[2024-01-24 11:35:22,541] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:35:22,545] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:35:22,545] [INFO] DQC Reference Directory: /var/lib/cwl/stg44f69924-05fb-41ee-a08f-b9b557eb8fd9/dqc_reference
[2024-01-24 11:35:26,240] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:35:26,242] [INFO] Task started: Prodigal
[2024-01-24 11:35:26,242] [INFO] Running command: gunzip -c /var/lib/cwl/stg52cc221f-efdc-4bae-82b1-8f7fdc4216f2/GCF_010726645.1_ASM1072664v1_genomic.fna.gz | prodigal -d GCF_010726645.1_ASM1072664v1_genomic.fna/cds.fna -a GCF_010726645.1_ASM1072664v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:35:44,196] [INFO] Task succeeded: Prodigal
[2024-01-24 11:35:44,196] [INFO] Task started: HMMsearch
[2024-01-24 11:35:44,196] [INFO] Running command: hmmsearch --tblout GCF_010726645.1_ASM1072664v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg44f69924-05fb-41ee-a08f-b9b557eb8fd9/dqc_reference/reference_markers.hmm GCF_010726645.1_ASM1072664v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:35:44,604] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:35:44,605] [INFO] Found 6/6 markers.
[2024-01-24 11:35:44,653] [INFO] Query marker FASTA was written to GCF_010726645.1_ASM1072664v1_genomic.fna/markers.fasta
[2024-01-24 11:35:44,654] [INFO] Task started: Blastn
[2024-01-24 11:35:44,654] [INFO] Running command: blastn -query GCF_010726645.1_ASM1072664v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg44f69924-05fb-41ee-a08f-b9b557eb8fd9/dqc_reference/reference_markers.fasta -out GCF_010726645.1_ASM1072664v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:35:45,964] [INFO] Task succeeded: Blastn
[2024-01-24 11:35:45,969] [INFO] Selected 26 target genomes.
[2024-01-24 11:35:45,970] [INFO] Target genome list was writen to GCF_010726645.1_ASM1072664v1_genomic.fna/target_genomes.txt
[2024-01-24 11:35:45,981] [INFO] Task started: fastANI
[2024-01-24 11:35:45,981] [INFO] Running command: fastANI --query /var/lib/cwl/stg52cc221f-efdc-4bae-82b1-8f7fdc4216f2/GCF_010726645.1_ASM1072664v1_genomic.fna.gz --refList GCF_010726645.1_ASM1072664v1_genomic.fna/target_genomes.txt --output GCF_010726645.1_ASM1072664v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:36:16,322] [INFO] Task succeeded: fastANI
[2024-01-24 11:36:16,323] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg44f69924-05fb-41ee-a08f-b9b557eb8fd9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:36:16,323] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg44f69924-05fb-41ee-a08f-b9b557eb8fd9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:36:16,344] [INFO] Found 26 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:36:16,345] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:36:16,345] [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 vaccae	strain=95051	GCA_001655245.1	1810	1810	type	True	82.572	1182	1885	95	below_threshold
Mycolicibacterium vaccae	strain=NBRC 14118	GCA_001552715.1	1810	1810	type	True	82.4525	1086	1885	95	below_threshold
Mycolicibacterium chubuense	strain=DSM 44219	GCA_002086595.1	1800	1800	type	True	81.9949	1119	1885	95	below_threshold
Mycolicibacterium chubuense	strain=DSM 44219	GCA_001044255.1	1800	1800	type	True	81.9889	1115	1885	95	below_threshold
Mycolicibacterium chubuense	strain=NCTC10819	GCA_900453455.1	1800	1800	type	True	81.9632	1133	1885	95	below_threshold
Mycolicibacterium psychrotolerans	strain=JCM 13323	GCA_010729305.1	216929	216929	type	True	81.9018	1123	1885	95	below_threshold
Mycolicibacterium phlei	strain=CCUG 21000	GCA_009192875.1	1771	1771	type	True	81.328	1054	1885	95	below_threshold
Mycolicibacterium phlei	strain=CCUG 21000	GCA_001583415.1	1771	1771	type	True	81.2927	1076	1885	95	below_threshold
