[2024-01-24 13:03:20,658] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:03:20,660] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:03:20,661] [INFO] DQC Reference Directory: /var/lib/cwl/stg4c129da3-129e-4451-b580-45ee9d528e46/dqc_reference
[2024-01-24 13:03:21,879] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:03:21,880] [INFO] Task started: Prodigal
[2024-01-24 13:03:21,880] [INFO] Running command: gunzip -c /var/lib/cwl/stgbf9182da-53a8-405f-a8da-9851e4eb253f/GCF_003688935.1_ASM368893v1_genomic.fna.gz | prodigal -d GCF_003688935.1_ASM368893v1_genomic.fna/cds.fna -a GCF_003688935.1_ASM368893v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:03:28,971] [INFO] Task succeeded: Prodigal
[2024-01-24 13:03:28,972] [INFO] Task started: HMMsearch
[2024-01-24 13:03:28,972] [INFO] Running command: hmmsearch --tblout GCF_003688935.1_ASM368893v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4c129da3-129e-4451-b580-45ee9d528e46/dqc_reference/reference_markers.hmm GCF_003688935.1_ASM368893v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:03:29,200] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:03:29,201] [INFO] Found 6/6 markers.
[2024-01-24 13:03:29,227] [INFO] Query marker FASTA was written to GCF_003688935.1_ASM368893v1_genomic.fna/markers.fasta
[2024-01-24 13:03:29,228] [INFO] Task started: Blastn
[2024-01-24 13:03:29,228] [INFO] Running command: blastn -query GCF_003688935.1_ASM368893v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4c129da3-129e-4451-b580-45ee9d528e46/dqc_reference/reference_markers.fasta -out GCF_003688935.1_ASM368893v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:03:30,018] [INFO] Task succeeded: Blastn
[2024-01-24 13:03:30,028] [INFO] Selected 8 target genomes.
[2024-01-24 13:03:30,029] [INFO] Target genome list was writen to GCF_003688935.1_ASM368893v1_genomic.fna/target_genomes.txt
[2024-01-24 13:03:30,035] [INFO] Task started: fastANI
[2024-01-24 13:03:30,035] [INFO] Running command: fastANI --query /var/lib/cwl/stgbf9182da-53a8-405f-a8da-9851e4eb253f/GCF_003688935.1_ASM368893v1_genomic.fna.gz --refList GCF_003688935.1_ASM368893v1_genomic.fna/target_genomes.txt --output GCF_003688935.1_ASM368893v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:03:35,027] [INFO] Task succeeded: fastANI
[2024-01-24 13:03:35,027] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4c129da3-129e-4451-b580-45ee9d528e46/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:03:35,028] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4c129da3-129e-4451-b580-45ee9d528e46/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:03:35,035] [INFO] Found 8 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:03:35,036] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:03:35,036] [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 macginleyi	strain=CCUG 32361	GCA_003688935.1	38290	38290	type	True	100.0	770	775	95	conclusive
Corynebacterium macginleyi	strain=FDAARGOS_1195	GCA_016889465.1	38290	38290	type	True	99.9993	775	775	95	conclusive
Corynebacterium accolens	strain=ATCC 49725	GCA_000159115.1	38284	38284	type	True	88.0851	667	775	95	below_threshold
Corynebacterium accolens	strain=DSM 44278	GCA_023520795.1	38284	38284	type	True	88.065	671	775	95	below_threshold
Corynebacterium tuberculostearicum	strain=FDAARGOS_1117	GCA_016728365.1	38304	38304	type	True	80.183	427	775	95	below_threshold
Corynebacterium striatum	strain=FDAARGOS_1054	GCA_016403285.1	43770	43770	type	True	78.7488	239	775	95	below_threshold
Corynebacterium vitaeruminis	strain=DSM 20294	GCA_000550805.1	38305	38305	type	True	77.3338	115	775	95	below_threshold
Corynebacterium ureicelerivorans	strain=IMMIB RIV-2301	GCA_000747315.1	401472	401472	type	True	77.2502	105	775	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:03:35,038] [INFO] DFAST Taxonomy check result was written to GCF_003688935.1_ASM368893v1_genomic.fna/tc_result.tsv
[2024-01-24 13:03:35,038] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:03:35,038] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:03:35,039] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4c129da3-129e-4451-b580-45ee9d528e46/dqc_reference/checkm_data
