[2024-01-25 20:27:05,685] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:27:05,686] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:27:05,686] [INFO] DQC Reference Directory: /var/lib/cwl/stg9ddb6b19-fc5a-49d2-8e2c-003779b11164/dqc_reference
[2024-01-25 20:27:06,917] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:27:06,918] [INFO] Task started: Prodigal
[2024-01-25 20:27:06,918] [INFO] Running command: gunzip -c /var/lib/cwl/stg34616e7b-c084-4e88-b52f-109117e706e8/GCF_027886095.1_ASM2788609v1_genomic.fna.gz | prodigal -d GCF_027886095.1_ASM2788609v1_genomic.fna/cds.fna -a GCF_027886095.1_ASM2788609v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:27:20,497] [INFO] Task succeeded: Prodigal
[2024-01-25 20:27:20,498] [INFO] Task started: HMMsearch
[2024-01-25 20:27:20,498] [INFO] Running command: hmmsearch --tblout GCF_027886095.1_ASM2788609v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9ddb6b19-fc5a-49d2-8e2c-003779b11164/dqc_reference/reference_markers.hmm GCF_027886095.1_ASM2788609v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:27:20,818] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:27:20,828] [INFO] Found 6/6 markers.
[2024-01-25 20:27:20,871] [INFO] Query marker FASTA was written to GCF_027886095.1_ASM2788609v1_genomic.fna/markers.fasta
[2024-01-25 20:27:20,871] [INFO] Task started: Blastn
[2024-01-25 20:27:20,871] [INFO] Running command: blastn -query GCF_027886095.1_ASM2788609v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9ddb6b19-fc5a-49d2-8e2c-003779b11164/dqc_reference/reference_markers.fasta -out GCF_027886095.1_ASM2788609v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:27:22,217] [INFO] Task succeeded: Blastn
[2024-01-25 20:27:22,220] [INFO] Selected 5 target genomes.
[2024-01-25 20:27:22,221] [INFO] Target genome list was writen to GCF_027886095.1_ASM2788609v1_genomic.fna/target_genomes.txt
[2024-01-25 20:27:22,222] [INFO] Task started: fastANI
[2024-01-25 20:27:22,222] [INFO] Running command: fastANI --query /var/lib/cwl/stg34616e7b-c084-4e88-b52f-109117e706e8/GCF_027886095.1_ASM2788609v1_genomic.fna.gz --refList GCF_027886095.1_ASM2788609v1_genomic.fna/target_genomes.txt --output GCF_027886095.1_ASM2788609v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:27:28,706] [INFO] Task succeeded: fastANI
[2024-01-25 20:27:28,706] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9ddb6b19-fc5a-49d2-8e2c-003779b11164/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:27:28,706] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9ddb6b19-fc5a-49d2-8e2c-003779b11164/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:27:28,711] [INFO] Found 5 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 20:27:28,712] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:27:28,712] [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
Mycolicibacterium hassiacum	strain=DSM 44199	GCA_000379865.1	46351	46351	type	True	99.9835	1624	1651	95	conclusive
Mycolicibacterium hassiacum	strain=DSM 44199	GCA_000300375.1	46351	46351	type	True	99.9219	1548	1651	95	conclusive
Mycolicibacterium phlei	strain=DSM 43239 = CCUG 21000	GCA_001582015.1	1771	1771	type	True	83.6419	1200	1651	95	below_threshold
Mycolicibacterium phlei	strain=CCUG 21000	GCA_001583415.1	1771	1771	type	True	83.6248	1204	1651	95	below_threshold
Mycolicibacterium phlei	strain=CCUG 21000	GCA_009192875.1	1771	1771	type	True	83.6216	1187	1651	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:27:28,713] [INFO] DFAST Taxonomy check result was written to GCF_027886095.1_ASM2788609v1_genomic.fna/tc_result.tsv
[2024-01-25 20:27:28,714] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:27:28,714] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:27:28,714] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9ddb6b19-fc5a-49d2-8e2c-003779b11164/dqc_reference/checkm_data
[2024-01-25 20:27:28,715] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:27:28,765] [INFO] Task started: CheckM
[2024-01-25 20:27:28,765] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_027886095.1_ASM2788609v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_027886095.1_ASM2788609v1_genomic.fna/checkm_input GCF_027886095.1_ASM2788609v1_genomic.fna/checkm_result
[2024-01-25 20:28:16,523] [INFO] Task succeeded: CheckM
[2024-01-25 20:28:16,524] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:28:16,538] [INFO] ===== Completeness check finished =====
[2024-01-25 20:28:16,538] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:28:16,539] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_027886095.1_ASM2788609v1_genomic.fna/markers.fasta)
[2024-01-25 20:28:16,539] [INFO] Task started: Blastn
[2024-01-25 20:28:16,539] [INFO] Running command: blastn -query GCF_027886095.1_ASM2788609v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9ddb6b19-fc5a-49d2-8e2c-003779b11164/dqc_reference/reference_markers_gtdb.fasta -out GCF_027886095.1_ASM2788609v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:28:18,396] [INFO] Task succeeded: Blastn
[2024-01-25 20:28:18,399] [INFO] Selected 18 target genomes.
