[2024-01-24 12:06:24,511] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:06:24,513] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:06:24,513] [INFO] DQC Reference Directory: /var/lib/cwl/stg78440dda-0e47-44b9-8205-37197bc4b67f/dqc_reference
[2024-01-24 12:06:25,828] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:06:25,829] [INFO] Task started: Prodigal
[2024-01-24 12:06:25,829] [INFO] Running command: gunzip -c /var/lib/cwl/stgea522f21-7917-4b26-9702-3a37668fa8f3/GCF_022374935.2_ASM2237493v2_genomic.fna.gz | prodigal -d GCF_022374935.2_ASM2237493v2_genomic.fna/cds.fna -a GCF_022374935.2_ASM2237493v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:06:44,541] [INFO] Task succeeded: Prodigal
[2024-01-24 12:06:44,541] [INFO] Task started: HMMsearch
[2024-01-24 12:06:44,541] [INFO] Running command: hmmsearch --tblout GCF_022374935.2_ASM2237493v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg78440dda-0e47-44b9-8205-37197bc4b67f/dqc_reference/reference_markers.hmm GCF_022374935.2_ASM2237493v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:06:44,783] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:06:44,784] [INFO] Found 6/6 markers.
[2024-01-24 12:06:44,830] [INFO] Query marker FASTA was written to GCF_022374935.2_ASM2237493v2_genomic.fna/markers.fasta
[2024-01-24 12:06:44,831] [INFO] Task started: Blastn
[2024-01-24 12:06:44,831] [INFO] Running command: blastn -query GCF_022374935.2_ASM2237493v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg78440dda-0e47-44b9-8205-37197bc4b67f/dqc_reference/reference_markers.fasta -out GCF_022374935.2_ASM2237493v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:06:46,108] [INFO] Task succeeded: Blastn
[2024-01-24 12:06:46,112] [INFO] Selected 10 target genomes.
[2024-01-24 12:06:46,113] [INFO] Target genome list was writen to GCF_022374935.2_ASM2237493v2_genomic.fna/target_genomes.txt
[2024-01-24 12:06:46,118] [INFO] Task started: fastANI
[2024-01-24 12:06:46,119] [INFO] Running command: fastANI --query /var/lib/cwl/stgea522f21-7917-4b26-9702-3a37668fa8f3/GCF_022374935.2_ASM2237493v2_genomic.fna.gz --refList GCF_022374935.2_ASM2237493v2_genomic.fna/target_genomes.txt --output GCF_022374935.2_ASM2237493v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:07:00,002] [INFO] Task succeeded: fastANI
[2024-01-24 12:07:00,003] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg78440dda-0e47-44b9-8205-37197bc4b67f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:07:00,003] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg78440dda-0e47-44b9-8205-37197bc4b67f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:07:00,013] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:07:00,013] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:07:00,013] [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
Mycolicibacter nonchromogenicus	strain=DSM 44164	GCA_002101775.1	1782	1782	type	True	88.9136	1238	1660	95	below_threshold
Mycolicibacter longobardus	strain=DSM 45394	GCA_002102265.1	1108812	1108812	type	True	86.7827	1255	1660	95	below_threshold
Mycolicibacter engbaekii	strain=ATCC 27353	GCA_002101585.1	188915	188915	type	True	86.2895	1178	1660	95	below_threshold
Mycolicibacter hiberniae	strain=JCM 13571	GCA_010729485.1	29314	29314	type	True	86.1772	1206	1660	95	below_threshold
Mycolicibacter hiberniae	strain=ATCC 49874	GCA_002101655.1	29314	29314	type	True	86.1624	1195	1660	95	below_threshold
Mycolicibacter arupensis	strain=DSM 44942	GCA_002086515.1	342002	342002	type	True	86.0241	1184	1660	95	below_threshold
Mycolicibacter minnesotensis	strain=JCM 17932	GCA_010731755.1	1118379	1118379	type	True	85.9258	1192	1660	95	below_threshold
Mycolicibacter minnesotensis	strain=DSM 45633	GCA_002086405.1	1118379	1118379	type	True	85.8971	1159	1660	95	below_threshold
Mycolicibacter kumamotonensis	strain=CST 7247	GCA_010093495.1	354243	354243	type	True	85.0549	1155	1660	95	below_threshold
