[2024-01-24 12:31:21,197] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:31:21,199] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:31:21,199] [INFO] DQC Reference Directory: /var/lib/cwl/stg2f48c1f4-3087-434d-a2c8-188cba39bf96/dqc_reference
[2024-01-24 12:31:22,474] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:31:22,475] [INFO] Task started: Prodigal
[2024-01-24 12:31:22,475] [INFO] Running command: gunzip -c /var/lib/cwl/stg0bc777f4-8f68-48b7-8220-94d4166f0eb8/GCF_008933115.1_ASM893311v1_genomic.fna.gz | prodigal -d GCF_008933115.1_ASM893311v1_genomic.fna/cds.fna -a GCF_008933115.1_ASM893311v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:31:38,911] [INFO] Task succeeded: Prodigal
[2024-01-24 12:31:38,911] [INFO] Task started: HMMsearch
[2024-01-24 12:31:38,911] [INFO] Running command: hmmsearch --tblout GCF_008933115.1_ASM893311v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2f48c1f4-3087-434d-a2c8-188cba39bf96/dqc_reference/reference_markers.hmm GCF_008933115.1_ASM893311v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:31:39,118] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:31:39,120] [INFO] Found 6/6 markers.
[2024-01-24 12:31:39,148] [INFO] Query marker FASTA was written to GCF_008933115.1_ASM893311v1_genomic.fna/markers.fasta
[2024-01-24 12:31:39,148] [INFO] Task started: Blastn
[2024-01-24 12:31:39,148] [INFO] Running command: blastn -query GCF_008933115.1_ASM893311v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2f48c1f4-3087-434d-a2c8-188cba39bf96/dqc_reference/reference_markers.fasta -out GCF_008933115.1_ASM893311v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:31:39,703] [INFO] Task succeeded: Blastn
[2024-01-24 12:31:39,706] [INFO] Selected 17 target genomes.
[2024-01-24 12:31:39,706] [INFO] Target genome list was writen to GCF_008933115.1_ASM893311v1_genomic.fna/target_genomes.txt
[2024-01-24 12:31:39,717] [INFO] Task started: fastANI
[2024-01-24 12:31:39,718] [INFO] Running command: fastANI --query /var/lib/cwl/stg0bc777f4-8f68-48b7-8220-94d4166f0eb8/GCF_008933115.1_ASM893311v1_genomic.fna.gz --refList GCF_008933115.1_ASM893311v1_genomic.fna/target_genomes.txt --output GCF_008933115.1_ASM893311v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:31:50,588] [INFO] Task succeeded: fastANI
[2024-01-24 12:31:50,589] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2f48c1f4-3087-434d-a2c8-188cba39bf96/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:31:50,589] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2f48c1f4-3087-434d-a2c8-188cba39bf96/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:31:50,594] [INFO] Found 3 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:31:50,595] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:31:50,595] [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
Phaeocystidibacter luteus	strain=LMG 25704	GCA_008933115.1	911197	911197	type	True	100.0	1053	1056	95	conclusive
Phaeocystidibacter marisrubri	strain=JCM 30614	GCA_008933165.1	1577780	1577780	type	True	77.9207	185	1056	95	below_threshold
Phaeocystidibacter marisrubri	strain=CGMCC 1.14954	GCA_014640415.1	1577780	1577780	type	True	77.9142	184	1056	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:31:50,597] [INFO] DFAST Taxonomy check result was written to GCF_008933115.1_ASM893311v1_genomic.fna/tc_result.tsv
[2024-01-24 12:31:50,598] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:31:50,598] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:31:50,598] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2f48c1f4-3087-434d-a2c8-188cba39bf96/dqc_reference/checkm_data
[2024-01-24 12:31:50,599] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:31:50,633] [INFO] Task started: CheckM
[2024-01-24 12:31:50,633] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008933115.1_ASM893311v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008933115.1_ASM893311v1_genomic.fna/checkm_input GCF_008933115.1_ASM893311v1_genomic.fna/checkm_result
[2024-01-24 12:32:39,727] [INFO] Task succeeded: CheckM
[2024-01-24 12:32:39,729] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:32:39,748] [INFO] ===== Completeness check finished =====
[2024-01-24 12:32:39,748] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:32:39,749] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008933115.1_ASM893311v1_genomic.fna/markers.fasta)
[2024-01-24 12:32:39,749] [INFO] Task started: Blastn
[2024-01-24 12:32:39,749] [INFO] Running command: blastn -query GCF_008933115.1_ASM893311v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2f48c1f4-3087-434d-a2c8-188cba39bf96/dqc_reference/reference_markers_gtdb.fasta -out GCF_008933115.1_ASM893311v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:32:40,550] [INFO] Task succeeded: Blastn
[2024-01-24 12:32:40,554] [INFO] Selected 20 target genomes.
[2024-01-24 12:32:40,554] [INFO] Target genome list was writen to GCF_008933115.1_ASM893311v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:32:40,593] [INFO] Task started: fastANI
[2024-01-24 12:32:40,593] [INFO] Running command: fastANI --query /var/lib/cwl/stg0bc777f4-8f68-48b7-8220-94d4166f0eb8/GCF_008933115.1_ASM893311v1_genomic.fna.gz --refList GCF_008933115.1_ASM893311v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008933115.1_ASM893311v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:32:50,433] [INFO] Task succeeded: fastANI
[2024-01-24 12:32:50,437] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:32:50,437] [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_008933115.1	s__Phaeocystidibacter luteus	100.0	1053	1056	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__Phaeocystidibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_013373425.1	s__Phaeocystidibacter sp013373425	77.9414	230	1056	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__Phaeocystidibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008933165.1	s__Phaeocystidibacter marisrubri	77.9207	185	1056	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__Phaeocystidibacter	95.0	99.07	98.14	0.97	0.95	3	-
--------------------------------------------------------------------------------
[2024-01-24 12:32:50,439] [INFO] GTDB search result was written to GCF_008933115.1_ASM893311v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:32:50,440] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:32:50,443] [INFO] DFAST_QC result json was written to GCF_008933115.1_ASM893311v1_genomic.fna/dqc_result.json
[2024-01-24 12:32:50,443] [INFO] DFAST_QC completed!
[2024-01-24 12:32:50,443] [INFO] Total running time: 0h1m29s