[2024-01-24 12:06:12,488] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:06:12,490] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:06:12,490] [INFO] DQC Reference Directory: /var/lib/cwl/stg767d6a7e-e09f-42d8-b092-0cac872f955f/dqc_reference
[2024-01-24 12:06:13,870] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:06:13,871] [INFO] Task started: Prodigal
[2024-01-24 12:06:13,871] [INFO] Running command: gunzip -c /var/lib/cwl/stge7c41553-ccd9-4b50-8394-128019ede876/GCF_030408395.1_ASM3040839v1_genomic.fna.gz | prodigal -d GCF_030408395.1_ASM3040839v1_genomic.fna/cds.fna -a GCF_030408395.1_ASM3040839v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:06:22,214] [INFO] Task succeeded: Prodigal
[2024-01-24 12:06:22,215] [INFO] Task started: HMMsearch
[2024-01-24 12:06:22,215] [INFO] Running command: hmmsearch --tblout GCF_030408395.1_ASM3040839v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg767d6a7e-e09f-42d8-b092-0cac872f955f/dqc_reference/reference_markers.hmm GCF_030408395.1_ASM3040839v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:06:22,442] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:06:22,443] [INFO] Found 6/6 markers.
[2024-01-24 12:06:22,467] [INFO] Query marker FASTA was written to GCF_030408395.1_ASM3040839v1_genomic.fna/markers.fasta
[2024-01-24 12:06:22,468] [INFO] Task started: Blastn
[2024-01-24 12:06:22,468] [INFO] Running command: blastn -query GCF_030408395.1_ASM3040839v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg767d6a7e-e09f-42d8-b092-0cac872f955f/dqc_reference/reference_markers.fasta -out GCF_030408395.1_ASM3040839v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:06:23,401] [INFO] Task succeeded: Blastn
[2024-01-24 12:06:23,405] [INFO] Selected 19 target genomes.
[2024-01-24 12:06:23,406] [INFO] Target genome list was writen to GCF_030408395.1_ASM3040839v1_genomic.fna/target_genomes.txt
[2024-01-24 12:06:23,430] [INFO] Task started: fastANI
[2024-01-24 12:06:23,431] [INFO] Running command: fastANI --query /var/lib/cwl/stge7c41553-ccd9-4b50-8394-128019ede876/GCF_030408395.1_ASM3040839v1_genomic.fna.gz --refList GCF_030408395.1_ASM3040839v1_genomic.fna/target_genomes.txt --output GCF_030408395.1_ASM3040839v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:06:32,641] [INFO] Task succeeded: fastANI
[2024-01-24 12:06:32,641] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg767d6a7e-e09f-42d8-b092-0cac872f955f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:06:32,642] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg767d6a7e-e09f-42d8-b092-0cac872f955f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:06:32,656] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:06:32,656] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:06:32,657] [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 aquatimens	strain=DSM 45632	GCA_015752125.1	1190508	1190508	type	True	99.9972	841	841	95	conclusive
Corynebacterium urinipleomorphum	strain=Marseille-P2799	GCA_900155535.1	1852380	1852380	type	True	79.8042	299	841	95	below_threshold
Corynebacterium jeddahense	strain=JCB	GCA_000577555.1	1414719	1414719	type	True	79.6564	241	841	95	below_threshold
Corynebacterium lipophiloflavum	strain=DSM 44291	GCA_000159635.1	161889	161889	type	True	79.4636	232	841	95	below_threshold
Corynebacterium appendicis	strain=DSM 44531	GCA_900156665.1	163202	163202	type	True	79.3915	293	841	95	below_threshold
Corynebacterium mycetoides	strain=DSM 20632	GCA_900103625.1	38302	38302	type	True	79.3727	265	841	95	below_threshold
Corynebacterium sanguinis	strain=CCUG 58655	GCA_007641235.1	2594913	2594913	type	True	79.2217	239	841	95	below_threshold
Corynebacterium senegalense	strain=Marseille-P4329	GCA_900411315.1	2080750	2080750	type	True	79.2001	258	841	95	below_threshold
Corynebacterium bouchesdurhonense	strain=SN14	GCA_900078305.2	1720192	1720192	type	True	79.0713	249	841	95	below_threshold
Corynebacterium tuscaniense	strain=CCUG 51321T	GCA_008693065.1	302449	302449	type	True	78.9646	222	841	95	below_threshold
Corynebacterium riegelii	strain=FDAARGOS_1114	GCA_016728505.1	156976	156976	type	True	78.8607	217	841	95	below_threshold
Corynebacterium qintianiae	strain=MC1420	GCA_011038645.2	2709392	2709392	type	True	78.3671	221	841	95	below_threshold
Corynebacterium humireducens	strain=NBRC 106098	GCA_001571025.1	1223514	1223514	type	True	77.4515	195	841	95	below_threshold
Corynebacterium variabile	strain=NBRC 15286	GCA_006539825.1	1727	1727	type	True	77.1708	98	841	95	below_threshold
Smaragdicoccus niigatensis	strain=DSM 44881	GCA_000380645.1	359359	359359	type	True	77.0573	56	841	95	below_threshold
