[2023-06-29 18:37:21,528] [INFO] DFAST_QC pipeline started.
[2023-06-29 18:37:21,532] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 18:37:21,532] [INFO] DQC Reference Directory: /var/lib/cwl/stgf7fc3e98-ad69-43b1-9779-d9e94079abe6/dqc_reference
[2023-06-29 18:37:22,771] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 18:37:22,772] [INFO] Task started: Prodigal
[2023-06-29 18:37:22,772] [INFO] Running command: gunzip -c /var/lib/cwl/stgce913a04-edcc-4486-9536-585c0dab3ae5/GCA_021619475.1_ASM2161947v1_genomic.fna.gz | prodigal -d GCA_021619475.1_ASM2161947v1_genomic.fna/cds.fna -a GCA_021619475.1_ASM2161947v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 18:37:26,070] [INFO] Task succeeded: Prodigal
[2023-06-29 18:37:26,071] [INFO] Task started: HMMsearch
[2023-06-29 18:37:26,071] [INFO] Running command: hmmsearch --tblout GCA_021619475.1_ASM2161947v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf7fc3e98-ad69-43b1-9779-d9e94079abe6/dqc_reference/reference_markers.hmm GCA_021619475.1_ASM2161947v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 18:37:26,260] [INFO] Task succeeded: HMMsearch
[2023-06-29 18:37:26,261] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgce913a04-edcc-4486-9536-585c0dab3ae5/GCA_021619475.1_ASM2161947v1_genomic.fna.gz]
[2023-06-29 18:37:26,283] [INFO] Query marker FASTA was written to GCA_021619475.1_ASM2161947v1_genomic.fna/markers.fasta
[2023-06-29 18:37:26,283] [INFO] Task started: Blastn
[2023-06-29 18:37:26,283] [INFO] Running command: blastn -query GCA_021619475.1_ASM2161947v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf7fc3e98-ad69-43b1-9779-d9e94079abe6/dqc_reference/reference_markers.fasta -out GCA_021619475.1_ASM2161947v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 18:37:26,768] [INFO] Task succeeded: Blastn
[2023-06-29 18:37:26,772] [INFO] Selected 11 target genomes.
[2023-06-29 18:37:26,772] [INFO] Target genome list was writen to GCA_021619475.1_ASM2161947v1_genomic.fna/target_genomes.txt
[2023-06-29 18:37:26,774] [INFO] Task started: fastANI
[2023-06-29 18:37:26,774] [INFO] Running command: fastANI --query /var/lib/cwl/stgce913a04-edcc-4486-9536-585c0dab3ae5/GCA_021619475.1_ASM2161947v1_genomic.fna.gz --refList GCA_021619475.1_ASM2161947v1_genomic.fna/target_genomes.txt --output GCA_021619475.1_ASM2161947v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 18:37:31,622] [INFO] Task succeeded: fastANI
[2023-06-29 18:37:31,622] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf7fc3e98-ad69-43b1-9779-d9e94079abe6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 18:37:31,623] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf7fc3e98-ad69-43b1-9779-d9e94079abe6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 18:37:31,627] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 18:37:31,627] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 18:37:31,627] [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
Anaerovibrio slackiae	strain=WCA-693-APC-5D-A	GCA_009695585.1	2652309	2652309	type	True	80.8561	70	125	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 18:37:31,629] [INFO] DFAST Taxonomy check result was written to GCA_021619475.1_ASM2161947v1_genomic.fna/tc_result.tsv
[2023-06-29 18:37:31,629] [INFO] ===== Taxonomy check completed =====
[2023-06-29 18:37:31,630] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 18:37:31,630] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf7fc3e98-ad69-43b1-9779-d9e94079abe6/dqc_reference/checkm_data
[2023-06-29 18:37:31,631] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 18:37:31,659] [INFO] Task started: CheckM
[2023-06-29 18:37:31,659] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_021619475.1_ASM2161947v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_021619475.1_ASM2161947v1_genomic.fna/checkm_input GCA_021619475.1_ASM2161947v1_genomic.fna/checkm_result
[2023-06-29 18:37:49,964] [INFO] Task succeeded: CheckM
[2023-06-29 18:37:49,967] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 76.18%
Contamintation: 6.25%
Strain heterogeneity: 33.33%
--------------------------------------------------------------------------------
[2023-06-29 18:37:49,991] [INFO] ===== Completeness check finished =====
[2023-06-29 18:37:49,992] [INFO] ===== Start GTDB Search =====
[2023-06-29 18:37:49,992] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_021619475.1_ASM2161947v1_genomic.fna/markers.fasta)
[2023-06-29 18:37:49,992] [INFO] Task started: Blastn
[2023-06-29 18:37:49,992] [INFO] Running command: blastn -query GCA_021619475.1_ASM2161947v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf7fc3e98-ad69-43b1-9779-d9e94079abe6/dqc_reference/reference_markers_gtdb.fasta -out GCA_021619475.1_ASM2161947v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 18:37:50,618] [INFO] Task succeeded: Blastn
[2023-06-29 18:37:50,622] [INFO] Selected 13 target genomes.
[2023-06-29 18:37:50,622] [INFO] Target genome list was writen to GCA_021619475.1_ASM2161947v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 18:37:50,648] [INFO] Task started: fastANI
[2023-06-29 18:37:50,648] [INFO] Running command: fastANI --query /var/lib/cwl/stgce913a04-edcc-4486-9536-585c0dab3ae5/GCA_021619475.1_ASM2161947v1_genomic.fna.gz --refList GCA_021619475.1_ASM2161947v1_genomic.fna/target_genomes_gtdb.txt --output GCA_021619475.1_ASM2161947v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 18:37:56,455] [INFO] Task succeeded: fastANI
[2023-06-29 18:37:56,460] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 18:37:56,460] [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
GCA_900548165.1	s__Anaerovibrio sp900548165	96.6552	110	125	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Anaerovibrio	95.0	96.97	96.65	0.86	0.85	4	conclusive
GCF_009695585.1	s__Anaerovibrio slackiae	80.8561	70	125	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Anaerovibrio	95.0	98.28	97.88	0.95	0.93	10	-
GCA_900768695.1	s__Anaerovibrio sp900768695	79.4896	51	125	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Anaerovibrio	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 18:37:56,462] [INFO] GTDB search result was written to GCA_021619475.1_ASM2161947v1_genomic.fna/result_gtdb.tsv
[2023-06-29 18:37:56,463] [INFO] ===== GTDB Search completed =====
[2023-06-29 18:37:56,467] [INFO] DFAST_QC result json was written to GCA_021619475.1_ASM2161947v1_genomic.fna/dqc_result.json
[2023-06-29 18:37:56,467] [INFO] DFAST_QC completed!
[2023-06-29 18:37:56,467] [INFO] Total running time: 0h0m35s