[2024-01-24 12:36:58,426] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:36:58,428] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:36:58,429] [INFO] DQC Reference Directory: /var/lib/cwl/stgcd207f0a-d651-4b8b-905c-b351daef3c7b/dqc_reference
[2024-01-24 12:36:59,703] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:36:59,703] [INFO] Task started: Prodigal
[2024-01-24 12:36:59,704] [INFO] Running command: gunzip -c /var/lib/cwl/stg72334d46-9256-484e-a643-6fe13ae24361/GCF_004762035.2_ASM476203v2_genomic.fna.gz | prodigal -d GCF_004762035.2_ASM476203v2_genomic.fna/cds.fna -a GCF_004762035.2_ASM476203v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:37:20,769] [INFO] Task succeeded: Prodigal
[2024-01-24 12:37:20,769] [INFO] Task started: HMMsearch
[2024-01-24 12:37:20,769] [INFO] Running command: hmmsearch --tblout GCF_004762035.2_ASM476203v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcd207f0a-d651-4b8b-905c-b351daef3c7b/dqc_reference/reference_markers.hmm GCF_004762035.2_ASM476203v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:37:21,187] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:37:21,189] [INFO] Found 6/6 markers.
[2024-01-24 12:37:21,248] [INFO] Query marker FASTA was written to GCF_004762035.2_ASM476203v2_genomic.fna/markers.fasta
[2024-01-24 12:37:21,248] [INFO] Task started: Blastn
[2024-01-24 12:37:21,249] [INFO] Running command: blastn -query GCF_004762035.2_ASM476203v2_genomic.fna/markers.fasta -db /var/lib/cwl/stgcd207f0a-d651-4b8b-905c-b351daef3c7b/dqc_reference/reference_markers.fasta -out GCF_004762035.2_ASM476203v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:37:21,867] [INFO] Task succeeded: Blastn
[2024-01-24 12:37:21,871] [INFO] Selected 18 target genomes.
[2024-01-24 12:37:21,872] [INFO] Target genome list was writen to GCF_004762035.2_ASM476203v2_genomic.fna/target_genomes.txt
[2024-01-24 12:37:21,880] [INFO] Task started: fastANI
[2024-01-24 12:37:21,881] [INFO] Running command: fastANI --query /var/lib/cwl/stg72334d46-9256-484e-a643-6fe13ae24361/GCF_004762035.2_ASM476203v2_genomic.fna.gz --refList GCF_004762035.2_ASM476203v2_genomic.fna/target_genomes.txt --output GCF_004762035.2_ASM476203v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:37:31,648] [INFO] Task succeeded: fastANI
[2024-01-24 12:37:31,649] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcd207f0a-d651-4b8b-905c-b351daef3c7b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:37:31,649] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcd207f0a-d651-4b8b-905c-b351daef3c7b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:37:31,653] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:37:31,654] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:37:31,654] [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
Oscillochloris trichoides	strain=DG-6	GCA_000152145.1	104176	104176	type	True	76.1647	138	2028	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:37:31,655] [INFO] DFAST Taxonomy check result was written to GCF_004762035.2_ASM476203v2_genomic.fna/tc_result.tsv
[2024-01-24 12:37:31,656] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:37:31,656] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:37:31,657] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcd207f0a-d651-4b8b-905c-b351daef3c7b/dqc_reference/checkm_data
[2024-01-24 12:37:31,658] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:37:31,721] [INFO] Task started: CheckM
[2024-01-24 12:37:31,721] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004762035.2_ASM476203v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004762035.2_ASM476203v2_genomic.fna/checkm_input GCF_004762035.2_ASM476203v2_genomic.fna/checkm_result
[2024-01-24 12:38:36,117] [INFO] Task succeeded: CheckM
[2024-01-24 12:38:36,118] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 2.08%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:38:36,145] [INFO] ===== Completeness check finished =====
[2024-01-24 12:38:36,145] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:38:36,146] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004762035.2_ASM476203v2_genomic.fna/markers.fasta)
[2024-01-24 12:38:36,146] [INFO] Task started: Blastn
[2024-01-24 12:38:36,146] [INFO] Running command: blastn -query GCF_004762035.2_ASM476203v2_genomic.fna/markers.fasta -db /var/lib/cwl/stgcd207f0a-d651-4b8b-905c-b351daef3c7b/dqc_reference/reference_markers_gtdb.fasta -out GCF_004762035.2_ASM476203v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:38:36,918] [INFO] Task succeeded: Blastn
[2024-01-24 12:38:36,922] [INFO] Selected 11 target genomes.
