[2023-06-18 23:43:00,055] [INFO] DFAST_QC pipeline started.
[2023-06-18 23:43:00,057] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 23:43:00,057] [INFO] DQC Reference Directory: /var/lib/cwl/stg7e438e2b-5333-4023-b4c9-8efa1639b24d/dqc_reference
[2023-06-18 23:43:01,305] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 23:43:01,306] [INFO] Task started: Prodigal
[2023-06-18 23:43:01,306] [INFO] Running command: gunzip -c /var/lib/cwl/stg62aa21f8-6273-464f-bd9b-3ae1bcf777a2/GCA_018606945.1_ASM1860694v1_genomic.fna.gz | prodigal -d GCA_018606945.1_ASM1860694v1_genomic.fna/cds.fna -a GCA_018606945.1_ASM1860694v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 23:43:03,048] [INFO] Task succeeded: Prodigal
[2023-06-18 23:43:03,049] [INFO] Task started: HMMsearch
[2023-06-18 23:43:03,049] [INFO] Running command: hmmsearch --tblout GCA_018606945.1_ASM1860694v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7e438e2b-5333-4023-b4c9-8efa1639b24d/dqc_reference/reference_markers.hmm GCA_018606945.1_ASM1860694v1_genomic.fna/protein.faa > /dev/null
[2023-06-18 23:43:03,247] [INFO] Task succeeded: HMMsearch
[2023-06-18 23:43:03,249] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg62aa21f8-6273-464f-bd9b-3ae1bcf777a2/GCA_018606945.1_ASM1860694v1_genomic.fna.gz]
[2023-06-18 23:43:03,270] [INFO] Query marker FASTA was written to GCA_018606945.1_ASM1860694v1_genomic.fna/markers.fasta
[2023-06-18 23:43:03,271] [INFO] Task started: Blastn
[2023-06-18 23:43:03,271] [INFO] Running command: blastn -query GCA_018606945.1_ASM1860694v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7e438e2b-5333-4023-b4c9-8efa1639b24d/dqc_reference/reference_markers.fasta -out GCA_018606945.1_ASM1860694v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 23:43:05,445] [INFO] Task succeeded: Blastn
[2023-06-18 23:43:05,449] [INFO] Selected 12 target genomes.
[2023-06-18 23:43:05,449] [INFO] Target genome list was writen to GCA_018606945.1_ASM1860694v1_genomic.fna/target_genomes.txt
[2023-06-18 23:43:05,463] [INFO] Task started: fastANI
[2023-06-18 23:43:05,463] [INFO] Running command: fastANI --query /var/lib/cwl/stg62aa21f8-6273-464f-bd9b-3ae1bcf777a2/GCA_018606945.1_ASM1860694v1_genomic.fna.gz --refList GCA_018606945.1_ASM1860694v1_genomic.fna/target_genomes.txt --output GCA_018606945.1_ASM1860694v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 23:43:12,177] [INFO] Task succeeded: fastANI
[2023-06-18 23:43:12,177] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7e438e2b-5333-4023-b4c9-8efa1639b24d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 23:43:12,177] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7e438e2b-5333-4023-b4c9-8efa1639b24d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 23:43:12,183] [INFO] Found 4 fastANI hits (1 hits with ANI > threshold)
[2023-06-18 23:43:12,183] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-18 23:43:12,183] [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
Actinotignum sanguinis	strain=DSM 26039	GCA_003957255.1	1445614	1445614	type	True	95.8872	174	187	95	conclusive
Actinotignum timonense	strain=type strain: Marseille-P2803	GCA_900155575.1	1870995	1870995	type	True	90.5082	177	187	95	below_threshold
Actinotignum schaalii	strain=DSM 15541	GCA_000429205.1	59505	59505	type	True	89.9524	175	187	95	below_threshold
Actinotignum schaalii	strain=CCUG 27420	GCA_000724605.1	59505	59505	type	True	89.9184	179	187	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-18 23:43:12,186] [INFO] DFAST Taxonomy check result was written to GCA_018606945.1_ASM1860694v1_genomic.fna/tc_result.tsv
[2023-06-18 23:43:12,186] [INFO] ===== Taxonomy check completed =====
[2023-06-18 23:43:12,186] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 23:43:12,187] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7e438e2b-5333-4023-b4c9-8efa1639b24d/dqc_reference/checkm_data
[2023-06-18 23:43:12,188] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 23:43:12,202] [INFO] Task started: CheckM
[2023-06-18 23:43:12,203] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018606945.1_ASM1860694v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018606945.1_ASM1860694v1_genomic.fna/checkm_input GCA_018606945.1_ASM1860694v1_genomic.fna/checkm_result
[2023-06-18 23:43:25,612] [INFO] Task succeeded: CheckM
[2023-06-18 23:43:25,613] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 49.12%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-18 23:43:25,646] [INFO] ===== Completeness check finished =====
[2023-06-18 23:43:25,646] [INFO] ===== Start GTDB Search =====
[2023-06-18 23:43:25,647] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018606945.1_ASM1860694v1_genomic.fna/markers.fasta)
[2023-06-18 23:43:25,647] [INFO] Task started: Blastn
[2023-06-18 23:43:25,647] [INFO] Running command: blastn -query GCA_018606945.1_ASM1860694v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7e438e2b-5333-4023-b4c9-8efa1639b24d/dqc_reference/reference_markers_gtdb.fasta -out GCA_018606945.1_ASM1860694v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 23:43:26,509] [INFO] Task succeeded: Blastn
[2023-06-18 23:43:26,514] [INFO] Selected 8 target genomes.
[2023-06-18 23:43:26,514] [INFO] Target genome list was writen to GCA_018606945.1_ASM1860694v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 23:43:26,519] [INFO] Task started: fastANI
[2023-06-18 23:43:26,519] [INFO] Running command: fastANI --query /var/lib/cwl/stg62aa21f8-6273-464f-bd9b-3ae1bcf777a2/GCA_018606945.1_ASM1860694v1_genomic.fna.gz --refList GCA_018606945.1_ASM1860694v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018606945.1_ASM1860694v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 23:43:29,483] [INFO] Task succeeded: fastANI
[2023-06-18 23:43:29,492] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-18 23:43:29,492] [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_003957255.1	s__Actinotignum sanguinis	95.8872	174	187	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinotignum	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000411135.1	s__Actinotignum schaalii_A	92.7804	172	187	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinotignum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900155575.1	s__Actinotignum timonense	90.4721	178	187	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinotignum	95.0	99.14	98.55	0.97	0.96	4	-
GCF_000724605.1	s__Actinotignum schaalii	89.9184	179	187	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinotignum	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2023-06-18 23:43:29,502] [INFO] GTDB search result was written to GCA_018606945.1_ASM1860694v1_genomic.fna/result_gtdb.tsv
[2023-06-18 23:43:29,503] [INFO] ===== GTDB Search completed =====
[2023-06-18 23:43:29,507] [INFO] DFAST_QC result json was written to GCA_018606945.1_ASM1860694v1_genomic.fna/dqc_result.json
[2023-06-18 23:43:29,508] [INFO] DFAST_QC completed!
[2023-06-18 23:43:29,508] [INFO] Total running time: 0h0m29s