[2024-01-24 13:09:51,614] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:09:51,616] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:09:51,617] [INFO] DQC Reference Directory: /var/lib/cwl/stg5982f9e0-0180-4ebd-811e-078e03343b23/dqc_reference
[2024-01-24 13:09:52,990] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:09:52,991] [INFO] Task started: Prodigal
[2024-01-24 13:09:52,992] [INFO] Running command: gunzip -c /var/lib/cwl/stg066011fd-b59f-4d88-8664-fafee969b252/GCF_002104795.1_ASM210479v1_genomic.fna.gz | prodigal -d GCF_002104795.1_ASM210479v1_genomic.fna/cds.fna -a GCF_002104795.1_ASM210479v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:10:05,267] [INFO] Task succeeded: Prodigal
[2024-01-24 13:10:05,268] [INFO] Task started: HMMsearch
[2024-01-24 13:10:05,268] [INFO] Running command: hmmsearch --tblout GCF_002104795.1_ASM210479v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5982f9e0-0180-4ebd-811e-078e03343b23/dqc_reference/reference_markers.hmm GCF_002104795.1_ASM210479v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:10:05,578] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:10:05,579] [INFO] Found 6/6 markers.
[2024-01-24 13:10:05,625] [INFO] Query marker FASTA was written to GCF_002104795.1_ASM210479v1_genomic.fna/markers.fasta
[2024-01-24 13:10:05,631] [INFO] Task started: Blastn
[2024-01-24 13:10:05,632] [INFO] Running command: blastn -query GCF_002104795.1_ASM210479v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5982f9e0-0180-4ebd-811e-078e03343b23/dqc_reference/reference_markers.fasta -out GCF_002104795.1_ASM210479v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:10:06,950] [INFO] Task succeeded: Blastn
[2024-01-24 13:10:06,953] [INFO] Selected 23 target genomes.
[2024-01-24 13:10:06,954] [INFO] Target genome list was writen to GCF_002104795.1_ASM210479v1_genomic.fna/target_genomes.txt
[2024-01-24 13:10:06,962] [INFO] Task started: fastANI
[2024-01-24 13:10:06,962] [INFO] Running command: fastANI --query /var/lib/cwl/stg066011fd-b59f-4d88-8664-fafee969b252/GCF_002104795.1_ASM210479v1_genomic.fna.gz --refList GCF_002104795.1_ASM210479v1_genomic.fna/target_genomes.txt --output GCF_002104795.1_ASM210479v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:10:27,928] [INFO] Task succeeded: fastANI
[2024-01-24 13:10:27,928] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5982f9e0-0180-4ebd-811e-078e03343b23/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:10:27,929] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5982f9e0-0180-4ebd-811e-078e03343b23/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:10:27,946] [INFO] Found 23 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:10:27,946] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:10:27,947] [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 senuensis	strain=DSM 44999	GCA_002101885.1	386913	386913	type	True	80.7478	729	1299	95	below_threshold
Mycolicibacter kumamotonensis	strain=DSM 45093	GCA_002086285.1	354243	354243	type	True	80.7323	740	1299	95	below_threshold
Mycolicibacter senuensis	strain=JCM 16017	GCA_010723225.1	386913	386913	type	True	80.6555	730	1299	95	below_threshold
Mycolicibacter kumamotonensis	strain=CST 7247	GCA_010093495.1	354243	354243	type	True	80.4057	701	1299	95	below_threshold
Mycolicibacter longobardus	strain=DSM 45394	GCA_002102265.1	1108812	1108812	type	True	80.3784	728	1299	95	below_threshold
Mycolicibacter terrae	strain=CIP 104321	GCA_002101955.1	1788	1788	type	True	80.3704	706	1299	95	below_threshold
Mycolicibacter terrae	strain=JCM 12143	GCA_010727125.1	1788	1788	type	True	80.3437	731	1299	95	below_threshold
Mycolicibacterium fallax	strain=DSM 44179	GCA_002101995.1	1793	1793	type	True	80.2381	643	1299	95	below_threshold
Mycolicibacterium fallax	strain=JCM 6405	GCA_010726955.1	1793	1793	type	True	80.2027	656	1299	95	below_threshold
Mycolicibacterium thermoresistibile	strain=ATCC 19527	GCA_000234585.2	1797	1797	type	True	79.9623	647	1299	95	below_threshold
Mycolicibacterium thermoresistibile	strain=NCTC10409	GCA_900187065.1	1797	1797	type	True	79.9623	655	1299	95	below_threshold
Mycolicibacter nonchromogenicus	strain=DSM 44164	GCA_002101775.1	1782	1782	type	True	79.9581	650	1299	95	below_threshold
Mycolicibacter hiberniae	strain=ATCC 49874	GCA_002101655.1	29314	29314	type	True	79.9358	649	1299	95	below_threshold
Mycolicibacterium thermoresistibile	strain=JCM6362	GCA_001570505.1	1797	1797	type	True	79.8899	653	1299	95	below_threshold
Mycolicibacterium chlorophenolicum	strain=NBRC 15527	GCA_001552315.1	37916	37916	type	True	79.8252	659	1299	95	below_threshold
Mycolicibacterium chlorophenolicum	strain=DSM 43826	GCA_001044235.1	37916	37916	type	True	79.7209	662	1299	95	below_threshold
Mycolicibacterium cosmeticum	strain=DSM 44829	GCA_000613185.1	258533	258533	type	True	79.6798	639	1299	95	below_threshold
Mycolicibacterium brumae	strain=ATCC 51384	GCA_025215495.1	85968	85968	type	True	79.6347	575	1299	95	below_threshold
Mycolicibacterium cosmeticum	strain=DSM 44829	GCA_005670675.1	258533	258533	type	True	79.5978	643	1299	95	below_threshold
Mycolicibacterium psychrotolerans	strain=JCM 13323	GCA_010729305.1	216929	216929	type	True	79.3144	622	1299	95	below_threshold
Mycobacterium kubicae	strain=JCM 13573	GCA_015689175.1	120959	120959	type	True	79.2452	575	1299	95	below_threshold
