[2023-06-29 00:37:22,012] [INFO] DFAST_QC pipeline started.
[2023-06-29 00:37:22,014] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 00:37:22,014] [INFO] DQC Reference Directory: /var/lib/cwl/stgfcd42b76-495a-4cd8-9e00-8ac33e55dab3/dqc_reference
[2023-06-29 00:37:23,532] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 00:37:23,533] [INFO] Task started: Prodigal
[2023-06-29 00:37:23,533] [INFO] Running command: gunzip -c /var/lib/cwl/stg90eaec55-512d-4a56-8a2b-4ccae292af57/GCA_002708415.1_ASM270841v1_genomic.fna.gz | prodigal -d GCA_002708415.1_ASM270841v1_genomic.fna/cds.fna -a GCA_002708415.1_ASM270841v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 00:37:26,587] [INFO] Task succeeded: Prodigal
[2023-06-29 00:37:26,587] [INFO] Task started: HMMsearch
[2023-06-29 00:37:26,587] [INFO] Running command: hmmsearch --tblout GCA_002708415.1_ASM270841v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfcd42b76-495a-4cd8-9e00-8ac33e55dab3/dqc_reference/reference_markers.hmm GCA_002708415.1_ASM270841v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 00:37:26,819] [INFO] Task succeeded: HMMsearch
[2023-06-29 00:37:26,821] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg90eaec55-512d-4a56-8a2b-4ccae292af57/GCA_002708415.1_ASM270841v1_genomic.fna.gz]
[2023-06-29 00:37:26,840] [INFO] Query marker FASTA was written to GCA_002708415.1_ASM270841v1_genomic.fna/markers.fasta
[2023-06-29 00:37:26,840] [INFO] Task started: Blastn
[2023-06-29 00:37:26,841] [INFO] Running command: blastn -query GCA_002708415.1_ASM270841v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfcd42b76-495a-4cd8-9e00-8ac33e55dab3/dqc_reference/reference_markers.fasta -out GCA_002708415.1_ASM270841v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 00:37:27,457] [INFO] Task succeeded: Blastn
[2023-06-29 00:37:27,465] [INFO] Selected 23 target genomes.
[2023-06-29 00:37:27,465] [INFO] Target genome list was writen to GCA_002708415.1_ASM270841v1_genomic.fna/target_genomes.txt
[2023-06-29 00:37:27,469] [INFO] Task started: fastANI
[2023-06-29 00:37:27,469] [INFO] Running command: fastANI --query /var/lib/cwl/stg90eaec55-512d-4a56-8a2b-4ccae292af57/GCA_002708415.1_ASM270841v1_genomic.fna.gz --refList GCA_002708415.1_ASM270841v1_genomic.fna/target_genomes.txt --output GCA_002708415.1_ASM270841v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 00:37:40,512] [INFO] Task succeeded: fastANI
[2023-06-29 00:37:40,513] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfcd42b76-495a-4cd8-9e00-8ac33e55dab3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 00:37:40,513] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfcd42b76-495a-4cd8-9e00-8ac33e55dab3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 00:37:40,514] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 00:37:40,515] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-29 00:37:40,515] [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
--------------------------------------------------------------------------------
[2023-06-29 00:37:40,517] [INFO] DFAST Taxonomy check result was written to GCA_002708415.1_ASM270841v1_genomic.fna/tc_result.tsv
[2023-06-29 00:37:40,517] [INFO] ===== Taxonomy check completed =====
[2023-06-29 00:37:40,518] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 00:37:40,518] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfcd42b76-495a-4cd8-9e00-8ac33e55dab3/dqc_reference/checkm_data
[2023-06-29 00:37:40,521] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 00:37:40,538] [INFO] Task started: CheckM
[2023-06-29 00:37:40,538] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_002708415.1_ASM270841v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_002708415.1_ASM270841v1_genomic.fna/checkm_input GCA_002708415.1_ASM270841v1_genomic.fna/checkm_result
[2023-06-29 00:37:59,205] [INFO] Task succeeded: CheckM
[2023-06-29 00:37:59,211] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 62.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 00:37:59,241] [INFO] ===== Completeness check finished =====
[2023-06-29 00:37:59,242] [INFO] ===== Start GTDB Search =====
[2023-06-29 00:37:59,242] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_002708415.1_ASM270841v1_genomic.fna/markers.fasta)
[2023-06-29 00:37:59,242] [INFO] Task started: Blastn
[2023-06-29 00:37:59,242] [INFO] Running command: blastn -query GCA_002708415.1_ASM270841v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfcd42b76-495a-4cd8-9e00-8ac33e55dab3/dqc_reference/reference_markers_gtdb.fasta -out GCA_002708415.1_ASM270841v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 00:38:00,101] [INFO] Task succeeded: Blastn
[2023-06-29 00:38:00,105] [INFO] Selected 12 target genomes.
[2023-06-29 00:38:00,105] [INFO] Target genome list was writen to GCA_002708415.1_ASM270841v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 00:38:00,113] [INFO] Task started: fastANI
[2023-06-29 00:38:00,113] [INFO] Running command: fastANI --query /var/lib/cwl/stg90eaec55-512d-4a56-8a2b-4ccae292af57/GCA_002708415.1_ASM270841v1_genomic.fna.gz --refList GCA_002708415.1_ASM270841v1_genomic.fna/target_genomes_gtdb.txt --output GCA_002708415.1_ASM270841v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 00:38:04,362] [INFO] Task succeeded: fastANI
[2023-06-29 00:38:04,371] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 00:38:04,371] [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_002708415.1	s__GCA-2708415 sp002708415	99.9999	425	426	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Micavibrionales;f__Micavibrionaceae;g__GCA-2708415	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_013215815.1	s__GCA-2708415 sp013215815	77.6462	161	426	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Micavibrionales;f__Micavibrionaceae;g__GCA-2708415	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009995595.1	s__GCA-2708415 sp009995595	77.4982	110	426	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Micavibrionales;f__Micavibrionaceae;g__GCA-2708415	95.0	100.00	100.00	1.00	1.00	2	-
GCA_018608245.1	s__GCA-2708415 sp018608245	76.8565	54	426	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Micavibrionales;f__Micavibrionaceae;g__GCA-2708415	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 00:38:04,373] [INFO] GTDB search result was written to GCA_002708415.1_ASM270841v1_genomic.fna/result_gtdb.tsv
[2023-06-29 00:38:04,374] [INFO] ===== GTDB Search completed =====
[2023-06-29 00:38:04,378] [INFO] DFAST_QC result json was written to GCA_002708415.1_ASM270841v1_genomic.fna/dqc_result.json
[2023-06-29 00:38:04,378] [INFO] DFAST_QC completed!
[2023-06-29 00:38:04,378] [INFO] Total running time: 0h0m42s