[2024-01-24 11:35:34,785] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:35:34,787] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:35:34,787] [INFO] DQC Reference Directory: /var/lib/cwl/stg230c8678-7090-4c14-880c-f9285b5cc147/dqc_reference
[2024-01-24 11:35:35,997] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:35:35,998] [INFO] Task started: Prodigal
[2024-01-24 11:35:35,998] [INFO] Running command: gunzip -c /var/lib/cwl/stg7331ddb7-938b-4a8f-8bd4-87abfbdddc53/GCF_000340435.2_ASM34043v3_genomic.fna.gz | prodigal -d GCF_000340435.2_ASM34043v3_genomic.fna/cds.fna -a GCF_000340435.2_ASM34043v3_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:35:51,705] [INFO] Task succeeded: Prodigal
[2024-01-24 11:35:51,706] [INFO] Task started: HMMsearch
[2024-01-24 11:35:51,706] [INFO] Running command: hmmsearch --tblout GCF_000340435.2_ASM34043v3_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg230c8678-7090-4c14-880c-f9285b5cc147/dqc_reference/reference_markers.hmm GCF_000340435.2_ASM34043v3_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:35:51,960] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:35:51,962] [INFO] Found 6/6 markers.
[2024-01-24 11:35:51,999] [INFO] Query marker FASTA was written to GCF_000340435.2_ASM34043v3_genomic.fna/markers.fasta
[2024-01-24 11:35:52,000] [INFO] Task started: Blastn
[2024-01-24 11:35:52,000] [INFO] Running command: blastn -query GCF_000340435.2_ASM34043v3_genomic.fna/markers.fasta -db /var/lib/cwl/stg230c8678-7090-4c14-880c-f9285b5cc147/dqc_reference/reference_markers.fasta -out GCF_000340435.2_ASM34043v3_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:35:52,935] [INFO] Task succeeded: Blastn
[2024-01-24 11:35:52,938] [INFO] Selected 19 target genomes.
[2024-01-24 11:35:52,938] [INFO] Target genome list was writen to GCF_000340435.2_ASM34043v3_genomic.fna/target_genomes.txt
[2024-01-24 11:35:52,956] [INFO] Task started: fastANI
[2024-01-24 11:35:52,956] [INFO] Running command: fastANI --query /var/lib/cwl/stg7331ddb7-938b-4a8f-8bd4-87abfbdddc53/GCF_000340435.2_ASM34043v3_genomic.fna.gz --refList GCF_000340435.2_ASM34043v3_genomic.fna/target_genomes.txt --output GCF_000340435.2_ASM34043v3_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:36:12,080] [INFO] Task succeeded: fastANI
[2024-01-24 11:36:12,081] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg230c8678-7090-4c14-880c-f9285b5cc147/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:36:12,081] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg230c8678-7090-4c14-880c-f9285b5cc147/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:36:12,107] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:36:12,107] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:36:12,107] [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 haemophilum	strain=ATCC 29548	GCA_000340435.3	29311	29311	type	True	100.0	1410	1411	95	conclusive
Mycobacterium lepromatosis	strain=FJ924	GCA_000975265.2	480418	480418	type	True	84.967	905	1411	95	below_threshold
Mycobacterium heidelbergense	strain=DSM 44471	GCA_002086215.1	53376	53376	type	True	82.1246	897	1411	95	below_threshold
Mycobacterium heidelbergense	strain=JCM 14842	GCA_010730745.1	53376	53376	type	True	82.0139	920	1411	95	below_threshold
Mycobacterium lacus	strain=DSM 44577	GCA_002102215.1	169765	169765	type	True	81.947	931	1411	95	below_threshold
Mycobacterium lacus	strain=JCM 15657	GCA_010731535.1	169765	169765	type	True	81.8317	969	1411	95	below_threshold
Mycobacterium shinjukuense	strain=CCUG 53584	GCA_002086755.1	398694	398694	type	True	81.2955	861	1411	95	below_threshold
Mycobacterium shinjukuense	strain=JCM 14233	GCA_010730055.1	398694	398694	type	True	81.2658	875	1411	95	below_threshold
Mycobacterium conspicuum	strain=DSM 44136	GCA_002102095.1	44010	44010	type	True	81.1589	868	1411	95	below_threshold
Mycobacterium conspicuum	strain=JCM 14738	GCA_010730195.1	44010	44010	type	True	81.0857	879	1411	95	below_threshold
Mycobacterium paraense	strain=IEC26	GCA_002101815.1	767916	767916	type	True	81.0057	880	1411	95	below_threshold
Mycobacterium tuberculosis variant africanum	strain=ATCC 25420	GCA_002982335.1	33894	1773	type	True	80.9172	849	1411	95	below_threshold
Mycobacterium tuberculosis variant microti	strain=ATCC 19422	GCA_002982215.1	1806	1773	type	True	80.8791	819	1411	95	below_threshold
Mycobacterium riyadhense	strain=DSM 45176	GCA_002101845.1	486698	486698	type	True	80.8687	893	1411	95	below_threshold
Mycobacterium tuberculosis	strain=H37Rv	GCA_000195955.2	1773	1773	type	True	80.846	871	1411	95	below_threshold
Mycobacterium innocens	strain=MK13	GCA_900566055.1	2341083	2341083	type	True	80.539	855	1411	95	below_threshold
Mycobacterium angelicum	strain=DSM 45057	GCA_002086155.1	470074	470074	type	True	80.4176	851	1411	95	below_threshold
Mycobacterium marseillense	strain=JCM 17324	GCA_010731675.1	701042	701042	type	True	80.3445	827	1411	95	below_threshold
