[2024-01-24 11:34:43,082] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:34:43,088] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:34:43,088] [INFO] DQC Reference Directory: /var/lib/cwl/stg54fb34ee-fba9-4a55-bf81-b1cdf9fb12d5/dqc_reference
[2024-01-24 11:34:44,586] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:34:44,587] [INFO] Task started: Prodigal
[2024-01-24 11:34:44,587] [INFO] Running command: gunzip -c /var/lib/cwl/stg21a0ca21-7c2a-481b-bd94-e9dc9e487c88/GCF_002086715.1_ASM208671v1_genomic.fna.gz | prodigal -d GCF_002086715.1_ASM208671v1_genomic.fna/cds.fna -a GCF_002086715.1_ASM208671v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:35:04,119] [INFO] Task succeeded: Prodigal
[2024-01-24 11:35:04,120] [INFO] Task started: HMMsearch
[2024-01-24 11:35:04,120] [INFO] Running command: hmmsearch --tblout GCF_002086715.1_ASM208671v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg54fb34ee-fba9-4a55-bf81-b1cdf9fb12d5/dqc_reference/reference_markers.hmm GCF_002086715.1_ASM208671v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:35:04,427] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:35:04,428] [INFO] Found 6/6 markers.
[2024-01-24 11:35:04,474] [INFO] Query marker FASTA was written to GCF_002086715.1_ASM208671v1_genomic.fna/markers.fasta
[2024-01-24 11:35:04,475] [INFO] Task started: Blastn
[2024-01-24 11:35:04,475] [INFO] Running command: blastn -query GCF_002086715.1_ASM208671v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg54fb34ee-fba9-4a55-bf81-b1cdf9fb12d5/dqc_reference/reference_markers.fasta -out GCF_002086715.1_ASM208671v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:35:05,602] [INFO] Task succeeded: Blastn
[2024-01-24 11:35:05,605] [INFO] Selected 14 target genomes.
[2024-01-24 11:35:05,606] [INFO] Target genome list was writen to GCF_002086715.1_ASM208671v1_genomic.fna/target_genomes.txt
[2024-01-24 11:35:05,611] [INFO] Task started: fastANI
[2024-01-24 11:35:05,611] [INFO] Running command: fastANI --query /var/lib/cwl/stg21a0ca21-7c2a-481b-bd94-e9dc9e487c88/GCF_002086715.1_ASM208671v1_genomic.fna.gz --refList GCF_002086715.1_ASM208671v1_genomic.fna/target_genomes.txt --output GCF_002086715.1_ASM208671v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:35:21,677] [INFO] Task succeeded: fastANI
[2024-01-24 11:35:21,678] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg54fb34ee-fba9-4a55-bf81-b1cdf9fb12d5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:35:21,678] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg54fb34ee-fba9-4a55-bf81-b1cdf9fb12d5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:35:21,699] [INFO] Found 14 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:35:21,700] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:35:21,700] [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
Mycobacteroides saopaulense	strain=CCUG 66554	GCA_002086715.1	1578165	1578165	type	True	100.0	1679	1683	95	conclusive
Mycobacteroides saopaulense	strain=EPM10906	GCA_001456355.1	1578165	1578165	type	True	99.4425	1471	1683	95	conclusive
Mycobacteroides franklinii	strain=DSM 45524	GCA_004355025.1	948102	948102	type	True	85.7355	1316	1683	95	below_threshold
Mycobacteroides franklinii	strain=DSM 45524	GCA_002086225.1	948102	948102	type	True	85.7028	1307	1683	95	below_threshold
Mycobacteroides franklinii	strain=CV002	GCA_002013895.1	948102	948102	type	True	85.6811	1307	1683	95	below_threshold
[Mycobacterium] chelonae subsp. chelonae	strain=DSM 43804	GCA_004355245.1	2099321	1774	type	True	85.5064	1306	1683	95	below_threshold
Mycobacteroides chelonae	strain=ATCC 35752	GCA_001942545.1	1774	1774	suspected-type	True	85.4972	1310	1683	95	below_threshold
Mycobacteroides chelonae	strain=CCUG 47445	GCA_001632805.1	1774	1774	suspected-type	True	85.4791	1315	1683	95	below_threshold
Mycobacteroides immunogenum	strain=ATCC 700505	GCA_002101665.1	83262	83262	type	True	85.3403	1289	1683	95	below_threshold
Mycobacteroides immunogenum	strain=MC 779	GCA_002013555.1	83262	83262	type	True	85.2934	1298	1683	95	below_threshold
Mycobacteroides immunogenum	strain=CCUG 47286	GCA_001605725.1	83262	83262	type	True	85.2638	1302	1683	95	below_threshold
Mycobacteroides abscessus subsp. bolletii	strain=BD	GCA_000239035.2	319705	36809	type	True	85.1385	1296	1683	95	below_threshold
