[2024-01-25 20:27:50,466] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:27:50,467] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:27:50,467] [INFO] DQC Reference Directory: /var/lib/cwl/stg22693e4d-693c-4194-a912-533061929b35/dqc_reference
[2024-01-25 20:27:51,582] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:27:51,583] [INFO] Task started: Prodigal
[2024-01-25 20:27:51,583] [INFO] Running command: gunzip -c /var/lib/cwl/stg327f8b9a-4202-4ad9-9f15-982f4a11d829/GCF_002102335.1_ASM210233v1_genomic.fna.gz | prodigal -d GCF_002102335.1_ASM210233v1_genomic.fna/cds.fna -a GCF_002102335.1_ASM210233v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:28:07,554] [INFO] Task succeeded: Prodigal
[2024-01-25 20:28:07,554] [INFO] Task started: HMMsearch
[2024-01-25 20:28:07,554] [INFO] Running command: hmmsearch --tblout GCF_002102335.1_ASM210233v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg22693e4d-693c-4194-a912-533061929b35/dqc_reference/reference_markers.hmm GCF_002102335.1_ASM210233v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:28:07,837] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:28:07,841] [INFO] Found 6/6 markers.
[2024-01-25 20:28:07,898] [INFO] Query marker FASTA was written to GCF_002102335.1_ASM210233v1_genomic.fna/markers.fasta
[2024-01-25 20:28:07,898] [INFO] Task started: Blastn
[2024-01-25 20:28:07,898] [INFO] Running command: blastn -query GCF_002102335.1_ASM210233v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg22693e4d-693c-4194-a912-533061929b35/dqc_reference/reference_markers.fasta -out GCF_002102335.1_ASM210233v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:28:09,042] [INFO] Task succeeded: Blastn
[2024-01-25 20:28:09,044] [INFO] Selected 18 target genomes.
[2024-01-25 20:28:09,045] [INFO] Target genome list was writen to GCF_002102335.1_ASM210233v1_genomic.fna/target_genomes.txt
[2024-01-25 20:28:09,068] [INFO] Task started: fastANI
[2024-01-25 20:28:09,068] [INFO] Running command: fastANI --query /var/lib/cwl/stg327f8b9a-4202-4ad9-9f15-982f4a11d829/GCF_002102335.1_ASM210233v1_genomic.fna.gz --refList GCF_002102335.1_ASM210233v1_genomic.fna/target_genomes.txt --output GCF_002102335.1_ASM210233v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:28:32,877] [INFO] Task succeeded: fastANI
[2024-01-25 20:28:32,878] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg22693e4d-693c-4194-a912-533061929b35/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:28:32,878] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg22693e4d-693c-4194-a912-533061929b35/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:28:32,890] [INFO] Found 18 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 20:28:32,890] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:28:32,890] [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=DSM 44553	GCA_002102335.1	185642	185642	type	True	100.0	1916	1922	95	conclusive
Mycobacterium parmense	strain=JCM 14742	GCA_010730575.1	185642	185642	type	True	99.996	1922	1922	95	conclusive
Mycobacterium nebraskense	strain=DSM 44803	GCA_002102255.1	244292	244292	type	True	84.6093	1362	1922	95	below_threshold
Mycobacterium helveticum	strain=16-83	GCA_007714205.1	2592811	2592811	type	True	84.5545	1218	1922	95	below_threshold
Mycobacterium heidelbergense	strain=JCM 14842	GCA_010730745.1	53376	53376	type	True	83.7157	1185	1922	95	below_threshold
Mycobacterium heidelbergense	strain=DSM 44471	GCA_002086215.1	53376	53376	type	True	83.6793	1152	1922	95	below_threshold
Mycobacterium paraense	strain=IEC26	GCA_002101815.1	767916	767916	type	True	83.6668	1278	1922	95	below_threshold
Mycobacterium avium subsp. avium	strain=DSM 44156	GCA_009741445.1	44454	1764	type	True	83.6214	1180	1922	95	below_threshold
Mycobacterium avium subsp. avium	strain=ATCC 25291	GCA_000174035.1	44454	1764	type	True	83.5701	1113	1922	95	below_threshold
Mycobacterium seoulense	strain=JCM 16018	GCA_010731595.1	386911	386911	type	True	83.477	1255	1922	95	below_threshold
Mycobacterium bohemicum	strain=DSM 44277	GCA_002102025.1	56425	56425	type	True	83.2983	1260	1922	95	below_threshold
Mycobacterium colombiense	strain=CECT 3035	GCA_000222105.4	339268	339268	suspected-type	True	83.2435	1238	1922	95	below_threshold
Mycobacterium bohemicum	strain=DSM 44277	GCA_001053185.1	56425	56425	type	True	83.2002	1212	1922	95	below_threshold
Mycobacterium colombiense	strain=CECT 3035	GCA_002105755.1	339268	339268	suspected-type	True	83.1883	1244	1922	95	below_threshold
Mycobacterium paraintracellulare	strain=MOTT64	GCA_000276825.1	1138383	1138383	suspected-type	True	83.1573	1227	1922	95	below_threshold
Mycobacterium paraintracellulare	strain=JCM 30622	GCA_010731935.1	1138383	1138383	suspected-type	True	83.1021	1243	1922	95	below_threshold
Mycobacterium marseillense	strain=JCM 17324	GCA_010731675.1	701042	701042	type	True	82.927	1199	1922	95	below_threshold
