[2024-01-24 13:01:18,996] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:01:19,001] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:01:19,001] [INFO] DQC Reference Directory: /var/lib/cwl/stg28c2b3f1-80c3-44e9-9c47-8a62757537f4/dqc_reference
[2024-01-24 13:01:20,292] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:01:20,293] [INFO] Task started: Prodigal
[2024-01-24 13:01:20,293] [INFO] Running command: gunzip -c /var/lib/cwl/stg86d6f98b-0a82-4565-8a80-f36cff79c9cb/GCF_000174035.1_ASM17403v1_genomic.fna.gz | prodigal -d GCF_000174035.1_ASM17403v1_genomic.fna/cds.fna -a GCF_000174035.1_ASM17403v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:01:34,608] [INFO] Task succeeded: Prodigal
[2024-01-24 13:01:34,608] [INFO] Task started: HMMsearch
[2024-01-24 13:01:34,608] [INFO] Running command: hmmsearch --tblout GCF_000174035.1_ASM17403v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg28c2b3f1-80c3-44e9-9c47-8a62757537f4/dqc_reference/reference_markers.hmm GCF_000174035.1_ASM17403v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:01:34,888] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:01:34,890] [INFO] Found 6/6 markers.
[2024-01-24 13:01:34,941] [INFO] Query marker FASTA was written to GCF_000174035.1_ASM17403v1_genomic.fna/markers.fasta
[2024-01-24 13:01:34,942] [INFO] Task started: Blastn
[2024-01-24 13:01:34,942] [INFO] Running command: blastn -query GCF_000174035.1_ASM17403v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg28c2b3f1-80c3-44e9-9c47-8a62757537f4/dqc_reference/reference_markers.fasta -out GCF_000174035.1_ASM17403v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:01:36,175] [INFO] Task succeeded: Blastn
[2024-01-24 13:01:36,179] [INFO] Selected 16 target genomes.
[2024-01-24 13:01:36,180] [INFO] Target genome list was writen to GCF_000174035.1_ASM17403v1_genomic.fna/target_genomes.txt
[2024-01-24 13:01:36,199] [INFO] Task started: fastANI
[2024-01-24 13:01:36,200] [INFO] Running command: fastANI --query /var/lib/cwl/stg86d6f98b-0a82-4565-8a80-f36cff79c9cb/GCF_000174035.1_ASM17403v1_genomic.fna.gz --refList GCF_000174035.1_ASM17403v1_genomic.fna/target_genomes.txt --output GCF_000174035.1_ASM17403v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:01:55,970] [INFO] Task succeeded: fastANI
[2024-01-24 13:01:55,971] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg28c2b3f1-80c3-44e9-9c47-8a62757537f4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:01:55,971] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg28c2b3f1-80c3-44e9-9c47-8a62757537f4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:01:55,989] [INFO] Found 16 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:01:55,989] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:01:55,990] [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=ATCC 25291	GCA_000174035.1	44454	1764	type	True	100.0	1500	1509	95	conclusive
Mycobacterium avium subsp. avium	strain=DSM 44156	GCA_009741445.1	44454	1764	type	True	99.9966	1509	1509	95	conclusive
Mycobacterium paraintracellulare	strain=KCTC 29084	GCA_002104735.1	1138383	1138383	suspected-type	True	87.9022	1316	1509	95	below_threshold
Mycobacterium paraintracellulare	strain=JCM 30622	GCA_010731935.1	1138383	1138383	suspected-type	True	87.8921	1354	1509	95	below_threshold
Mycobacterium intracellulare	strain=ATCC 13950	GCA_000172115.1	1767	1767	suspected-type	True	87.8692	1205	1509	95	below_threshold
Mycobacterium paraintracellulare	strain=MOTT64	GCA_000276825.1	1138383	1138383	suspected-type	True	87.8687	1349	1509	95	below_threshold
Mycobacterium intracellulare	strain=ATCC 13950	GCA_023278525.1	1767	1767	suspected-type	True	87.8342	1350	1509	95	below_threshold
Mycobacterium intracellulare	strain=ATCC 13950	GCA_000277125.1	1767	1767	suspected-type	True	87.8211	1350	1509	95	below_threshold
Mycobacterium marseillense	strain=JCM 17324	GCA_010731675.1	701042	701042	type	True	87.1178	1336	1509	95	below_threshold
Mycobacterium colombiense	strain=CECT 3035	GCA_002105755.1	339268	339268	suspected-type	True	87.0668	1357	1509	95	below_threshold
Mycobacterium colombiense	strain=CECT 3035	GCA_000222105.4	339268	339268	suspected-type	True	87.0558	1355	1509	95	below_threshold
Mycobacterium marseillense	strain=DSM 45437	GCA_002086345.1	701042	701042	type	True	87.0453	1324	1509	95	below_threshold
Mycobacterium mantenii	strain=JCM 18113	GCA_010731775.1	560555	560555	type	True	86.5842	1325	1509	95	below_threshold