Mycolicibacterium phlei	strain=DSM 43239 = CCUG 21000	GCA_001582015.1	1771	1771	type	True	81.2921	1058	1885	95	below_threshold
Mycolicibacterium rutilum	strain=DSM 45405	GCA_900108565.1	370526	370526	type	True	81.2139	1039	1885	95	below_threshold
Mycolicibacterium aurum	strain=NCTC 10437	GCA_001049355.1	1791	1791	type	True	81.0893	1093	1885	95	below_threshold
Mycolicibacterium aurum	strain=NCTC10437	GCA_900637195.1	1791	1791	type	True	81.0762	1103	1885	95	below_threshold
Mycolicibacterium malmesburyense	strain=WCM 7299	GCA_001050015.1	1566886	1566886	type	True	80.5394	998	1885	95	below_threshold
Mycobacterium doricum	strain=JCM 12405	GCA_010728155.1	126673	126673	type	True	80.3514	709	1885	95	below_threshold
Mycolicibacterium baixiangningiae	strain=LJ126	GCA_016313185.1	2761578	2761578	type	True	80.3415	968	1885	95	below_threshold
Mycolicibacterium baixiangningiae	strain=LJ126	GCA_014893035.1	2761578	2761578	type	True	80.2593	966	1885	95	below_threshold
Mycobacterium doricum	strain=DSM 44339	GCA_002102115.1	126673	126673	type	True	80.2267	702	1885	95	below_threshold
Mycolicibacterium houstonense	strain=type strain: ATCC 49403	GCA_900078665.2	146021	146021	type	True	80.018	907	1885	95	below_threshold
Mycolicibacterium moriokaense	strain=JCM 6375	GCA_010726085.1	39691	39691	type	True	79.9456	935	1885	95	below_threshold
Mycolicibacterium fortuitum subsp. fortuitum	strain=JCM 6387	GCA_022179545.1	144549	1766	type	True	79.8776	845	1885	95	below_threshold
Mycolicibacterium moriokaense	strain=CIP105393	GCA_002086395.1	39691	39691	type	True	79.8489	928	1885	95	below_threshold
Mycolicibacterium mageritense	strain=CIP 104973	GCA_000612825.1	53462	53462	type	True	79.8176	887	1885	95	below_threshold
Mycolicibacterium lacusdiani	strain=JXJ CY 35	GCA_021916785.1	2895283	2895283	type	True	79.7527	920	1885	95	below_threshold
Mycobacterium pallens	strain=JCM 16370	GCA_019456675.1	370524	370524	type	True	79.6547	855	1885	95	below_threshold
Mycobacterium crocinum	strain=JCM 16369	GCA_022370635.3	388459	388459	type	True	79.6241	850	1885	95	below_threshold
Mycolicibacterium anyangense	strain=JCM 30275	GCA_010731855.1	1431246	1431246	type	True	79.5672	790	1885	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:36:16,347] [INFO] DFAST Taxonomy check result was written to GCF_010726645.1_ASM1072664v1_genomic.fna/tc_result.tsv
[2024-01-24 11:36:16,347] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:36:16,347] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:36:16,347] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg44f69924-05fb-41ee-a08f-b9b557eb8fd9/dqc_reference/checkm_data
[2024-01-24 11:36:16,348] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:36:16,399] [INFO] Task started: CheckM
[2024-01-24 11:36:16,399] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_010726645.1_ASM1072664v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_010726645.1_ASM1072664v1_genomic.fna/checkm_input GCF_010726645.1_ASM1072664v1_genomic.fna/checkm_result
[2024-01-24 11:37:26,348] [INFO] Task succeeded: CheckM
[2024-01-24 11:37:26,350] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:37:26,370] [INFO] ===== Completeness check finished =====
[2024-01-24 11:37:26,371] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:37:26,371] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_010726645.1_ASM1072664v1_genomic.fna/markers.fasta)
[2024-01-24 11:37:26,371] [INFO] Task started: Blastn
[2024-01-24 11:37:26,372] [INFO] Running command: blastn -query GCF_010726645.1_ASM1072664v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg44f69924-05fb-41ee-a08f-b9b557eb8fd9/dqc_reference/reference_markers_gtdb.fasta -out GCF_010726645.1_ASM1072664v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:37:28,392] [INFO] Task succeeded: Blastn
[2024-01-24 11:37:28,397] [INFO] Selected 21 target genomes.
