QC completed!
[2024-01-24 13:26:12,644] [INFO] Total running time: 0h2m0s