[2024-01-24 15:17:49,729] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:17:49,732] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:17:49,732] [INFO] DQC Reference Directory: /var/lib/cwl/stgee075ad0-7d69-468c-a390-56c7db5bfccd/dqc_reference
[2024-01-24 15:17:51,533] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:17:51,535] [INFO] Task started: Prodigal
[2024-01-24 15:17:51,536] [INFO] Running command: gunzip -c /var/lib/cwl/stg76015a35-29de-4608-9df5-0d94deeb73af/GCF_003614435.1_ASM361443v1_genomic.fna.gz | prodigal -d GCF_003614435.1_ASM361443v1_genomic.fna/cds.fna -a GCF_003614435.1_ASM361443v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:18:21,315] [INFO] Task succeeded: Prodigal
[2024-01-24 15:18:21,316] [INFO] Task started: HMMsearch
[2024-01-24 15:18:21,316] [INFO] Running command: hmmsearch --tblout GCF_003614435.1_ASM361443v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgee075ad0-7d69-468c-a390-56c7db5bfccd/dqc_reference/reference_markers.hmm GCF_003614435.1_ASM361443v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:18:21,688] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:18:21,690] [INFO] Found 6/6 markers.
[2024-01-24 15:18:21,753] [INFO] Query marker FASTA was written to GCF_003614435.1_ASM361443v1_genomic.fna/markers.fasta
[2024-01-24 15:18:21,753] [INFO] Task started: Blastn
[2024-01-24 15:18:21,754] [INFO] Running command: blastn -query GCF_003614435.1_ASM361443v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgee075ad0-7d69-468c-a390-56c7db5bfccd/dqc_reference/reference_markers.fasta -out GCF_003614435.1_ASM361443v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:18:22,857] [INFO] Task succeeded: Blastn
[2024-01-24 15:18:22,861] [INFO] Selected 13 target genomes.
[2024-01-24 15:18:22,862] [INFO] Target genome list was writen to GCF_003614435.1_ASM361443v1_genomic.fna/target_genomes.txt
[2024-01-24 15:18:22,874] [INFO] Task started: fastANI
[2024-01-24 15:18:22,875] [INFO] Running command: fastANI --query /var/lib/cwl/stg76015a35-29de-4608-9df5-0d94deeb73af/GCF_003614435.1_ASM361443v1_genomic.fna.gz --refList GCF_003614435.1_ASM361443v1_genomic.fna/target_genomes.txt --output GCF_003614435.1_ASM361443v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:18:48,672] [INFO] Task succeeded: fastANI
[2024-01-24 15:18:48,673] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgee075ad0-7d69-468c-a390-56c7db5bfccd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:18:48,673] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgee075ad0-7d69-468c-a390-56c7db5bfccd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:18:48,690] [INFO] Found 13 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 15:18:48,690] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:18:48,691] [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 paragordonae	strain=49061	GCA_003614435.1	1389713	1389713	type	True	100.0	2405	2405	95	conclusive
Mycobacterium paragordonae	strain=JCM 18565	GCA_010723415.1	1389713	1389713	type	True	99.9892	2394	2405	95	conclusive
Mycobacterium gordonae	strain=DSM 44160	GCA_002101675.1	1778	1778	type	True	86.7536	1831	2405	95	below_threshold
Mycobacterium asiaticum	strain=DSM 44297	GCA_002086545.1	1790	1790	suspected-type	True	81.9184	1411	2405	95	below_threshold
Mycobacterium asiaticum	strain=DSM 44297	GCA_000613245.1	1790	1790	suspected-type	True	81.9183	1435	2405	95	below_threshold
Mycobacterium vicinigordonae	strain=24	GCA_013466425.1	1719132	1719132	type	True	81.3333	1313	2405	95	below_threshold
Mycobacterium angelicum	strain=DSM 45057	GCA_002086155.1	470074	470074	type	True	81.2	1260	2405	95	below_threshold
Mycobacterium kubicae	strain=JCM 13573	GCA_015689175.1	120959	120959	type	True	81.0398	1138	2405	95	below_threshold
Mycobacterium kubicae	strain=JCM 13573	GCA_010723135.1	120959	120959	type	True	80.9753	1148	2405	95	below_threshold
Mycobacterium kubicae	strain=CIP 106428	GCA_002101745.1	120959	120959	type	True	80.9739	1144	2405	95	below_threshold
Mycobacterium szulgai	strain=DSM 44166	GCA_002116635.1	1787	1787	type	True	80.8433	1242	2405	95	below_threshold
