[2024-01-25 19:45:21,067] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:45:21,068] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:45:21,068] [INFO] DQC Reference Directory: /var/lib/cwl/stg6f8826da-9e9e-497a-a786-7493e2b15b4a/dqc_reference
[2024-01-25 19:45:22,229] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:45:22,230] [INFO] Task started: Prodigal
[2024-01-25 19:45:22,230] [INFO] Running command: gunzip -c /var/lib/cwl/stg9f3a4b79-07b0-4463-91cd-b1dee8a52e2a/GCF_027570155.1_ASM2757015v1_genomic.fna.gz | prodigal -d GCF_027570155.1_ASM2757015v1_genomic.fna/cds.fna -a GCF_027570155.1_ASM2757015v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:45:28,884] [INFO] Task succeeded: Prodigal
[2024-01-25 19:45:28,884] [INFO] Task started: HMMsearch
[2024-01-25 19:45:28,885] [INFO] Running command: hmmsearch --tblout GCF_027570155.1_ASM2757015v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6f8826da-9e9e-497a-a786-7493e2b15b4a/dqc_reference/reference_markers.hmm GCF_027570155.1_ASM2757015v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:45:29,062] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:45:29,063] [INFO] Found 6/6 markers.
[2024-01-25 19:45:29,084] [INFO] Query marker FASTA was written to GCF_027570155.1_ASM2757015v1_genomic.fna/markers.fasta
[2024-01-25 19:45:29,084] [INFO] Task started: Blastn
[2024-01-25 19:45:29,084] [INFO] Running command: blastn -query GCF_027570155.1_ASM2757015v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6f8826da-9e9e-497a-a786-7493e2b15b4a/dqc_reference/reference_markers.fasta -out GCF_027570155.1_ASM2757015v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:45:29,779] [INFO] Task succeeded: Blastn
[2024-01-25 19:45:29,783] [INFO] Selected 16 target genomes.
[2024-01-25 19:45:29,783] [INFO] Target genome list was writen to GCF_027570155.1_ASM2757015v1_genomic.fna/target_genomes.txt
[2024-01-25 19:45:29,804] [INFO] Task started: fastANI
[2024-01-25 19:45:29,804] [INFO] Running command: fastANI --query /var/lib/cwl/stg9f3a4b79-07b0-4463-91cd-b1dee8a52e2a/GCF_027570155.1_ASM2757015v1_genomic.fna.gz --refList GCF_027570155.1_ASM2757015v1_genomic.fna/target_genomes.txt --output GCF_027570155.1_ASM2757015v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:45:37,629] [INFO] Task succeeded: fastANI
[2024-01-25 19:45:37,629] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6f8826da-9e9e-497a-a786-7493e2b15b4a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:45:37,630] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6f8826da-9e9e-497a-a786-7493e2b15b4a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:45:37,640] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 19:45:37,640] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 19:45:37,640] [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 tuberculostearicum	strain=FDAARGOS_1117	GCA_016728365.1	38304	38304	type	True	94.3221	708	804	95	below_threshold
Corynebacterium tuberculostearicum	strain=DSM 44922	GCA_013408445.1	38304	38304	type	True	94.2898	708	804	95	below_threshold
Corynebacterium accolens	strain=ATCC 49725	GCA_000159115.1	38284	38284	type	True	81.4869	539	804	95	below_threshold
Corynebacterium accolens	strain=DSM 44278	GCA_023520795.1	38284	38284	type	True	81.4285	549	804	95	below_threshold
Corynebacterium macginleyi	strain=CCUG 32361	GCA_003688935.1	38290	38290	type	True	79.9005	417	804	95	below_threshold
Corynebacterium aurimucosum	strain=FDAARGOS_1109	GCA_016728705.1	169292	169292	suspected-type	True	79.8835	362	804	95	below_threshold
Corynebacterium aurimucosum	strain=DSM 44532	GCA_024138775.1	169292	169292	suspected-type	True	79.843	365	804	95	below_threshold
Corynebacterium striatum	strain=FDAARGOS_1054	GCA_016403285.1	43770	43770	type	True	79.5929	347	804	95	below_threshold
Corynebacterium phoceense	strain=MC1	GCA_900092335.1	1686286	1686286	type	True	79.0092	297	804	95	below_threshold
Corynebacterium massiliense	strain=DSM 45435	GCA_000420605.1	441501	441501	type	True	78.7343	257	804	95	below_threshold
Corynebacterium flavescens	strain=OJ8	GCA_001941465.1	28028	28028	type	True	78.6354	258	804	95	below_threshold
