[2024-01-24 12:15:03,433] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:15:03,438] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:15:03,438] [INFO] DQC Reference Directory: /var/lib/cwl/stg02a2d2ab-6df1-48b2-bbaf-747b6e59294e/dqc_reference
[2024-01-24 12:15:04,861] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:15:04,862] [INFO] Task started: Prodigal
[2024-01-24 12:15:04,862] [INFO] Running command: gunzip -c /var/lib/cwl/stg089f7ea2-ef71-4ca4-8f97-771d4ea1b398/GCF_030408415.1_ASM3040841v1_genomic.fna.gz | prodigal -d GCF_030408415.1_ASM3040841v1_genomic.fna/cds.fna -a GCF_030408415.1_ASM3040841v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:15:12,043] [INFO] Task succeeded: Prodigal
[2024-01-24 12:15:12,043] [INFO] Task started: HMMsearch
[2024-01-24 12:15:12,044] [INFO] Running command: hmmsearch --tblout GCF_030408415.1_ASM3040841v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg02a2d2ab-6df1-48b2-bbaf-747b6e59294e/dqc_reference/reference_markers.hmm GCF_030408415.1_ASM3040841v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:15:12,346] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:15:12,347] [INFO] Found 6/6 markers.
[2024-01-24 12:15:12,371] [INFO] Query marker FASTA was written to GCF_030408415.1_ASM3040841v1_genomic.fna/markers.fasta
[2024-01-24 12:15:12,371] [INFO] Task started: Blastn
[2024-01-24 12:15:12,372] [INFO] Running command: blastn -query GCF_030408415.1_ASM3040841v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg02a2d2ab-6df1-48b2-bbaf-747b6e59294e/dqc_reference/reference_markers.fasta -out GCF_030408415.1_ASM3040841v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:13,480] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:13,483] [INFO] Selected 16 target genomes.
[2024-01-24 12:15:13,483] [INFO] Target genome list was writen to GCF_030408415.1_ASM3040841v1_genomic.fna/target_genomes.txt
[2024-01-24 12:15:13,486] [INFO] Task started: fastANI
[2024-01-24 12:15:13,486] [INFO] Running command: fastANI --query /var/lib/cwl/stg089f7ea2-ef71-4ca4-8f97-771d4ea1b398/GCF_030408415.1_ASM3040841v1_genomic.fna.gz --refList GCF_030408415.1_ASM3040841v1_genomic.fna/target_genomes.txt --output GCF_030408415.1_ASM3040841v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:15:23,003] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:23,004] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg02a2d2ab-6df1-48b2-bbaf-747b6e59294e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:15:23,004] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg02a2d2ab-6df1-48b2-bbaf-747b6e59294e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:15:23,017] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:15:23,017] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:15:23,017] [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
Corynebacterium appendicis	strain=DSM 44531	GCA_900156665.1	163202	163202	type	True	99.9647	729	761	95	conclusive
Corynebacterium urinipleomorphum	strain=Marseille-P2799	GCA_900155535.1	1852380	1852380	type	True	85.0907	605	761	95	below_threshold
Corynebacterium mycetoides	strain=DSM 20632	GCA_900103625.1	38302	38302	type	True	81.3596	388	761	95	below_threshold
Corynebacterium senegalense	strain=Marseille-P4329	GCA_900411315.1	2080750	2080750	type	True	80.9137	402	761	95	below_threshold
Corynebacterium haemomassiliense	strain=Marseille-Q3615	GCA_013978595.1	2754726	2754726	type	True	80.7093	406	761	95	below_threshold
Corynebacterium afermentans subsp. lipophilum	strain=CCUG 32105	GCA_015351335.1	144184	38286	type	True	80.4127	366	761	95	below_threshold
Corynebacterium jeddahense	strain=JCB	GCA_000577555.1	1414719	1414719	type	True	80.3887	357	761	95	below_threshold
Corynebacterium fournieri	strain=Marseille-P2948	GCA_900176865.1	1852390	1852390	type	True	80.3336	374	761	95	below_threshold
Corynebacterium lujinxingii	strain=zg-917	GCA_014490555.1	2763010	2763010	type	True	80.279	377	761	95	below_threshold
Corynebacterium ihumii	strain=GD7	GCA_000403725.2	1232427	1232427	type	True	80.1396	372	761	95	below_threshold
Corynebacterium bouchesdurhonense	strain=SN14	GCA_900078305.2	1720192	1720192	type	True	80.1267	371	761	95	below_threshold
Corynebacterium tuscaniense	strain=CCUG 51321T	GCA_008693065.1	302449	302449	type	True	80.0358	333	761	95	below_threshold
Corynebacterium marinum	strain=DSM 44953	GCA_000835165.1	349751	349751	type	True	79.6806	329	761	95	below_threshold