Mycobacterium arosiense	strain=DSM 45069	GCA_002086125.1	425468	425468	type	True	86.3172	1226	1509	95	below_threshold
Mycobacterium parmense	strain=DSM 44553	GCA_002102335.1	185642	185642	type	True	83.6853	1116	1509	95	below_threshold
Mycobacterium parmense	strain=JCM 14742	GCA_010730575.1	185642	185642	type	True	83.6774	1126	1509	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:01:55,991] [INFO] DFAST Taxonomy check result was written to GCF_000174035.1_ASM17403v1_genomic.fna/tc_result.tsv
[2024-01-24 13:01:55,992] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:01:55,992] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:01:55,992] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg28c2b3f1-80c3-44e9-9c47-8a62757537f4/dqc_reference/checkm_data
[2024-01-24 13:01:55,993] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:01:56,039] [INFO] Task started: CheckM
[2024-01-24 13:01:56,039] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000174035.1_ASM17403v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000174035.1_ASM17403v1_genomic.fna/checkm_input GCF_000174035.1_ASM17403v1_genomic.fna/checkm_result
[2024-01-24 13:02:40,778] [INFO] Task succeeded: CheckM
[2024-01-24 13:02:40,780] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:02:40,801] [INFO] ===== Completeness check finished =====
[2024-01-24 13:02:40,802] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:02:40,802] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000174035.1_ASM17403v1_genomic.fna/markers.fasta)
[2024-01-24 13:02:40,803] [INFO] Task started: Blastn
[2024-01-24 13:02:40,803] [INFO] Running command: blastn -query GCF_000174035.1_ASM17403v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg28c2b3f1-80c3-44e9-9c47-8a62757537f4/dqc_reference/reference_markers_gtdb.fasta -out GCF_000174035.1_ASM17403v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:02:42,606] [INFO] Task succeeded: Blastn
[2024-01-24 13:02:42,610] [INFO] Selected 17 target genomes.
[2024-01-24 13:02:42,611] [INFO] Target genome list was writen to GCF_000174035.1_ASM17403v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:02:42,627] [INFO] Task started: fastANI
[2024-01-24 13:02:42,627] [INFO] Running command: fastANI --query /var/lib/cwl/stg86d6f98b-0a82-4565-8a80-f36cff79c9cb/GCF_000174035.1_ASM17403v1_genomic.fna.gz --refList GCF_000174035.1_ASM17403v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000174035.1_ASM17403v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:03:05,720] [INFO] Task succeeded: fastANI
[2024-01-24 13:03:05,739] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:03:05,739] [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	99.9966	1509	1509	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	96.7839	1224	1509	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	87.8211	1350	1509	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	87.1434	1332	1509	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	87.0612	1357	1509	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.60	97.75	0.94	0.91	4	-
GCF_001667315.1	s__Mycobacterium sp001667315	86.9542	1278	1509	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	86.9078	1253	1509	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001672755.1	s__Mycobacterium colombiense_C	86.8982	1298	1509	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	86.8836	1261	1509	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	86.8392	1317	1509	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	84.9298	1198	1509	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	84.8745	1190	1509	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	84.7355	1224	1509	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	84.666	1192	1509	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	84.3287	1197	1509	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	84.0613	1167	1509	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	83.7057	1122	1509	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 13:03:05,741] [INFO] GTDB search result was written to GCF_000174035.1_ASM17403v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:03:05,741] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:03:05,745] [INFO] DFAST_QC result json was written to GCF_000174035.1_ASM17403v1_genomic.fna/dqc_result.json
[2024-01-24 13:03:05,745] [INFO] DFAST_QC completed!
[2024-01-24 13:03:05,745] [INFO] Total running time: 0h1m47s