Mycobacteroides abscessus subsp. bolletii	strain=CIP 108541	GCA_001792615.1	319705	36809	type	True	85.1226	1266	1683	95	below_threshold
Mycobacteroides abscessus subsp. bolletii	strain=CCUG 50184	GCA_006409125.1	319705	36809	type	True	85.0866	1279	1683	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:35:21,702] [INFO] DFAST Taxonomy check result was written to GCF_002086715.1_ASM208671v1_genomic.fna/tc_result.tsv
[2024-01-24 11:35:21,703] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:35:21,703] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:35:21,703] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg54fb34ee-fba9-4a55-bf81-b1cdf9fb12d5/dqc_reference/checkm_data
[2024-01-24 11:35:21,705] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:35:21,759] [INFO] Task started: CheckM
[2024-01-24 11:35:21,759] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002086715.1_ASM208671v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002086715.1_ASM208671v1_genomic.fna/checkm_input GCF_002086715.1_ASM208671v1_genomic.fna/checkm_result
[2024-01-24 11:36:17,217] [INFO] Task succeeded: CheckM
[2024-01-24 11:36:17,218] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:36:17,235] [INFO] ===== Completeness check finished =====
[2024-01-24 11:36:17,235] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:36:17,236] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002086715.1_ASM208671v1_genomic.fna/markers.fasta)
[2024-01-24 11:36:17,236] [INFO] Task started: Blastn
[2024-01-24 11:36:17,236] [INFO] Running command: blastn -query GCF_002086715.1_ASM208671v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg54fb34ee-fba9-4a55-bf81-b1cdf9fb12d5/dqc_reference/reference_markers_gtdb.fasta -out GCF_002086715.1_ASM208671v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:36:18,947] [INFO] Task succeeded: Blastn
[2024-01-24 11:36:18,950] [INFO] Selected 8 target genomes.
[2024-01-24 11:36:18,951] [INFO] Target genome list was writen to GCF_002086715.1_ASM208671v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:36:18,958] [INFO] Task started: fastANI
[2024-01-24 11:36:18,958] [INFO] Running command: fastANI --query /var/lib/cwl/stg21a0ca21-7c2a-481b-bd94-e9dc9e487c88/GCF_002086715.1_ASM208671v1_genomic.fna.gz --refList GCF_002086715.1_ASM208671v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002086715.1_ASM208671v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:36:28,610] [INFO] Task succeeded: fastANI
[2024-01-24 11:36:28,622] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:36:28,622] [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_001456355.1	s__Mycobacterium saopaulense	99.4425	1471	1683	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.82	98.51	0.95	0.95	4	conclusive
GCF_014204435.1	s__Mycobacterium chelonae_A	94.3882	1164	1683	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002013895.1	s__Mycobacterium franklinii	85.7072	1303	1683	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.20	95.66	0.94	0.87	12	-
GCF_002356335.1	s__Mycobacterium stephanolepidis	85.5626	1286	1683	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001632805.1	s__Mycobacterium chelonae	85.4791	1315	1683	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	95.73	95.27	0.90	0.84	73	-
GCF_002013465.1	s__Mycobacterium sp002013465	85.4526	1315	1683	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	95.45	95.17	0.93	0.91	7	-
GCA_000069185.1	s__Mycobacterium abscessus	85.3268	1305	1683	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.55	96.83	0.93	0.86	1820	-
GCF_001605725.1	s__Mycobacterium immunogenum	85.2625	1303	1683	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.78	96.59	0.98	0.90	18	-
--------------------------------------------------------------------------------
[2024-01-24 11:36:28,623] [INFO] GTDB search result was written to GCF_002086715.1_ASM208671v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:36:28,624] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:36:28,627] [INFO] DFAST_QC result json was written to GCF_002086715.1_ASM208671v1_genomic.fna/dqc_result.json
[2024-01-24 11:36:28,627] [INFO] DFAST_QC completed!
[2024-01-24 11:36:28,627] [INFO] Total running time: 0h1m46s