Corynebacterium ureicelerivorans	strain=IMMIB RIV-2301	GCA_000747315.1	401472	401472	type	True	78.119	164	804	95	below_threshold
Corynebacterium mucifaciens	strain=ATCC 700355	GCA_012396315.1	57171	57171	type	True	78.0366	160	804	95	below_threshold
Corynebacterium imitans	strain=DSM 44264	GCA_000739455.1	156978	156978	type	True	77.7717	172	804	95	below_threshold
Corynebacterium imitans	strain=NCTC13015	GCA_900187215.1	156978	156978	type	True	77.7104	167	804	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:45:37,643] [INFO] DFAST Taxonomy check result was written to GCF_027570155.1_ASM2757015v1_genomic.fna/tc_result.tsv
[2024-01-25 19:45:37,644] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:45:37,644] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:45:37,644] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6f8826da-9e9e-497a-a786-7493e2b15b4a/dqc_reference/checkm_data
[2024-01-25 19:45:37,645] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:45:37,672] [INFO] Task started: CheckM
[2024-01-25 19:45:37,672] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_027570155.1_ASM2757015v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_027570155.1_ASM2757015v1_genomic.fna/checkm_input GCF_027570155.1_ASM2757015v1_genomic.fna/checkm_result
[2024-01-25 19:46:00,651] [INFO] Task succeeded: CheckM
[2024-01-25 19:46:00,652] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:46:00,677] [INFO] ===== Completeness check finished =====
[2024-01-25 19:46:00,677] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:46:00,678] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_027570155.1_ASM2757015v1_genomic.fna/markers.fasta)
[2024-01-25 19:46:00,678] [INFO] Task started: Blastn
[2024-01-25 19:46:00,678] [INFO] Running command: blastn -query GCF_027570155.1_ASM2757015v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6f8826da-9e9e-497a-a786-7493e2b15b4a/dqc_reference/reference_markers_gtdb.fasta -out GCF_027570155.1_ASM2757015v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:46:01,692] [INFO] Task succeeded: Blastn
[2024-01-25 19:46:01,695] [INFO] Selected 6 target genomes.
[2024-01-25 19:46:01,695] [INFO] Target genome list was writen to GCF_027570155.1_ASM2757015v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:46:01,703] [INFO] Task started: fastANI
[2024-01-25 19:46:01,704] [INFO] Running command: fastANI --query /var/lib/cwl/stg9f3a4b79-07b0-4463-91cd-b1dee8a52e2a/GCF_027570155.1_ASM2757015v1_genomic.fna.gz --refList GCF_027570155.1_ASM2757015v1_genomic.fna/target_genomes_gtdb.txt --output GCF_027570155.1_ASM2757015v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:46:05,196] [INFO] Task succeeded: fastANI
[2024-01-25 19:46:05,201] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:46:05,202] [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_016127015.1	s__Corynebacterium aurimucosum_E	96.4464	711	804	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	96.91	96.45	0.92	0.89	6	conclusive
GCA_900539985.1	s__Corynebacterium sp900539985	94.7033	627	804	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	99.98	99.98	0.92	0.92	2	-
GCF_000175635.1	s__Corynebacterium tuberculostearicum_C	94.4068	710	804	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	96.3332	96.71	96.71	0.91	0.91	2	-
GCF_013408445.1	s__Corynebacterium tuberculostearicum	94.2898	708	804	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	96.3332	98.29	96.59	0.96	0.92	3	-
GCF_016894265.1	s__Corynebacterium tuberculostearicum_D	94.2709	695	804	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.1108	N/A	N/A	N/A	N/A	1	-
GCF_002154655.1	s__Corynebacterium kefirresidentii	89.3273	694	804	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	96.23	95.39	0.90	0.89	9	-
--------------------------------------------------------------------------------
[2024-01-25 19:46:05,203] [INFO] GTDB search result was written to GCF_027570155.1_ASM2757015v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:46:05,203] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:46:05,206] [INFO] DFAST_QC result json was written to GCF_027570155.1_ASM2757015v1_genomic.fna/dqc_result.json
[2024-01-25 19:46:05,206] [INFO] DFAST_QC completed!
[2024-01-25 19:46:05,206] [INFO] Total running time: 0h0m44s