Mycobacterium kubicae	strain=JCM 13573	GCA_010723135.1	120959	120959	type	True	79.2095	586	1299	95	below_threshold
Mycobacterium kubicae	strain=CIP 106428	GCA_002101745.1	120959	120959	type	True	79.1819	576	1299	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:10:27,948] [INFO] DFAST Taxonomy check result was written to GCF_002104795.1_ASM210479v1_genomic.fna/tc_result.tsv
[2024-01-24 13:10:27,949] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:10:27,949] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:10:27,949] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5982f9e0-0180-4ebd-811e-078e03343b23/dqc_reference/checkm_data
[2024-01-24 13:10:27,951] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:10:27,992] [INFO] Task started: CheckM
[2024-01-24 13:10:27,993] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002104795.1_ASM210479v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002104795.1_ASM210479v1_genomic.fna/checkm_input GCF_002104795.1_ASM210479v1_genomic.fna/checkm_result
[2024-01-24 13:11:09,583] [INFO] Task succeeded: CheckM
[2024-01-24 13:11:09,585] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:11:09,607] [INFO] ===== Completeness check finished =====
[2024-01-24 13:11:09,607] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:11:09,608] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002104795.1_ASM210479v1_genomic.fna/markers.fasta)
[2024-01-24 13:11:09,608] [INFO] Task started: Blastn
[2024-01-24 13:11:09,609] [INFO] Running command: blastn -query GCF_002104795.1_ASM210479v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5982f9e0-0180-4ebd-811e-078e03343b23/dqc_reference/reference_markers_gtdb.fasta -out GCF_002104795.1_ASM210479v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:11:11,240] [INFO] Task succeeded: Blastn
[2024-01-24 13:11:11,243] [INFO] Selected 20 target genomes.
[2024-01-24 13:11:11,244] [INFO] Target genome list was writen to GCF_002104795.1_ASM210479v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:11:11,255] [INFO] Task started: fastANI
[2024-01-24 13:11:11,256] [INFO] Running command: fastANI --query /var/lib/cwl/stg066011fd-b59f-4d88-8664-fafee969b252/GCF_002104795.1_ASM210479v1_genomic.fna.gz --refList GCF_002104795.1_ASM210479v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002104795.1_ASM210479v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:11:30,561] [INFO] Task succeeded: fastANI
[2024-01-24 13:11:30,584] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:11:30,584] [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_002104795.1	s__Mycobacterium koreense	100.0	1294	1299	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.42	98.84	0.96	0.92	3	conclusive
GCF_001668625.1	s__Mycobacterium sp001668625	84.054	869	1299	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002102395.1	s__Mycobacterium triviale	83.7194	920	1299	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004354905.1	s__Mycobacterium eburneum	81.4725	805	1299	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.68	99.68	0.92	0.92	2	-
GCF_018455725.1	s__Mycobacterium sp018455725	80.7663	744	1299	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002101885.1	s__Mycobacterium senuense	80.7181	733	1299	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002086455.1	s__Mycobacterium algericum	80.6904	713	1299	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.66	97.92	0.93	0.90	4	-
GCF_002102265.1	s__Mycobacterium longobardum	80.3867	727	1299	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010727125.1	s__Mycobacterium terrae	80.3321	734	1299	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	100.00	99.99	1.00	1.00	3	-
GCF_010726955.1	s__Mycobacterium fallax	80.2371	651	1299	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.99	99.99	0.97	0.97	2	-
GCF_001021505.1	s__Mycobacterium heraklionense_B	80.1231	703	1299	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003284935.1	s__Mycobacterium arosiense_A	80.0193	640	1299	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	79.974	653	1299	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.98	99.97	1.00	1.00	3	-
GCF_004570325.1	s__Mycobacterium sp004570325	79.738	644	1299	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000613185.1	s__Mycobacterium cosmeticum	79.676	640	1299	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.89	98.33	0.93	0.89	4	-
GCF_010731755.1	s__Mycobacterium minnesotense	79.3996	603	1299	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_015689175.1	s__Mycobacterium kubicae	79.2447	574	1299	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.05	97.98	0.96	0.92	7	-
GCA_019245755.1	s__Mycobacterium sp019245755	78.8143	543	1299	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.79	99.79	0.94	0.94	2	-
GCF_001673155.1	s__Mycobacterium sp001673155	78.7982	545	1299	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018401645.1	s__Mycobacterium sp018401645	77.7668	329	1299	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 13:11:30,586] [INFO] GTDB search result was written to GCF_002104795.1_ASM210479v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:11:30,586] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:11:30,592] [INFO] DFAST_QC result json was written to GCF_002104795.1_ASM210479v1_genomic.fna/dqc_result.json
[2024-01-24 13:11:30,592] [INFO] DFAST_QC completed!
[2024-01-24 13:11:30,593] [INFO] Total running time: 0h1m39s