Corynebacterium marinum	strain=CGMCC 1.6998	GCA_014645275.1	349751	349751	type	True	79.6274	323	761	95	below_threshold
Corynebacterium liangguodongii	strain=2184	GCA_003070865.1	2079535	2079535	type	True	79.1502	329	761	95	below_threshold
Corynebacterium striatum	strain=FDAARGOS_1054	GCA_016403285.1	43770	43770	type	True	78.556	178	761	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:15:23,019] [INFO] DFAST Taxonomy check result was written to GCF_030408415.1_ASM3040841v1_genomic.fna/tc_result.tsv
[2024-01-24 12:15:23,019] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:15:23,019] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:15:23,020] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg02a2d2ab-6df1-48b2-bbaf-747b6e59294e/dqc_reference/checkm_data
[2024-01-24 12:15:23,020] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:15:23,047] [INFO] Task started: CheckM
[2024-01-24 12:15:23,047] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030408415.1_ASM3040841v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030408415.1_ASM3040841v1_genomic.fna/checkm_input GCF_030408415.1_ASM3040841v1_genomic.fna/checkm_result
[2024-01-24 12:15:49,105] [INFO] Task succeeded: CheckM
[2024-01-24 12:15:49,106] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.52%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2024-01-24 12:15:49,128] [INFO] ===== Completeness check finished =====
[2024-01-24 12:15:49,129] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:15:49,129] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030408415.1_ASM3040841v1_genomic.fna/markers.fasta)
[2024-01-24 12:15:49,129] [INFO] Task started: Blastn
[2024-01-24 12:15:49,130] [INFO] Running command: blastn -query GCF_030408415.1_ASM3040841v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg02a2d2ab-6df1-48b2-bbaf-747b6e59294e/dqc_reference/reference_markers_gtdb.fasta -out GCF_030408415.1_ASM3040841v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:50,728] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:50,733] [INFO] Selected 10 target genomes.
[2024-01-24 12:15:50,733] [INFO] Target genome list was writen to GCF_030408415.1_ASM3040841v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:15:50,738] [INFO] Task started: fastANI
[2024-01-24 12:15:50,738] [INFO] Running command: fastANI --query /var/lib/cwl/stg089f7ea2-ef71-4ca4-8f97-771d4ea1b398/GCF_030408415.1_ASM3040841v1_genomic.fna.gz --refList GCF_030408415.1_ASM3040841v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030408415.1_ASM3040841v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:15:55,968] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:55,979] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:15:55,979] [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_900156665.1	s__Corynebacterium appendicis	99.9647	729	761	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_017942225.1	s__Corynebacterium sp017942225	87.8987	640	761	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900155535.1	s__Corynebacterium urinipleomorphum	85.0899	608	761	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000143825.1	s__Corynebacterium genitalium_A	81.5198	487	761	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900618065.1	s__Corynebacterium sp900618065	81.0139	463	761	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015351335.1	s__Corynebacterium lipophilum	80.3902	367	761	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900078305.2	s__Corynebacterium bouchesdurhonense	80.1291	371	761	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	100.00	100.00	0.99	0.99	2	-
GCF_008693065.1	s__Corynebacterium tuscaniense	80.0479	333	761	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.42	98.40	0.94	0.94	3	-
GCF_000835165.1	s__Corynebacterium marinum	79.6968	328	761	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	99.21	98.42	0.97	0.94	3	-
GCF_000159135.1	s__Corynebacterium striatum	78.1317	175	761	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.44	95.19	0.92	0.85	41	-
--------------------------------------------------------------------------------
[2024-01-24 12:15:55,981] [INFO] GTDB search result was written to GCF_030408415.1_ASM3040841v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:15:55,982] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:15:55,985] [INFO] DFAST_QC result json was written to GCF_030408415.1_ASM3040841v1_genomic.fna/dqc_result.json
[2024-01-24 12:15:55,985] [INFO] DFAST_QC completed!
[2024-01-24 12:15:55,985] [INFO] Total running time: 0h0m53s