Mycobacterium bohemicum	strain=DSM 44277	GCA_002102025.1	56425	56425	type	True	80.2728	808	1411	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:36:12,109] [INFO] DFAST Taxonomy check result was written to GCF_000340435.2_ASM34043v3_genomic.fna/tc_result.tsv
[2024-01-24 11:36:12,109] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:36:12,109] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:36:12,110] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg230c8678-7090-4c14-880c-f9285b5cc147/dqc_reference/checkm_data
[2024-01-24 11:36:12,112] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:36:12,154] [INFO] Task started: CheckM
[2024-01-24 11:36:12,154] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000340435.2_ASM34043v3_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000340435.2_ASM34043v3_genomic.fna/checkm_input GCF_000340435.2_ASM34043v3_genomic.fna/checkm_result
[2024-01-24 11:36:59,312] [INFO] Task succeeded: CheckM
[2024-01-24 11:36:59,313] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:36:59,332] [INFO] ===== Completeness check finished =====
[2024-01-24 11:36:59,333] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:36:59,333] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000340435.2_ASM34043v3_genomic.fna/markers.fasta)
[2024-01-24 11:36:59,334] [INFO] Task started: Blastn
[2024-01-24 11:36:59,334] [INFO] Running command: blastn -query GCF_000340435.2_ASM34043v3_genomic.fna/markers.fasta -db /var/lib/cwl/stg230c8678-7090-4c14-880c-f9285b5cc147/dqc_reference/reference_markers_gtdb.fasta -out GCF_000340435.2_ASM34043v3_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:37:00,659] [INFO] Task succeeded: Blastn
[2024-01-24 11:37:00,663] [INFO] Selected 18 target genomes.
[2024-01-24 11:37:00,663] [INFO] Target genome list was writen to GCF_000340435.2_ASM34043v3_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:37:00,679] [INFO] Task started: fastANI
[2024-01-24 11:37:00,679] [INFO] Running command: fastANI --query /var/lib/cwl/stg7331ddb7-938b-4a8f-8bd4-87abfbdddc53/GCF_000340435.2_ASM34043v3_genomic.fna.gz --refList GCF_000340435.2_ASM34043v3_genomic.fna/target_genomes_gtdb.txt --output GCF_000340435.2_ASM34043v3_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:37:20,003] [INFO] Task succeeded: fastANI
[2024-01-24 11:37:20,028] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:37:20,028] [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_000340435.2	s__Mycobacterium haemophilum	100.0	1410	1411	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.07	99.06	0.94	0.94	5	conclusive
GCF_000195855.1	s__Mycobacterium leprae	85.2544	908	1411	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.97	99.91	1.00	0.99	6	-
GCF_000966355.1	s__Mycobacterium lepromatosis	85.1208	863	1411	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.85	99.85	0.96	0.96	2	-
GCF_003408705.1	s__Mycobacterium uberis	84.9891	880	1411	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	82.1043	928	1411	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.01	99.01	0.95	0.95	2	-
GCF_010730745.1	s__Mycobacterium heidelbergense	82.0374	916	1411	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_010731535.1	s__Mycobacterium lacus	81.8274	969	1411	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.99	99.99	0.99	0.99	2	-
GCF_010730055.1	s__Mycobacterium shinjukuense	81.2624	875	1411	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.98	99.98	1.00	1.00	2	-
GCF_001667035.1	s__Mycobacterium sp001667035	81.2225	883	1411	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010730195.1	s__Mycobacterium conspicuum	81.0765	880	1411	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.99	99.99	1.00	1.00	2	-
GCF_001667015.1	s__Mycobacterium sp001667015	81.0499	834	1411	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002101815.1	s__Mycobacterium paraense	80.9957	882	1411	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.85	98.84	0.95	0.95	4	-
GCF_002101845.1	s__Mycobacterium riyadhense	80.8639	894	1411	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.42	99.30	0.97	0.96	10	-
GCF_000195955.2	s__Mycobacterium tuberculosis	80.8412	871	1411	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.92	97.88	0.99	0.91	6836	-
GCF_001667115.1	s__Mycobacterium sp001667115	80.8189	815	1411	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900566055.1	s__Mycobacterium innocens	80.5712	849	1411	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.27	98.57	0.94	0.90	3	-
GCF_002086155.1	s__Mycobacterium angelicum	80.4256	848	1411	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008370645.1	s__Mycobacterium simiae_A	79.593	723	1411	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 11:37:20,030] [INFO] GTDB search result was written to GCF_000340435.2_ASM34043v3_genomic.fna/result_gtdb.tsv
[2024-01-24 11:37:20,030] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:37:20,034] [INFO] DFAST_QC result json was written to GCF_000340435.2_ASM34043v3_genomic.fna/dqc_result.json
[2024-01-24 11:37:20,034] [INFO] DFAST_QC completed!
[2024-01-24 11:37:20,034] [INFO] Total running time: 0h1m45s