[2024-01-24 13:03:35,039] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:03:35,073] [INFO] Task started: CheckM
[2024-01-24 13:03:35,074] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003688935.1_ASM368893v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003688935.1_ASM368893v1_genomic.fna/checkm_input GCF_003688935.1_ASM368893v1_genomic.fna/checkm_result
[2024-01-24 13:04:01,349] [INFO] Task succeeded: CheckM
[2024-01-24 13:04:01,350] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:04:01,371] [INFO] ===== Completeness check finished =====
[2024-01-24 13:04:01,371] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:04:01,372] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003688935.1_ASM368893v1_genomic.fna/markers.fasta)
[2024-01-24 13:04:01,372] [INFO] Task started: Blastn
[2024-01-24 13:04:01,372] [INFO] Running command: blastn -query GCF_003688935.1_ASM368893v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4c129da3-129e-4451-b580-45ee9d528e46/dqc_reference/reference_markers_gtdb.fasta -out GCF_003688935.1_ASM368893v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:04:02,466] [INFO] Task succeeded: Blastn
[2024-01-24 13:04:02,470] [INFO] Selected 11 target genomes.
[2024-01-24 13:04:02,470] [INFO] Target genome list was writen to GCF_003688935.1_ASM368893v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:04:02,478] [INFO] Task started: fastANI
[2024-01-24 13:04:02,478] [INFO] Running command: fastANI --query /var/lib/cwl/stgbf9182da-53a8-405f-a8da-9851e4eb253f/GCF_003688935.1_ASM368893v1_genomic.fna.gz --refList GCF_003688935.1_ASM368893v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003688935.1_ASM368893v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:04:08,902] [INFO] Task succeeded: fastANI
[2024-01-24 13:04:08,918] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:04:08,918] [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_003688935.1	s__Corynebacterium macginleyi	100.0	770	775	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.68	97.89	0.95	0.93	26	conclusive
GCF_000159115.1	s__Corynebacterium accolens	88.086	668	775	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	97.20	96.99	0.95	0.94	10	-
GCF_000478175.1	s__Corynebacterium sp000478175	88.0133	677	775	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	99.95	99.95	0.99	0.98	3	-
GCF_016894265.1	s__Corynebacterium tuberculostearicum_D	80.1047	423	775	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.1108	N/A	N/A	N/A	N/A	1	-
GCF_000175635.1	s__Corynebacterium tuberculostearicum_C	80.0967	407	775	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	96.3332	96.71	96.71	0.91	0.91	2	-
GCF_016127015.1	s__Corynebacterium aurimucosum_E	79.951	420	775	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	96.91	96.45	0.92	0.89	6	-
GCA_900539985.1	s__Corynebacterium sp900539985	79.8799	377	775	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	99.98	99.98	0.92	0.92	2	-
GCF_000022905.1	s__Corynebacterium aurimucosum	78.7502	247	775	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	99.99	99.99	1.00	1.00	3	-
GCF_000159135.1	s__Corynebacterium striatum	78.4805	224	775	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.44	95.19	0.92	0.85	41	-
GCF_001836165.1	s__Corynebacterium sp001836165	78.3503	237	775	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	97.96	97.92	0.93	0.93	3	-
GCF_001941425.1	s__Corynebacterium ammoniagenes	77.3831	125	775	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	99.70	98.81	0.99	0.95	5	-
--------------------------------------------------------------------------------
[2024-01-24 13:04:08,920] [INFO] GTDB search result was written to GCF_003688935.1_ASM368893v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:04:08,920] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:04:08,923] [INFO] DFAST_QC result json was written to GCF_003688935.1_ASM368893v1_genomic.fna/dqc_result.json
[2024-01-24 13:04:08,924] [INFO] DFAST_QC completed!
[2024-01-24 13:04:08,924] [INFO] Total running time: 0h0m48s