Smaragdicoccus niigatensis	strain=NBRC 103563	GCA_001552795.1	359359	359359	type	True	76.5642	54	841	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:06:32,658] [INFO] DFAST Taxonomy check result was written to GCF_030408395.1_ASM3040839v1_genomic.fna/tc_result.tsv
[2024-01-24 12:06:32,659] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:06:32,659] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:06:32,659] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg767d6a7e-e09f-42d8-b092-0cac872f955f/dqc_reference/checkm_data
[2024-01-24 12:06:32,660] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:06:32,698] [INFO] Task started: CheckM
[2024-01-24 12:06:32,699] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030408395.1_ASM3040839v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030408395.1_ASM3040839v1_genomic.fna/checkm_input GCF_030408395.1_ASM3040839v1_genomic.fna/checkm_result
[2024-01-24 12:07:02,784] [INFO] Task succeeded: CheckM
[2024-01-24 12:07:02,785] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:07:02,804] [INFO] ===== Completeness check finished =====
[2024-01-24 12:07:02,804] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:07:02,805] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030408395.1_ASM3040839v1_genomic.fna/markers.fasta)
[2024-01-24 12:07:02,805] [INFO] Task started: Blastn
[2024-01-24 12:07:02,805] [INFO] Running command: blastn -query GCF_030408395.1_ASM3040839v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg767d6a7e-e09f-42d8-b092-0cac872f955f/dqc_reference/reference_markers_gtdb.fasta -out GCF_030408395.1_ASM3040839v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:07:04,051] [INFO] Task succeeded: Blastn
[2024-01-24 12:07:04,054] [INFO] Selected 20 target genomes.
[2024-01-24 12:07:04,054] [INFO] Target genome list was writen to GCF_030408395.1_ASM3040839v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:07:04,071] [INFO] Task started: fastANI
[2024-01-24 12:07:04,071] [INFO] Running command: fastANI --query /var/lib/cwl/stge7c41553-ccd9-4b50-8394-128019ede876/GCF_030408395.1_ASM3040839v1_genomic.fna.gz --refList GCF_030408395.1_ASM3040839v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030408395.1_ASM3040839v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:07:14,489] [INFO] Task succeeded: fastANI
[2024-01-24 12:07:14,508] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:07:14,509] [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_015752125.1	s__Corynebacterium aquatimens	99.9972	841	841	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_900618065.1	s__Corynebacterium sp900618065	79.915	304	841	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	79.7819	299	841	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_903645305.1	s__Corynebacterium sp001764565	79.551	237	841	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.10	98.10	0.96	0.96	2	-
GCF_017942225.1	s__Corynebacterium sp017942225	79.5486	295	841	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900103625.1	s__Corynebacterium mycetoides	79.4232	265	841	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900156665.1	s__Corynebacterium appendicis	79.3915	293	841	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	79.3338	304	841	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900411315.1	s__Corynebacterium senegalense	79.2638	260	841	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007641235.1	s__Corynebacterium sanguinis	79.2378	237	841	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.27	97.90	0.92	0.90	7	-
GCF_900078305.2	s__Corynebacterium bouchesdurhonense	79.079	247	841	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	78.9646	222	841	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.42	98.40	0.94	0.94	3	-
GCF_016728505.1	s__Corynebacterium riegelii	78.9544	217	841	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	97.34	97.30	0.92	0.92	4	-
GCF_011038645.2	s__Corynebacterium qintianiae	78.3671	221	841	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.90	98.90	0.92	0.92	2	-
GCA_002339505.1	s__Corynebacterium sp002339505	78.317	217	841	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006539825.1	s__Corynebacterium variabile	77.1708	98	841	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.53	98.15	0.92	0.86	8	-
GCA_012838985.1	s__Corynebacterium sp012838985	76.6722	161	841	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:07:14,511] [INFO] GTDB search result was written to GCF_030408395.1_ASM3040839v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:07:14,511] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:07:14,516] [INFO] DFAST_QC result json was written to GCF_030408395.1_ASM3040839v1_genomic.fna/dqc_result.json
[2024-01-24 12:07:14,517] [INFO] DFAST_QC completed!
[2024-01-24 12:07:14,517] [INFO] Total running time: 0h1m2s