[2024-01-25 19:50:50,613] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:50:50,618] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:50:50,618] [INFO] DQC Reference Directory: /var/lib/cwl/stgdf23c02e-affa-4c61-b3d5-a184724c7990/dqc_reference
[2024-01-25 19:50:51,785] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:50:51,786] [INFO] Task started: Prodigal
[2024-01-25 19:50:51,786] [INFO] Running command: gunzip -c /var/lib/cwl/stg0e5fffcb-49d1-4366-9205-eee0fb002ba1/GCF_025823225.1_ASM2582322v1_genomic.fna.gz | prodigal -d GCF_025823225.1_ASM2582322v1_genomic.fna/cds.fna -a GCF_025823225.1_ASM2582322v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:51:15,140] [INFO] Task succeeded: Prodigal
[2024-01-25 19:51:15,140] [INFO] Task started: HMMsearch
[2024-01-25 19:51:15,140] [INFO] Running command: hmmsearch --tblout GCF_025823225.1_ASM2582322v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdf23c02e-affa-4c61-b3d5-a184724c7990/dqc_reference/reference_markers.hmm GCF_025823225.1_ASM2582322v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:51:15,405] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:51:15,409] [INFO] Found 6/6 markers.
[2024-01-25 19:51:15,462] [INFO] Query marker FASTA was written to GCF_025823225.1_ASM2582322v1_genomic.fna/markers.fasta
[2024-01-25 19:51:15,463] [INFO] Task started: Blastn
[2024-01-25 19:51:15,463] [INFO] Running command: blastn -query GCF_025823225.1_ASM2582322v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdf23c02e-affa-4c61-b3d5-a184724c7990/dqc_reference/reference_markers.fasta -out GCF_025823225.1_ASM2582322v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:51:16,659] [INFO] Task succeeded: Blastn
[2024-01-25 19:51:16,662] [INFO] Selected 22 target genomes.
[2024-01-25 19:51:16,662] [INFO] Target genome list was writen to GCF_025823225.1_ASM2582322v1_genomic.fna/target_genomes.txt
[2024-01-25 19:51:16,681] [INFO] Task started: fastANI
[2024-01-25 19:51:16,681] [INFO] Running command: fastANI --query /var/lib/cwl/stg0e5fffcb-49d1-4366-9205-eee0fb002ba1/GCF_025823225.1_ASM2582322v1_genomic.fna.gz --refList GCF_025823225.1_ASM2582322v1_genomic.fna/target_genomes.txt --output GCF_025823225.1_ASM2582322v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:51:45,943] [INFO] Task succeeded: fastANI
[2024-01-25 19:51:45,944] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdf23c02e-affa-4c61-b3d5-a184724c7990/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:51:45,944] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdf23c02e-affa-4c61-b3d5-a184724c7990/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:51:45,956] [INFO] Found 22 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:51:45,957] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:51:45,957] [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 arabiense	strain=JCM 18538	GCA_010731815.2	1286181	1286181	type	True	99.998	2124	2124	95	conclusive
Mycolicibacterium lacusdiani	strain=JXJ CY 35	GCA_021916785.1	2895283	2895283	type	True	93.5255	1776	2124	95	below_threshold
Mycolicibacterium chlorophenolicum	strain=DSM 43826	GCA_001044235.1	37916	37916	type	True	80.7828	1098	2124	95	below_threshold
Mycolicibacterium phlei	strain=DSM 43239 = CCUG 21000	GCA_001582015.1	1771	1771	type	True	80.7315	1028	2124	95	below_threshold
Mycolicibacterium phlei	strain=CCUG 21000	GCA_009192875.1	1771	1771	type	True	80.7201	1039	2124	95	below_threshold
Mycolicibacterium phlei	strain=CCUG 21000	GCA_001583415.1	1771	1771	type	True	80.6956	1041	2124	95	below_threshold
Mycolicibacterium chlorophenolicum	strain=NBRC 15527	GCA_001552315.1	37916	37916	type	True	80.6802	1112	2124	95	below_threshold
Mycolicibacterium vaccae	strain=NBRC 14118	GCA_001552715.1	1810	1810	type	True	80.5686	940	2124	95	below_threshold
Mycolicibacterium baixiangningiae	strain=LJ126	GCA_014893035.1	2761578	2761578	type	True	80.3869	1032	2124	95	below_threshold
Mycolicibacterium baixiangningiae	strain=LJ126	GCA_016313185.1	2761578	2761578	type	True	80.3712	1042	2124	95	below_threshold
Mycolicibacterium chitae	strain=NCTC10485	GCA_900637205.1	1792	1792	type	True	80.1036	878	2124	95	below_threshold
Mycolicibacterium mageritense	strain=JCM 12375	GCA_010727475.1	53462	53462	type	True	80.0559	1001	2124	95	below_threshold
Mycolicibacterium malmesburyense	strain=WCM 7299	GCA_001050015.1	1566886	1566886	type	True	80.0395	944	2124	95	below_threshold
Mycolicibacterium confluentis	strain=JCM 13671	GCA_010729895.1	28047	28047	type	True	80.0234	876	2124	95	below_threshold
Mycolicibacterium chitae	strain=JCM 12403	GCA_010727725.1	1792	1792	type	True	80.0232	899	2124	95	below_threshold
Mycolicibacterium aurum	strain=NCTC10437	GCA_900637195.1	1791	1791	type	True	79.9741	1045	2124	95	below_threshold
Mycolicibacterium mageritense	strain=CIP 104973	GCA_000612825.1	53462	53462	type	True	79.9731	1027	2124	95	below_threshold
Mycolicibacterium aurum	strain=NCTC 10437	GCA_001049355.1	1791	1791	type	True	79.9001	1048	2124	95	below_threshold
