[2024-01-24 14:19:32,012] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:19:32,014] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:19:32,015] [INFO] DQC Reference Directory: /var/lib/cwl/stg7cc12d8e-de3c-45f8-b970-7b680a133175/dqc_reference
[2024-01-24 14:19:33,490] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:19:33,491] [INFO] Task started: Prodigal
[2024-01-24 14:19:33,491] [INFO] Running command: gunzip -c /var/lib/cwl/stg10c8943f-f372-40b3-a59c-3f29f81f7e1e/GCF_000420445.1_ASM42044v1_genomic.fna.gz | prodigal -d GCF_000420445.1_ASM42044v1_genomic.fna/cds.fna -a GCF_000420445.1_ASM42044v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:19:39,633] [INFO] Task succeeded: Prodigal
[2024-01-24 14:19:39,633] [INFO] Task started: HMMsearch
[2024-01-24 14:19:39,633] [INFO] Running command: hmmsearch --tblout GCF_000420445.1_ASM42044v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7cc12d8e-de3c-45f8-b970-7b680a133175/dqc_reference/reference_markers.hmm GCF_000420445.1_ASM42044v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:19:39,881] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:19:39,883] [INFO] Found 6/6 markers.
[2024-01-24 14:19:39,917] [INFO] Query marker FASTA was written to GCF_000420445.1_ASM42044v1_genomic.fna/markers.fasta
[2024-01-24 14:19:39,918] [INFO] Task started: Blastn
[2024-01-24 14:19:39,918] [INFO] Running command: blastn -query GCF_000420445.1_ASM42044v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7cc12d8e-de3c-45f8-b970-7b680a133175/dqc_reference/reference_markers.fasta -out GCF_000420445.1_ASM42044v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:19:40,547] [INFO] Task succeeded: Blastn
[2024-01-24 14:19:40,555] [INFO] Selected 25 target genomes.
[2024-01-24 14:19:40,555] [INFO] Target genome list was writen to GCF_000420445.1_ASM42044v1_genomic.fna/target_genomes.txt
[2024-01-24 14:19:40,599] [INFO] Task started: fastANI
[2024-01-24 14:19:40,600] [INFO] Running command: fastANI --query /var/lib/cwl/stg10c8943f-f372-40b3-a59c-3f29f81f7e1e/GCF_000420445.1_ASM42044v1_genomic.fna.gz --refList GCF_000420445.1_ASM42044v1_genomic.fna/target_genomes.txt --output GCF_000420445.1_ASM42044v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:19:53,408] [INFO] Task succeeded: fastANI
[2024-01-24 14:19:53,409] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7cc12d8e-de3c-45f8-b970-7b680a133175/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:19:53,409] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7cc12d8e-de3c-45f8-b970-7b680a133175/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:19:53,415] [INFO] Found 4 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:19:53,415] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:19:53,416] [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	76.8709	54	624	95	below_threshold
Actinotignum schaalii	strain=CCUG 27420	GCA_000724605.1	59505	59505	type	True	76.8383	55	624	95	below_threshold
Actinotignum schaalii	strain=DSM 15541	GCA_000429205.1	59505	59505	type	True	76.8373	54	624	95	below_threshold
Actinotignum timonense	strain=type strain: Marseille-P2803	GCA_900155575.1	1870995	1870995	type	True	76.7728	56	624	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:19:53,418] [INFO] DFAST Taxonomy check result was written to GCF_000420445.1_ASM42044v1_genomic.fna/tc_result.tsv
[2024-01-24 14:19:53,418] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:19:53,418] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:19:53,419] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7cc12d8e-de3c-45f8-b970-7b680a133175/dqc_reference/checkm_data
[2024-01-24 14:19:53,420] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:19:53,443] [INFO] Task started: CheckM
[2024-01-24 14:19:53,443] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000420445.1_ASM42044v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000420445.1_ASM42044v1_genomic.fna/checkm_input GCF_000420445.1_ASM42044v1_genomic.fna/checkm_result
[2024-01-24 14:20:17,923] [INFO] Task succeeded: CheckM
[2024-01-24 14:20:17,925] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:20:17,946] [INFO] ===== Completeness check finished =====
[2024-01-24 14:20:17,947] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:20:17,948] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000420445.1_ASM42044v1_genomic.fna/markers.fasta)
[2024-01-24 14:20:17,948] [INFO] Task started: Blastn
[2024-01-24 14:20:17,948] [INFO] Running command: blastn -query GCF_000420445.1_ASM42044v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7cc12d8e-de3c-45f8-b970-7b680a133175/dqc_reference/reference_markers_gtdb.fasta -out GCF_000420445.1_ASM42044v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:20:18,731] [INFO] Task succeeded: Blastn
[2024-01-24 14:20:18,736] [INFO] Selected 23 target genomes.
[2024-01-24 14:20:18,737] [INFO] Target genome list was writen to GCF_000420445.1_ASM42044v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:20:18,774] [INFO] Task started: fastANI
[2024-01-24 14:20:18,774] [INFO] Running command: fastANI --query /var/lib/cwl/stg10c8943f-f372-40b3-a59c-3f29f81f7e1e/GCF_000420445.1_ASM42044v1_genomic.fna.gz --refList GCF_000420445.1_ASM42044v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000420445.1_ASM42044v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:20:28,736] [INFO] Task succeeded: fastANI
[2024-01-24 14:20:28,745] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:20:28,745] [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_000420445.1	s__Actinotignum urinale	100.0	621	624	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinotignum	95.0	99.41	99.41	0.92	0.92	2	conclusive
GCF_000411135.1	s__Actinotignum schaalii_A	76.9481	50	624	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinotignum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003957255.1	s__Actinotignum sanguinis	76.8709	54	624	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinotignum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000724605.1	s__Actinotignum schaalii	76.8383	55	624	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinotignum	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900155575.1	s__Actinotignum timonense	76.7728	56	624	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinotignum	95.0	99.14	98.55	0.97	0.96	4	-
--------------------------------------------------------------------------------
[2024-01-24 14:20:28,747] [INFO] GTDB search result was written to GCF_000420445.1_ASM42044v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:20:28,748] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:20:28,751] [INFO] DFAST_QC result json was written to GCF_000420445.1_ASM42044v1_genomic.fna/dqc_result.json
[2024-01-24 14:20:28,751] [INFO] DFAST_QC completed!
[2024-01-24 14:20:28,751] [INFO] Total running time: 0h0m57s