[2024-01-25 20:28:18,399] [INFO] Target genome list was writen to GCF_027886095.1_ASM2788609v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:28:18,426] [INFO] Task started: fastANI
[2024-01-25 20:28:18,426] [INFO] Running command: fastANI --query /var/lib/cwl/stg34616e7b-c084-4e88-b52f-109117e706e8/GCF_027886095.1_ASM2788609v1_genomic.fna.gz --refList GCF_027886095.1_ASM2788609v1_genomic.fna/target_genomes_gtdb.txt --output GCF_027886095.1_ASM2788609v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:28:42,030] [INFO] Task succeeded: fastANI
[2024-01-25 20:28:42,041] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:28:42,041] [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_900603025.1	s__Mycobacterium hassiacum	99.9789	1650	1651	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.99	99.99	1.00	1.00	3	conclusive
GCF_001583415.1	s__Mycobacterium phlei	83.6217	1204	1651	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.86	99.38	0.98	0.91	10	-
GCF_900108565.1	s__Mycobacterium rutilum	82.1086	1098	1651	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900187065.1	s__Mycobacterium thermoresistibile	82.0408	1017	1651	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.98	99.97	1.00	1.00	3	-
GCF_004014805.1	s__Mycobacterium elephantis	81.7239	1057	1651	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	96.23	96.21	0.87	0.85	6	-
GCF_010725725.1	s__Mycobacterium pulveris	81.6504	1061	1651	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001050015.1	s__Mycobacterium malmesburyense	81.3788	1032	1651	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014218295.1	s__Mycobacterium litorale_B	81.2497	954	1651	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001044235.1	s__Mycobacterium chlorophenolicum	81.0192	960	1651	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.8643	98.88	97.93	0.94	0.90	4	-
GCA_000762985.1	s__Mycobacterium rufum_A	80.9195	949	1651	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002553505.1	s__Mycobacterium agri	80.9121	916	1651	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.99	99.99	1.00	1.00	2	-
GCF_001457595.1	s__Mycobacterium smegmatis	80.581	959	1651	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.88	98.06	0.95	0.91	32	-
GCF_002592005.1	s__Mycobacterium palauense	80.4352	875	1651	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900078665.2	s__Mycobacterium houstonense	80.3228	918	1651	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010731295.1	s__Mycobacterium boenickei	80.138	924	1651	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.98	99.96	1.00	1.00	3	-
GCF_002086285.1	s__Mycobacterium kumamotonense	79.9424	717	1651	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.55	98.48	0.89	0.87	4	-
GCF_010727475.1	s__Mycobacterium mageritense	79.915	912	1651	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.88	98.33	0.91	0.85	5	-
GCF_900157375.1	s__Mycobacterium rhizamassiliense	79.5917	787	1651	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:28:42,042] [INFO] GTDB search result was written to GCF_027886095.1_ASM2788609v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:28:42,043] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:28:42,046] [INFO] DFAST_QC result json was written to GCF_027886095.1_ASM2788609v1_genomic.fna/dqc_result.json
[2024-01-25 20:28:42,046] [INFO] DFAST_QC completed!
[2024-01-25 20:28:42,046] [INFO] Total running time: 0h1m36s