[2024-01-24 12:38:36,922] [INFO] Target genome list was writen to GCF_004762035.2_ASM476203v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:38:36,951] [INFO] Task started: fastANI
[2024-01-24 12:38:36,951] [INFO] Running command: fastANI --query /var/lib/cwl/stg72334d46-9256-484e-a643-6fe13ae24361/GCF_004762035.2_ASM476203v2_genomic.fna.gz --refList GCF_004762035.2_ASM476203v2_genomic.fna/target_genomes_gtdb.txt --output GCF_004762035.2_ASM476203v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:38:51,210] [INFO] Task succeeded: fastANI
[2024-01-24 12:38:51,220] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:38:51,220] [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_004762035.2	s__Chloroploca sp004762035	100.0	2019	2028	d__Bacteria;p__Chloroflexota;c__Chloroflexia;o__Chloroflexales;f__Chloroflexaceae;g__Chloroploca	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002532075.1	s__Chloroploca asiatica	94.0061	1567	2028	d__Bacteria;p__Chloroflexota;c__Chloroflexia;o__Chloroflexales;f__Chloroflexaceae;g__Chloroploca	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004138165.1	s__Chloroploca sp004138165	92.1662	1606	2028	d__Bacteria;p__Chloroflexota;c__Chloroflexia;o__Chloroflexales;f__Chloroflexaceae;g__Chloroploca	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002532535.1	s__Viridilinea mediisalina	76.8705	223	2028	d__Bacteria;p__Chloroflexota;c__Chloroflexia;o__Chloroflexales;f__Chloroflexaceae;g__Viridilinea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013388805.1	s__JACAEO01 sp013388805	76.5326	186	2028	d__Bacteria;p__Chloroflexota;c__Chloroflexia;o__Chloroflexales;f__Chloroflexaceae;g__JACAEO01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004138135.1	s__Oscillochloris fontis	76.3034	145	2028	d__Bacteria;p__Chloroflexota;c__Chloroflexia;o__Chloroflexales;f__Chloroflexaceae;g__Oscillochloris	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000152145.1	s__Oscillochloris trichoides	76.1647	138	2028	d__Bacteria;p__Chloroflexota;c__Chloroflexia;o__Chloroflexales;f__Chloroflexaceae;g__Oscillochloris	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903887465.1	s__Oscillochloris sp903887465	76.1152	119	2028	d__Bacteria;p__Chloroflexota;c__Chloroflexia;o__Chloroflexales;f__Chloroflexaceae;g__Oscillochloris	95.0	99.82	99.74	0.95	0.93	6	-
GCA_004367505.1	s__OHK40 sp004367505	76.0345	149	2028	d__Bacteria;p__Chloroflexota;c__Chloroflexia;o__Chloroflexales;f__Chloroflexaceae;g__OHK40	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903920315.1	s__Oscillochloris sp903920315	75.715	116	2028	d__Bacteria;p__Chloroflexota;c__Chloroflexia;o__Chloroflexales;f__Chloroflexaceae;g__Oscillochloris	95.0	98.25	98.25	0.71	0.71	2	-
GCA_016717335.1	s__JADKFS01 sp016717335	75.2755	84	2028	d__Bacteria;p__Chloroflexota;c__Chloroflexia;o__Chloroflexales;f__Roseiflexaceae;g__JADKFS01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:38:51,221] [INFO] GTDB search result was written to GCF_004762035.2_ASM476203v2_genomic.fna/result_gtdb.tsv
[2024-01-24 12:38:51,222] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:38:51,225] [INFO] DFAST_QC result json was written to GCF_004762035.2_ASM476203v2_genomic.fna/dqc_result.json
[2024-01-24 12:38:51,225] [INFO] DFAST_QC completed!
[2024-01-24 12:38:51,225] [INFO] Total running time: 0h1m53s