[2023-06-30 00:33:19,360] [INFO] DFAST_QC pipeline started.
[2023-06-30 00:33:19,363] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 00:33:19,364] [INFO] DQC Reference Directory: /var/lib/cwl/stgb1d87fb7-8202-4874-96b3-9b726a2271ca/dqc_reference
[2023-06-30 00:33:20,724] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 00:33:20,725] [INFO] Task started: Prodigal
[2023-06-30 00:33:20,726] [INFO] Running command: gunzip -c /var/lib/cwl/stg502bf66e-bc4b-449e-818e-b1c170ea6aca/GCA_900769665.1_SRS476271_15_genomic.fna.gz | prodigal -d GCA_900769665.1_SRS476271_15_genomic.fna/cds.fna -a GCA_900769665.1_SRS476271_15_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 00:33:28,340] [INFO] Task succeeded: Prodigal
[2023-06-30 00:33:28,341] [INFO] Task started: HMMsearch
[2023-06-30 00:33:28,341] [INFO] Running command: hmmsearch --tblout GCA_900769665.1_SRS476271_15_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb1d87fb7-8202-4874-96b3-9b726a2271ca/dqc_reference/reference_markers.hmm GCA_900769665.1_SRS476271_15_genomic.fna/protein.faa > /dev/null
[2023-06-30 00:33:28,611] [INFO] Task succeeded: HMMsearch
[2023-06-30 00:33:28,612] [INFO] Found 6/6 markers.
[2023-06-30 00:33:28,637] [INFO] Query marker FASTA was written to GCA_900769665.1_SRS476271_15_genomic.fna/markers.fasta
[2023-06-30 00:33:28,637] [INFO] Task started: Blastn
[2023-06-30 00:33:28,637] [INFO] Running command: blastn -query GCA_900769665.1_SRS476271_15_genomic.fna/markers.fasta -db /var/lib/cwl/stgb1d87fb7-8202-4874-96b3-9b726a2271ca/dqc_reference/reference_markers.fasta -out GCA_900769665.1_SRS476271_15_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 00:33:29,276] [INFO] Task succeeded: Blastn
[2023-06-30 00:33:29,279] [INFO] Selected 18 target genomes.
[2023-06-30 00:33:29,280] [INFO] Target genome list was writen to GCA_900769665.1_SRS476271_15_genomic.fna/target_genomes.txt
[2023-06-30 00:33:29,283] [INFO] Task started: fastANI
[2023-06-30 00:33:29,283] [INFO] Running command: fastANI --query /var/lib/cwl/stg502bf66e-bc4b-449e-818e-b1c170ea6aca/GCA_900769665.1_SRS476271_15_genomic.fna.gz --refList GCA_900769665.1_SRS476271_15_genomic.fna/target_genomes.txt --output GCA_900769665.1_SRS476271_15_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 00:33:40,455] [INFO] Task succeeded: fastANI
[2023-06-30 00:33:40,456] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb1d87fb7-8202-4874-96b3-9b726a2271ca/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 00:33:40,456] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb1d87fb7-8202-4874-96b3-9b726a2271ca/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 00:33:40,458] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 00:33:40,458] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-30 00:33:40,458] [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
--------------------------------------------------------------------------------
[2023-06-30 00:33:40,461] [INFO] DFAST Taxonomy check result was written to GCA_900769665.1_SRS476271_15_genomic.fna/tc_result.tsv
[2023-06-30 00:33:40,462] [INFO] ===== Taxonomy check completed =====
[2023-06-30 00:33:40,462] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 00:33:40,462] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb1d87fb7-8202-4874-96b3-9b726a2271ca/dqc_reference/checkm_data
[2023-06-30 00:33:40,466] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 00:33:40,493] [INFO] Task started: CheckM
[2023-06-30 00:33:40,493] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_900769665.1_SRS476271_15_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_900769665.1_SRS476271_15_genomic.fna/checkm_input GCA_900769665.1_SRS476271_15_genomic.fna/checkm_result
[2023-06-30 00:34:08,349] [INFO] Task succeeded: CheckM
[2023-06-30 00:34:08,351] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 00:34:08,409] [INFO] ===== Completeness check finished =====
[2023-06-30 00:34:08,409] [INFO] ===== Start GTDB Search =====
[2023-06-30 00:34:08,409] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_900769665.1_SRS476271_15_genomic.fna/markers.fasta)
[2023-06-30 00:34:08,410] [INFO] Task started: Blastn
[2023-06-30 00:34:08,410] [INFO] Running command: blastn -query GCA_900769665.1_SRS476271_15_genomic.fna/markers.fasta -db /var/lib/cwl/stgb1d87fb7-8202-4874-96b3-9b726a2271ca/dqc_reference/reference_markers_gtdb.fasta -out GCA_900769665.1_SRS476271_15_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 00:34:09,200] [INFO] Task succeeded: Blastn
[2023-06-30 00:34:09,205] [INFO] Selected 15 target genomes.
[2023-06-30 00:34:09,206] [INFO] Target genome list was writen to GCA_900769665.1_SRS476271_15_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 00:34:09,211] [INFO] Task started: fastANI
[2023-06-30 00:34:09,211] [INFO] Running command: fastANI --query /var/lib/cwl/stg502bf66e-bc4b-449e-818e-b1c170ea6aca/GCA_900769665.1_SRS476271_15_genomic.fna.gz --refList GCA_900769665.1_SRS476271_15_genomic.fna/target_genomes_gtdb.txt --output GCA_900769665.1_SRS476271_15_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 00:34:14,140] [INFO] Task succeeded: fastANI
[2023-06-30 00:34:14,150] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 00:34:14,151] [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_900769665.1	s__Fimimonas sp900769665	100.0	733	736	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-314;g__Fimimonas	95.0	96.81	96.81	0.74	0.74	2	conclusive
GCA_003537755.1	s__Fimimonas sp003537755	81.6352	312	736	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-314;g__Fimimonas	95.0	97.28	97.18	0.87	0.84	4	-
GCA_000433775.1	s__Fimimonas gallinarum	77.6282	82	736	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-314;g__Fimimonas	95.0	98.11	97.98	0.92	0.91	5	-
GCA_910586625.1	s__Fimimonas sp910586625	77.0897	62	736	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-314;g__Fimimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017500855.1	s__Fimimonas sp017500855	76.7256	70	736	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-314;g__Fimimonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 00:34:14,153] [INFO] GTDB search result was written to GCA_900769665.1_SRS476271_15_genomic.fna/result_gtdb.tsv
[2023-06-30 00:34:14,153] [INFO] ===== GTDB Search completed =====
[2023-06-30 00:34:14,156] [INFO] DFAST_QC result json was written to GCA_900769665.1_SRS476271_15_genomic.fna/dqc_result.json
[2023-06-30 00:34:14,157] [INFO] DFAST_QC completed!
[2023-06-30 00:34:14,157] [INFO] Total running time: 0h0m55s