[2024-01-24 13:32:41,991] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:32:41,992] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:32:41,993] [INFO] DQC Reference Directory: /var/lib/cwl/stgb15e1bf0-0012-4f3b-803f-7777a5d02dc6/dqc_reference
[2024-01-24 13:32:43,264] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:32:43,265] [INFO] Task started: Prodigal
[2024-01-24 13:32:43,265] [INFO] Running command: gunzip -c /var/lib/cwl/stgf9750db1-5eda-4286-9e24-6a6ac8725411/GCF_010723675.1_ASM1072367v1_genomic.fna.gz | prodigal -d GCF_010723675.1_ASM1072367v1_genomic.fna/cds.fna -a GCF_010723675.1_ASM1072367v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:33:09,344] [INFO] Task succeeded: Prodigal
[2024-01-24 13:33:09,344] [INFO] Task started: HMMsearch
[2024-01-24 13:33:09,344] [INFO] Running command: hmmsearch --tblout GCF_010723675.1_ASM1072367v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb15e1bf0-0012-4f3b-803f-7777a5d02dc6/dqc_reference/reference_markers.hmm GCF_010723675.1_ASM1072367v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:33:10,000] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:33:10,001] [INFO] Found 6/6 markers.
[2024-01-24 13:33:10,068] [INFO] Query marker FASTA was written to GCF_010723675.1_ASM1072367v1_genomic.fna/markers.fasta
[2024-01-24 13:33:10,069] [INFO] Task started: Blastn
[2024-01-24 13:33:10,069] [INFO] Running command: blastn -query GCF_010723675.1_ASM1072367v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb15e1bf0-0012-4f3b-803f-7777a5d02dc6/dqc_reference/reference_markers.fasta -out GCF_010723675.1_ASM1072367v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:33:11,292] [INFO] Task succeeded: Blastn
[2024-01-24 13:33:11,298] [INFO] Selected 15 target genomes.
[2024-01-24 13:33:11,299] [INFO] Target genome list was writen to GCF_010723675.1_ASM1072367v1_genomic.fna/target_genomes.txt
[2024-01-24 13:33:11,311] [INFO] Task started: fastANI
[2024-01-24 13:33:11,311] [INFO] Running command: fastANI --query /var/lib/cwl/stgf9750db1-5eda-4286-9e24-6a6ac8725411/GCF_010723675.1_ASM1072367v1_genomic.fna.gz --refList GCF_010723675.1_ASM1072367v1_genomic.fna/target_genomes.txt --output GCF_010723675.1_ASM1072367v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:33:33,312] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:33,312] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb15e1bf0-0012-4f3b-803f-7777a5d02dc6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:33:33,313] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb15e1bf0-0012-4f3b-803f-7777a5d02dc6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:33:33,338] [INFO] Found 15 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:33:33,338] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:33:33,338] [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 marseillense	strain=JCM 17324	GCA_010731675.1	701042	701042	type	True	95.5228	1656	1897	95	conclusive
Mycobacterium marseillense	strain=DSM 45437	GCA_002086345.1	701042	701042	type	True	95.5225	1594	1897	95	conclusive
Mycobacterium intracellulare	strain=ATCC 13950	GCA_000277125.1	1767	1767	suspected-type	True	93.1517	1631	1897	95	below_threshold
Mycobacterium intracellulare	strain=ATCC 13950	GCA_023278525.1	1767	1767	suspected-type	True	93.1484	1629	1897	95	below_threshold
Mycobacterium intracellulare subsp. yongonense	strain=05-1390	GCA_000418535.2	1203599	1767	type	True	93.1067	1634	1897	95	below_threshold
Mycobacterium intracellulare	strain=ATCC 13950	GCA_000172115.1	1767	1767	suspected-type	True	93.0849	1439	1897	95	below_threshold
Mycobacterium intracellulare subsp. chimaera	strain=JCM_14737	GCA_001938095.1	222805	1767	type	True	92.8805	1587	1897	95	below_threshold
Mycobacterium paraintracellulare	strain=KCTC 29084	GCA_002104735.1	1138383	1138383	suspected-type	True	92.8588	1563	1897	95	below_threshold
Mycobacterium intracellulare subsp. chimaera	strain=DSM 44623	GCA_002101575.1	222805	1767	type	True	92.8488	1570	1897	95	below_threshold
Mycobacterium intracellulare subsp. chimaera	strain=DSM 44623	GCA_002219285.1	222805	1767	type	True	92.8381	1602	1897	95	below_threshold
Mycobacterium paraintracellulare	strain=MOTT64	GCA_000276825.1	1138383	1138383	suspected-type	True	92.83	1606	1897	95	below_threshold
Mycobacterium paraintracellulare	strain=JCM 30622	GCA_010731935.1	1138383	1138383	suspected-type	True	92.8141	1608	1897	95	below_threshold
Mycobacterium mantenii	strain=DSM 45255	GCA_002086335.1	560555	560555	type	True	86.9684	1485	1897	95	below_threshold
Mycobacterium mantenii	strain=JCM 18113	GCA_010731775.1	560555	560555	type	True	86.9203	1524	1897	95	below_threshold
Mycobacterium palustre	strain=DSM 44572	GCA_002101785.1	153971	153971	type	True	83.5006	1203	1897	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:33:33,340] [INFO] DFAST Taxonomy check result was written to GCF_010723675.1_ASM1072367v1_genomic.fna/tc_result.tsv