[2024-01-24 11:37:28,397] [INFO] Target genome list was writen to GCF_010726645.1_ASM1072664v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:37:28,439] [INFO] Task started: fastANI
[2024-01-24 11:37:28,439] [INFO] Running command: fastANI --query /var/lib/cwl/stg52cc221f-efdc-4bae-82b1-8f7fdc4216f2/GCF_010726645.1_ASM1072664v1_genomic.fna.gz --refList GCF_010726645.1_ASM1072664v1_genomic.fna/target_genomes_gtdb.txt --output GCF_010726645.1_ASM1072664v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:37:54,302] [INFO] Task succeeded: fastANI
[2024-01-24 11:37:54,322] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:37:54,322] [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_010726645.1	s__Mycobacterium duvalii	100.0	1885	1885	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_001545925.1	s__Mycobacterium sp001545925	82.5377	1015	1885	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001552715.1	s__Mycobacterium vaccae	82.487	1080	1885	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.99	99.97	1.00	1.00	3	-
GCF_900454025.1	s__Mycobacterium gilvum	82.4819	1211	1885	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	97.87	97.81	0.88	0.86	5	-
GCF_000612725.1	s__Mycobacterium austroafricanum	82.1556	1190	1885	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.53	98.42	0.88	0.88	3	-
GCF_002086815.1	s__Mycobacterium parafortuitum	82.1412	1183	1885	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001722335.1	s__Mycobacterium flavescens_A	82.0585	1123	1885	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000762985.1	s__Mycobacterium rufum_A	81.9919	1150	1885	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000266905.1	s__Mycobacterium chubuense_A	81.9688	1161	1885	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010725485.1	s__Mycobacterium sp002946335	81.8809	1191	1885	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.86	98.86	0.96	0.96	2	-
GCF_001583415.1	s__Mycobacterium phlei	81.3037	1075	1885	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.86	99.38	0.98	0.91	10	-
GCF_007096635.1	s__Mycobacterium sp007096635	81.2628	976	1885	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	81.23	1036	1885	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900637195.1	s__Mycobacterium aurum	81.0315	1105	1885	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.99	99.99	1.00	1.00	2	-
GCF_001500125.1	s__Mycobacterium sp001500125	80.8459	990	1885	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	80.5366	999	1885	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010728155.1	s__Mycobacterium doricum	80.3495	709	1885	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_016313185.1	s__Mycobacterium sp016313185	80.3254	969	1885	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.68	97.36	0.93	0.85	3	-
GCA_900637135.1	s__Mycobacterium flavescens	80.3152	949	1885	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.2034	98.19	96.77	0.93	0.88	4	-
GCF_001499905.1	s__Mycobacterium sp001499905	80.2736	893	1885	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001500025.1	s__Mycobacterium sp001500025	80.2681	990	1885	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 11:37:54,324] [INFO] GTDB search result was written to GCF_010726645.1_ASM1072664v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:37:54,325] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:37:54,330] [INFO] DFAST_QC result json was written to GCF_010726645.1_ASM1072664v1_genomic.fna/dqc_result.json
[2024-01-24 11:37:54,330] [INFO] DFAST_QC completed!
[2024-01-24 11:37:54,330] [INFO] Total running time: 0h2m32s