Mycobacterium ahvazicum	strain=AFP003	GCA_900176255.2	1964395	1964395	type	True	82.0485	1177	1922	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:28:32,892] [INFO] DFAST Taxonomy check result was written to GCF_002102335.1_ASM210233v1_genomic.fna/tc_result.tsv
[2024-01-25 20:28:32,892] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:28:32,892] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:28:32,892] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg22693e4d-693c-4194-a912-533061929b35/dqc_reference/checkm_data
[2024-01-25 20:28:32,893] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:28:32,949] [INFO] Task started: CheckM
[2024-01-25 20:28:32,949] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002102335.1_ASM210233v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002102335.1_ASM210233v1_genomic.fna/checkm_input GCF_002102335.1_ASM210233v1_genomic.fna/checkm_result
[2024-01-25 20:29:28,440] [INFO] Task succeeded: CheckM
[2024-01-25 20:29:28,441] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:29:28,460] [INFO] ===== Completeness check finished =====
[2024-01-25 20:29:28,460] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:29:28,461] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002102335.1_ASM210233v1_genomic.fna/markers.fasta)
[2024-01-25 20:29:28,461] [INFO] Task started: Blastn
[2024-01-25 20:29:28,461] [INFO] Running command: blastn -query GCF_002102335.1_ASM210233v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg22693e4d-693c-4194-a912-533061929b35/dqc_reference/reference_markers_gtdb.fasta -out GCF_002102335.1_ASM210233v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:29:30,101] [INFO] Task succeeded: Blastn
[2024-01-25 20:29:30,104] [INFO] Selected 19 target genomes.
[2024-01-25 20:29:30,105] [INFO] Target genome list was writen to GCF_002102335.1_ASM210233v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:29:30,183] [INFO] Task started: fastANI
[2024-01-25 20:29:30,183] [INFO] Running command: fastANI --query /var/lib/cwl/stg327f8b9a-4202-4ad9-9f15-982f4a11d829/GCF_002102335.1_ASM210233v1_genomic.fna.gz --refList GCF_002102335.1_ASM210233v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002102335.1_ASM210233v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:29:56,406] [INFO] Task succeeded: fastANI
[2024-01-25 20:29:56,429] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:29:56,429] [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	99.996	1922	1922	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	84.8097	1386	1922	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	84.6092	1362	1922	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.58	99.42	0.93	0.92	4	-
GCF_002101815.1	s__Mycobacterium paraense	83.6936	1275	1922	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.85	98.84	0.95	0.95	4	-
GCF_010730745.1	s__Mycobacterium heidelbergense	83.6927	1188	1922	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_009741445.1	s__Mycobacterium avium	83.5998	1184	1922	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	83.5446	1215	1922	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	83.4075	1274	1922	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.46	99.46	0.97	0.97	2	-
GCF_001667015.1	s__Mycobacterium sp001667015	83.4048	1238	1922	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	83.3979	1280	1922	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.26	99.26	0.97	0.97	2	-
GCF_900157385.1	s__Mycobacterium terramassiliense	83.3729	1301	1922	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002104765.1	s__Mycobacterium vulneris	83.3455	1308	1922	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001667185.1	s__Mycobacterium sp001667185	83.2964	1244	1922	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	83.2941	1255	1922	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	97.65	95.35	0.92	0.88	4	-
GCF_001053185.1	s__Mycobacterium bohemicum	83.2283	1208	1922	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.81	99.81	0.97	0.97	2	-
GCF_001666835.1	s__Mycobacterium sp001666835	83.1143	1208	1922	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	83.0693	1155	1922	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	82.8742	1218	1922	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	82.8004	1132	1922	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 20:29:56,431] [INFO] GTDB search result was written to GCF_002102335.1_ASM210233v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:29:56,431] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:29:56,435] [INFO] DFAST_QC result json was written to GCF_002102335.1_ASM210233v1_genomic.fna/dqc_result.json
[2024-01-25 20:29:56,435] [INFO] DFAST_QC completed!
[2024-01-25 20:29:56,435] [INFO] Total running time: 0h2m6s