[2024-01-24 13:33:33,341] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:33:33,341] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:33:33,341] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb15e1bf0-0012-4f3b-803f-7777a5d02dc6/dqc_reference/checkm_data
[2024-01-24 13:33:33,342] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:33:33,406] [INFO] Task started: CheckM
[2024-01-24 13:33:33,406] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_010723675.1_ASM1072367v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_010723675.1_ASM1072367v1_genomic.fna/checkm_input GCF_010723675.1_ASM1072367v1_genomic.fna/checkm_result
[2024-01-24 13:34:52,030] [INFO] Task succeeded: CheckM
[2024-01-24 13:34:52,032] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.52%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:34:52,060] [INFO] ===== Completeness check finished =====
[2024-01-24 13:34:52,060] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:34:52,060] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_010723675.1_ASM1072367v1_genomic.fna/markers.fasta)
[2024-01-24 13:34:52,061] [INFO] Task started: Blastn
[2024-01-24 13:34:52,061] [INFO] Running command: blastn -query GCF_010723675.1_ASM1072367v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb15e1bf0-0012-4f3b-803f-7777a5d02dc6/dqc_reference/reference_markers_gtdb.fasta -out GCF_010723675.1_ASM1072367v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:34:53,878] [INFO] Task succeeded: Blastn
[2024-01-24 13:34:53,881] [INFO] Selected 19 target genomes.
[2024-01-24 13:34:53,881] [INFO] Target genome list was writen to GCF_010723675.1_ASM1072367v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:34:53,891] [INFO] Task started: fastANI
[2024-01-24 13:34:53,891] [INFO] Running command: fastANI --query /var/lib/cwl/stgf9750db1-5eda-4286-9e24-6a6ac8725411/GCF_010723675.1_ASM1072367v1_genomic.fna.gz --refList GCF_010723675.1_ASM1072367v1_genomic.fna/target_genomes_gtdb.txt --output GCF_010723675.1_ASM1072367v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:35:20,938] [INFO] Task succeeded: fastANI
[2024-01-24 13:35:20,983] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:35:20,984] [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_010731675.1	s__Mycobacterium marseillense	95.5125	1657	1897	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.64	95.51	0.95	0.90	6	conclusive
GCF_000277125.1	s__Mycobacterium intracellulare	93.1517	1631	1897	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.48	95.71	0.93	0.84	82	-
GCF_001667315.1	s__Mycobacterium sp001667315	90.9147	1480	1897	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	89.8573	1433	1897	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	87.5259	1477	1897	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001953985.1	s__Mycobacterium colombiense_B	87.4889	1470	1897	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	97.54	96.91	0.93	0.88	12	-
GCF_001665835.1	s__Mycobacterium colombiense_A	87.4495	1449	1897	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	87.2989	1409	1897	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003284975.1	s__Mycobacterium europaeum_A	86.9998	1351	1897	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	95.84	95.70	0.84	0.79	6	-
GCF_010731775.1	s__Mycobacterium mantenii	86.9151	1525	1897	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	96.19	95.22	0.92	0.90	6	-
GCF_000164135.1	s__Mycobacterium parascrofulaceum	84.3939	1389	1897	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	97.18	96.53	0.89	0.85	6	-
GCF_002101815.1	s__Mycobacterium paraense	83.9252	1287	1897	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.85	98.84	0.95	0.95	4	-
GCF_001667775.1	s__Mycobacterium sp001667775	83.8614	1170	1897	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	83.8045	1218	1897	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002086305.1	s__Mycobacterium malmoense_B	83.8013	1174	1897	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.01	99.01	0.95	0.95	2	-
GCF_001665295.1	s__Mycobacterium sp001665295	83.5488	1242	1897	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002101785.1	s__Mycobacterium palustre	83.4789	1205	1897	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	82.6988	1185	1897	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	81.0806	1070	1897	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:35:20,986] [INFO] GTDB search result was written to GCF_010723675.1_ASM1072367v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:35:20,987] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:35:20,994] [INFO] DFAST_QC result json was written to GCF_010723675.1_ASM1072367v1_genomic.fna/dqc_result.json
[2024-01-24 13:35:20,995] [INFO] DFAST_QC completed!
[2024-01-24 13:35:20,995] [INFO] Total running time: 0h2m39s