[2024-01-25 20:27:20,694] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:27:20,696] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:27:20,696] [INFO] DQC Reference Directory: /var/lib/cwl/stg8a8d76a0-a92e-4354-afd8-2e1d221fbeac/dqc_reference
[2024-01-25 20:27:21,833] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:27:21,834] [INFO] Task started: Prodigal
[2024-01-25 20:27:21,834] [INFO] Running command: gunzip -c /var/lib/cwl/stgfc7013f5-386d-4b5e-a433-9e389aadd923/GCF_025822765.1_ASM2582276v1_genomic.fna.gz | prodigal -d GCF_025822765.1_ASM2582276v1_genomic.fna/cds.fna -a GCF_025822765.1_ASM2582276v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:27:38,173] [INFO] Task succeeded: Prodigal
[2024-01-25 20:27:38,173] [INFO] Task started: HMMsearch
[2024-01-25 20:27:38,173] [INFO] Running command: hmmsearch --tblout GCF_025822765.1_ASM2582276v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8a8d76a0-a92e-4354-afd8-2e1d221fbeac/dqc_reference/reference_markers.hmm GCF_025822765.1_ASM2582276v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:27:38,453] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:27:38,454] [INFO] Found 6/6 markers.
[2024-01-25 20:27:38,502] [INFO] Query marker FASTA was written to GCF_025822765.1_ASM2582276v1_genomic.fna/markers.fasta
[2024-01-25 20:27:38,503] [INFO] Task started: Blastn
[2024-01-25 20:27:38,503] [INFO] Running command: blastn -query GCF_025822765.1_ASM2582276v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8a8d76a0-a92e-4354-afd8-2e1d221fbeac/dqc_reference/reference_markers.fasta -out GCF_025822765.1_ASM2582276v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:27:39,593] [INFO] Task succeeded: Blastn
[2024-01-25 20:27:39,595] [INFO] Selected 22 target genomes.
[2024-01-25 20:27:39,595] [INFO] Target genome list was writen to GCF_025822765.1_ASM2582276v1_genomic.fna/target_genomes.txt
[2024-01-25 20:27:39,614] [INFO] Task started: fastANI
[2024-01-25 20:27:39,614] [INFO] Running command: fastANI --query /var/lib/cwl/stgfc7013f5-386d-4b5e-a433-9e389aadd923/GCF_025822765.1_ASM2582276v1_genomic.fna.gz --refList GCF_025822765.1_ASM2582276v1_genomic.fna/target_genomes.txt --output GCF_025822765.1_ASM2582276v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:28:05,898] [INFO] Task succeeded: fastANI
[2024-01-25 20:28:05,898] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8a8d76a0-a92e-4354-afd8-2e1d221fbeac/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:28:05,899] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8a8d76a0-a92e-4354-afd8-2e1d221fbeac/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:28:05,913] [INFO] Found 22 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 20:28:05,914] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 20:28:05,914] [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 moriokaense	strain=JCM 6375	GCA_010726085.1	39691	39691	type	True	90.7887	1630	1946	95	below_threshold
Mycolicibacterium moriokaense	strain=CIP105393	GCA_002086395.1	39691	39691	type	True	90.7623	1606	1946	95	below_threshold
Mycolicibacterium tusciae	strain=DSM 44338	GCA_002086795.1	75922	75922	type	True	83.8289	1375	1946	95	below_threshold
Mycolicibacterium gadium	strain=JCM 12688	GCA_010728925.1	1794	1794	type	True	83.5961	1411	1946	95	below_threshold
Mycolicibacterium phlei	strain=DSM 43239 = CCUG 21000	GCA_001582015.1	1771	1771	type	True	81.568	1089	1946	95	below_threshold
Mycolicibacterium malmesburyense	strain=WCM 7299	GCA_001050015.1	1566886	1566886	type	True	81.4098	1085	1946	95	below_threshold
Mycolicibacterium komanii	strain=GPK 1020	GCA_001050035.1	1566885	1566885	type	True	81.2298	1146	1946	95	below_threshold
Mycobacterium neumannii	strain=CECT 8766	GCA_002245615.1	2048551	2048551	type	True	81.0998	1066	1946	95	below_threshold
Mycolicibacterium celeriflavum	strain=JCM 18439	GCA_010731795.1	1249101	1249101	type	True	81.0894	1097	1946	95	below_threshold
Mycolicibacterium celeriflavum	strain=DSM 46765	GCA_002086175.1	1249101	1249101	type	True	81.0533	1076	1946	95	below_threshold
Mycolicibacterium chlorophenolicum	strain=NBRC 15527	GCA_001552315.1	37916	37916	type	True	80.4468	1016	1946	95	below_threshold
Mycolicibacterium chlorophenolicum	strain=DSM 43826	GCA_001044235.1	37916	37916	type	True	80.3459	1024	1946	95	below_threshold
Mycolicibacterium psychrotolerans	strain=JCM 13323	GCA_010729305.1	216929	216929	type	True	80.1619	981	1946	95	below_threshold
Mycolicibacterium mageritense	strain=CIP 104973	GCA_000612825.1	53462	53462	type	True	79.7367	944	1946	95	below_threshold
Mycolicibacterium thermoresistibile	strain=NCTC10409	GCA_900187065.1	1797	1797	type	True	79.7147	816	1946	95	below_threshold
Mycolicibacterium thermoresistibile	strain=ATCC 19527	GCA_000234585.2	1797	1797	type	True	79.6981	800	1946	95	below_threshold
Mycolicibacterium mageritense	strain=JCM 12375	GCA_010727475.1	53462	53462	type	True	79.6052	957	1946	95	below_threshold
Mycobacterium paraintracellulare	strain=MOTT64	GCA_000276825.1	1138383	1138383	suspected-type	True	79.2343	734	1946	95	below_threshold
Mycobacterium paraintracellulare	strain=KCTC 29084	GCA_002104735.1	1138383	1138383	suspected-type	True	79.2057	723	1946	95	below_threshold
Mycobacterium paraintracellulare	strain=JCM 30622	GCA_010731935.1	1138383	1138383	suspected-type	True	79.1858	745	1946	95	below_threshold