Mycolicibacterium elephantis	strain=DSM 44368	GCA_004014805.1	81858	81858	type	True	79.8606	884	2124	95	below_threshold
Mycobacterium pallens	strain=JCM 16370	GCA_019456675.1	370524	370524	type	True	79.6449	861	2124	95	below_threshold
Mycobacterium crocinum	strain=JCM 16369	GCA_022370635.3	388459	388459	type	True	79.6062	866	2124	95	below_threshold
Mycolicibacterium vinylchloridicum	strain=CECT 8761	GCA_013404075.1	2736928	2736928	type	True	79.3661	850	2124	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:51:45,958] [INFO] DFAST Taxonomy check result was written to GCF_025823225.1_ASM2582322v1_genomic.fna/tc_result.tsv
[2024-01-25 19:51:45,959] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:51:45,959] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:51:45,959] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdf23c02e-affa-4c61-b3d5-a184724c7990/dqc_reference/checkm_data
[2024-01-25 19:51:45,960] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:51:46,019] [INFO] Task started: CheckM
[2024-01-25 19:51:46,019] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025823225.1_ASM2582322v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025823225.1_ASM2582322v1_genomic.fna/checkm_input GCF_025823225.1_ASM2582322v1_genomic.fna/checkm_result
[2024-01-25 19:53:09,094] [INFO] Task succeeded: CheckM
[2024-01-25 19:53:09,095] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2024-01-25 19:53:09,123] [INFO] ===== Completeness check finished =====
[2024-01-25 19:53:09,123] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:53:09,124] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025823225.1_ASM2582322v1_genomic.fna/markers.fasta)
[2024-01-25 19:53:09,125] [INFO] Task started: Blastn
[2024-01-25 19:53:09,125] [INFO] Running command: blastn -query GCF_025823225.1_ASM2582322v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdf23c02e-affa-4c61-b3d5-a184724c7990/dqc_reference/reference_markers_gtdb.fasta -out GCF_025823225.1_ASM2582322v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:53:10,970] [INFO] Task succeeded: Blastn
[2024-01-25 19:53:10,973] [INFO] Selected 16 target genomes.
[2024-01-25 19:53:10,973] [INFO] Target genome list was writen to GCF_025823225.1_ASM2582322v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:53:10,988] [INFO] Task started: fastANI
[2024-01-25 19:53:10,988] [INFO] Running command: fastANI --query /var/lib/cwl/stg0e5fffcb-49d1-4366-9205-eee0fb002ba1/GCF_025823225.1_ASM2582322v1_genomic.fna.gz --refList GCF_025823225.1_ASM2582322v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025823225.1_ASM2582322v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:53:34,675] [INFO] Task succeeded: fastANI
[2024-01-25 19:53:34,685] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:53:34,685] [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_010731815.2	s__Mycobacterium arabiense	99.998	2124	2124	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_010731735.1	s__Mycobacterium sediminis	83.3217	1418	2124	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008329645.1	s__Mycobacterium grossiae	82.8683	1345	2124	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.93	99.93	0.94	0.94	2	-
GCF_008329535.1	s__Mycobacterium sp008329535	81.5298	1186	2124	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010729665.1	s__Mycobacterium madagascariense	81.1387	1108	2124	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000620625.1	s__Mycobacterium sp000620625	81.1199	1192	2124	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002043095.1	s__Mycobacterium sp002043095	80.9413	1145	2124	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	95.25	95.25	0.79	0.79	2	-
GCF_008329605.1	s__Mycobacterium sp008329605	80.9405	1102	2124	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014202335.1	s__Mycobacterium sp014202335	80.8151	1129	2124	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	80.7792	1100	2124	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	80.722	1089	2124	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	80.6574	1046	2124	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.86	99.38	0.98	0.91	10	-
GCF_010729305.1	s__Mycobacterium psychrotolerans	80.6281	1030	2124	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	96.53	96.53	0.90	0.90	2	-
GCF_006439015.1	s__Mycobacterium hodleri_A	80.0913	991	2124	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	80.0825	997	2124	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.88	98.33	0.91	0.85	5	-
GCF_900637195.1	s__Mycobacterium aurum	79.9703	1045	2124	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.99	99.99	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-25 19:53:34,687] [INFO] GTDB search result was written to GCF_025823225.1_ASM2582322v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:53:34,687] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:53:34,691] [INFO] DFAST_QC result json was written to GCF_025823225.1_ASM2582322v1_genomic.fna/dqc_result.json
[2024-01-25 19:53:34,691] [INFO] DFAST_QC completed!
[2024-01-25 19:53:34,691] [INFO] Total running time: 0h2m44s