Mycobacterium bohemicum	strain=DSM 44277	GCA_002102025.1	56425	56425	type	True	80.79	1123	2405	95	below_threshold
Mycobacterium bohemicum	strain=DSM 44277	GCA_001053185.1	56425	56425	type	True	80.784	1073	2405	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:18:48,693] [INFO] DFAST Taxonomy check result was written to GCF_003614435.1_ASM361443v1_genomic.fna/tc_result.tsv
[2024-01-24 15:18:48,693] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:18:48,694] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:18:48,694] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgee075ad0-7d69-468c-a390-56c7db5bfccd/dqc_reference/checkm_data
[2024-01-24 15:18:48,695] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:18:48,794] [INFO] Task started: CheckM
[2024-01-24 15:18:48,795] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003614435.1_ASM361443v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003614435.1_ASM361443v1_genomic.fna/checkm_input GCF_003614435.1_ASM361443v1_genomic.fna/checkm_result
[2024-01-24 15:20:16,247] [INFO] Task succeeded: CheckM
[2024-01-24 15:20:16,248] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:20:16,271] [INFO] ===== Completeness check finished =====
[2024-01-24 15:20:16,271] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:20:16,272] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003614435.1_ASM361443v1_genomic.fna/markers.fasta)
[2024-01-24 15:20:16,272] [INFO] Task started: Blastn
[2024-01-24 15:20:16,272] [INFO] Running command: blastn -query GCF_003614435.1_ASM361443v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgee075ad0-7d69-468c-a390-56c7db5bfccd/dqc_reference/reference_markers_gtdb.fasta -out GCF_003614435.1_ASM361443v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:20:17,817] [INFO] Task succeeded: Blastn
[2024-01-24 15:20:17,821] [INFO] Selected 8 target genomes.
[2024-01-24 15:20:17,821] [INFO] Target genome list was writen to GCF_003614435.1_ASM361443v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:20:17,829] [INFO] Task started: fastANI
[2024-01-24 15:20:17,829] [INFO] Running command: fastANI --query /var/lib/cwl/stg76015a35-29de-4608-9df5-0d94deeb73af/GCF_003614435.1_ASM361443v1_genomic.fna.gz --refList GCF_003614435.1_ASM361443v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003614435.1_ASM361443v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:20:36,269] [INFO] Task succeeded: fastANI
[2024-01-24 15:20:36,287] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:20:36,288] [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_003614435.1	s__Mycobacterium paragordonae	100.0	2405	2405	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.23	97.83	0.93	0.88	9	conclusive
GCF_001417955.2	s__Mycobacterium gordonae_B	89.2605	1917	2405	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003987775.1	s__Mycobacterium sp003987775	88.4796	1962	2405	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002101675.1	s__Mycobacterium gordonae	86.7785	1824	2405	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.22	98.97	0.90	0.87	6	-
GCF_017086405.1	s__Mycobacterium gordonae_D	86.3548	1824	2405	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000613245.1	s__Mycobacterium asiaticum	81.9339	1432	2405	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.95	98.52	0.95	0.93	5	-
GCF_013466425.1	s__Mycobacterium vicinigordonae	81.3413	1315	2405	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015689175.1	s__Mycobacterium kubicae	81.0178	1138	2405	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.05	97.98	0.96	0.92	7	-
--------------------------------------------------------------------------------
[2024-01-24 15:20:36,289] [INFO] GTDB search result was written to GCF_003614435.1_ASM361443v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:20:36,290] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:20:36,293] [INFO] DFAST_QC result json was written to GCF_003614435.1_ASM361443v1_genomic.fna/dqc_result.json
[2024-01-24 15:20:36,293] [INFO] DFAST_QC completed!
[2024-01-24 15:20:36,293] [INFO] Total running time: 0h2m47s