Mycolicibacter kumamotonensis	strain=DSM 45093	GCA_002086285.1	354243	354243	type	True	85.0544	1200	1660	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:07:00,015] [INFO] DFAST Taxonomy check result was written to GCF_022374935.2_ASM2237493v2_genomic.fna/tc_result.tsv
[2024-01-24 12:07:00,015] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:07:00,016] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:07:00,016] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg78440dda-0e47-44b9-8205-37197bc4b67f/dqc_reference/checkm_data
[2024-01-24 12:07:00,017] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:07:00,066] [INFO] Task started: CheckM
[2024-01-24 12:07:00,067] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_022374935.2_ASM2237493v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_022374935.2_ASM2237493v2_genomic.fna/checkm_input GCF_022374935.2_ASM2237493v2_genomic.fna/checkm_result
[2024-01-24 12:07:59,464] [INFO] Task succeeded: CheckM
[2024-01-24 12:07:59,465] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:07:59,487] [INFO] ===== Completeness check finished =====
[2024-01-24 12:07:59,487] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:07:59,487] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_022374935.2_ASM2237493v2_genomic.fna/markers.fasta)
[2024-01-24 12:07:59,488] [INFO] Task started: Blastn
[2024-01-24 12:07:59,488] [INFO] Running command: blastn -query GCF_022374935.2_ASM2237493v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg78440dda-0e47-44b9-8205-37197bc4b67f/dqc_reference/reference_markers_gtdb.fasta -out GCF_022374935.2_ASM2237493v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:08:01,225] [INFO] Task succeeded: Blastn
[2024-01-24 12:08:01,228] [INFO] Selected 8 target genomes.
[2024-01-24 12:08:01,229] [INFO] Target genome list was writen to GCF_022374935.2_ASM2237493v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:08:01,235] [INFO] Task started: fastANI
[2024-01-24 12:08:01,235] [INFO] Running command: fastANI --query /var/lib/cwl/stgea522f21-7917-4b26-9702-3a37668fa8f3/GCF_022374935.2_ASM2237493v2_genomic.fna.gz --refList GCF_022374935.2_ASM2237493v2_genomic.fna/target_genomes_gtdb.txt --output GCF_022374935.2_ASM2237493v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:08:13,064] [INFO] Task succeeded: fastANI
[2024-01-24 12:08:13,072] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:08:13,072] [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_001673105.1	s__Mycobacterium heraklionense_A	98.9102	1489	1660	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.02	95.09	0.92	0.90	5	conclusive
GCF_000455125.1	s__Mycobacterium sp000455125	91.591	1312	1660	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.70	98.55	0.90	0.88	3	-
GCF_001021505.1	s__Mycobacterium heraklionense_B	90.4799	1378	1660	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900078685.2	s__Mycobacterium icosiumassiliensis	90.43	1261	1660	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002101775.1	s__Mycobacterium nonchromogenicum	88.9107	1238	1660	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	97.25	96.26	0.92	0.92	3	-
GCF_002101585.1	s__Mycobacterium engbaekii	86.2905	1178	1660	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.4017	N/A	N/A	N/A	N/A	1	-
GCF_002086515.1	s__Mycobacterium arupense	86.0372	1182	1660	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.89	98.19	0.91	0.89	5	-
GCF_010731755.1	s__Mycobacterium minnesotense	85.9337	1191	1660	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 12:08:13,074] [INFO] GTDB search result was written to GCF_022374935.2_ASM2237493v2_genomic.fna/result_gtdb.tsv
[2024-01-24 12:08:13,074] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:08:13,077] [INFO] DFAST_QC result json was written to GCF_022374935.2_ASM2237493v2_genomic.fna/dqc_result.json
[2024-01-24 12:08:13,077] [INFO] DFAST_QC completed!
[2024-01-24 12:08:13,077] [INFO] Total running time: 0h1m49s