Mycobacterium mantenii	strain=DSM 45255	GCA_002086335.1	560555	560555	type	True	78.9508	705	1946	95	below_threshold
Mycobacterium mantenii	strain=JCM 18113	GCA_010731775.1	560555	560555	type	True	78.9144	712	1946	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:28:05,916] [INFO] DFAST Taxonomy check result was written to GCF_025822765.1_ASM2582276v1_genomic.fna/tc_result.tsv
[2024-01-25 20:28:05,916] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:28:05,916] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:28:05,916] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8a8d76a0-a92e-4354-afd8-2e1d221fbeac/dqc_reference/checkm_data
[2024-01-25 20:28:05,917] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:28:05,973] [INFO] Task started: CheckM
[2024-01-25 20:28:05,973] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025822765.1_ASM2582276v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025822765.1_ASM2582276v1_genomic.fna/checkm_input GCF_025822765.1_ASM2582276v1_genomic.fna/checkm_result
[2024-01-25 20:28:57,333] [INFO] Task succeeded: CheckM
[2024-01-25 20:28:57,334] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:28:57,354] [INFO] ===== Completeness check finished =====
[2024-01-25 20:28:57,354] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:28:57,355] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025822765.1_ASM2582276v1_genomic.fna/markers.fasta)
[2024-01-25 20:28:57,355] [INFO] Task started: Blastn
[2024-01-25 20:28:57,355] [INFO] Running command: blastn -query GCF_025822765.1_ASM2582276v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8a8d76a0-a92e-4354-afd8-2e1d221fbeac/dqc_reference/reference_markers_gtdb.fasta -out GCF_025822765.1_ASM2582276v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:28:58,918] [INFO] Task succeeded: Blastn
[2024-01-25 20:28:58,921] [INFO] Selected 20 target genomes.
[2024-01-25 20:28:58,921] [INFO] Target genome list was writen to GCF_025822765.1_ASM2582276v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:28:58,954] [INFO] Task started: fastANI
[2024-01-25 20:28:58,954] [INFO] Running command: fastANI --query /var/lib/cwl/stgfc7013f5-386d-4b5e-a433-9e389aadd923/GCF_025822765.1_ASM2582276v1_genomic.fna.gz --refList GCF_025822765.1_ASM2582276v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025822765.1_ASM2582276v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:29:27,149] [INFO] Task succeeded: fastANI
[2024-01-25 20:29:27,165] [INFO] Found 20 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 20:29:27,165] [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_010726085.1	s__Mycobacterium moriokaense	90.7802	1631	1946	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002591975.1	s__Mycobacterium neglectum	83.983	1417	1946	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000243415.2	s__Mycobacterium tusciae_A	83.8836	1456	1946	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002086795.1	s__Mycobacterium tusciae	83.82	1376	1946	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010726765.1	s__Mycobacterium gallinarum	83.776	1429	1946	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010728925.1	s__Mycobacterium gadium	83.5897	1412	1946	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900108565.1	s__Mycobacterium rutilum	81.9406	1182	1946	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001583415.1	s__Mycobacterium phlei	81.492	1106	1946	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.86	99.38	0.98	0.91	10	-
GCF_001722335.1	s__Mycobacterium flavescens_A	81.424	1117	1946	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	81.4068	1086	1946	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001665535.1	s__Mycobacterium sp001665535	81.3589	1108	1946	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	96.97	96.97	0.90	0.90	2	-
GCF_001500025.1	s__Mycobacterium sp001500025	81.2001	1080	1946	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900637135.1	s__Mycobacterium flavescens	81.1029	1089	1946	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.2034	98.19	96.77	0.93	0.88	4	-
GCF_001570485.1	s__Mycobacterium novocastrense	81.098	1101	1946	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	97.10	95.11	0.87	0.87	5	-
GCF_900240945.1	s__Mycobacterium sp900240945	80.9743	1154	1946	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014873705.1	s__Mycobacterium sp014873705	80.8797	1107	1946	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.28	98.28	0.92	0.92	2	-
GCA_000762985.1	s__Mycobacterium rufum_A	80.5057	975	1946	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010727475.1	s__Mycobacterium mageritense	79.6132	956	1946	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.88	98.33	0.91	0.85	5	-
GCF_013337765.1	s__Mycobacterium sp003053865	79.2905	868	1946	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	95.43	95.41	0.83	0.83	3	-
GCF_002250655.1	s__Mycobacterium sphagni	79.1629	765	1946	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 20:29:27,174] [INFO] GTDB search result was written to GCF_025822765.1_ASM2582276v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:29:27,175] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:29:27,182] [INFO] DFAST_QC result json was written to GCF_025822765.1_ASM2582276v1_genomic.fna/dqc_result.json
[2024-01-25 20:29:27,182] [INFO] DFAST_QC completed!
[2024-01-25 20:29:27,182] [INFO] Total running time: 0h2m6s