[2023-06-08 11:22:49,458] [INFO] DFAST_QC pipeline started.
[2023-06-08 11:22:49,464] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 11:22:49,464] [INFO] DQC Reference Directory: /var/lib/cwl/stgc9b38de6-3846-4daa-be7a-fd77ccc594ea/dqc_reference
[2023-06-08 11:22:50,686] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 11:22:50,688] [INFO] Task started: Prodigal
[2023-06-08 11:22:50,689] [INFO] Running command: gunzip -c /var/lib/cwl/stg46077187-0642-4268-9e54-f15953916190/GCA_902526895.1_AG-337-K22_genomic.fna.gz | prodigal -d GCA_902526895.1_AG-337-K22_genomic.fna/cds.fna -a GCA_902526895.1_AG-337-K22_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 11:22:51,712] [INFO] Task succeeded: Prodigal
[2023-06-08 11:22:51,712] [INFO] Task started: HMMsearch
[2023-06-08 11:22:51,713] [INFO] Running command: hmmsearch --tblout GCA_902526895.1_AG-337-K22_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc9b38de6-3846-4daa-be7a-fd77ccc594ea/dqc_reference/reference_markers.hmm GCA_902526895.1_AG-337-K22_genomic.fna/protein.faa > /dev/null
[2023-06-08 11:22:51,852] [INFO] Task succeeded: HMMsearch
[2023-06-08 11:22:51,853] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg46077187-0642-4268-9e54-f15953916190/GCA_902526895.1_AG-337-K22_genomic.fna.gz]
[2023-06-08 11:22:51,872] [INFO] Query marker FASTA was written to GCA_902526895.1_AG-337-K22_genomic.fna/markers.fasta
[2023-06-08 11:22:51,872] [INFO] Task started: Blastn
[2023-06-08 11:22:51,873] [INFO] Running command: blastn -query GCA_902526895.1_AG-337-K22_genomic.fna/markers.fasta -db /var/lib/cwl/stgc9b38de6-3846-4daa-be7a-fd77ccc594ea/dqc_reference/reference_markers.fasta -out GCA_902526895.1_AG-337-K22_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 11:22:52,424] [INFO] Task succeeded: Blastn
[2023-06-08 11:22:52,432] [INFO] Selected 7 target genomes.
[2023-06-08 11:22:52,432] [INFO] Target genome list was writen to GCA_902526895.1_AG-337-K22_genomic.fna/target_genomes.txt
[2023-06-08 11:22:52,434] [INFO] Task started: fastANI
[2023-06-08 11:22:52,434] [INFO] Running command: fastANI --query /var/lib/cwl/stg46077187-0642-4268-9e54-f15953916190/GCA_902526895.1_AG-337-K22_genomic.fna.gz --refList GCA_902526895.1_AG-337-K22_genomic.fna/target_genomes.txt --output GCA_902526895.1_AG-337-K22_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 11:22:56,154] [INFO] Task succeeded: fastANI
[2023-06-08 11:22:56,154] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc9b38de6-3846-4daa-be7a-fd77ccc594ea/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 11:22:56,155] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc9b38de6-3846-4daa-be7a-fd77ccc594ea/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 11:22:56,156] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 11:22:56,156] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-08 11:22:56,156] [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
--------------------------------------------------------------------------------
[2023-06-08 11:22:56,158] [INFO] DFAST Taxonomy check result was written to GCA_902526895.1_AG-337-K22_genomic.fna/tc_result.tsv
[2023-06-08 11:22:56,159] [INFO] ===== Taxonomy check completed =====
[2023-06-08 11:22:56,159] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 11:22:56,159] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc9b38de6-3846-4daa-be7a-fd77ccc594ea/dqc_reference/checkm_data
[2023-06-08 11:22:56,162] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 11:22:56,172] [INFO] Task started: CheckM
[2023-06-08 11:22:56,172] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902526895.1_AG-337-K22_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902526895.1_AG-337-K22_genomic.fna/checkm_input GCA_902526895.1_AG-337-K22_genomic.fna/checkm_result
[2023-06-08 11:23:07,205] [INFO] Task succeeded: CheckM
[2023-06-08 11:23:07,206] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 29.17%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 11:23:07,222] [INFO] ===== Completeness check finished =====
[2023-06-08 11:23:07,223] [INFO] ===== Start GTDB Search =====
[2023-06-08 11:23:07,223] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902526895.1_AG-337-K22_genomic.fna/markers.fasta)
[2023-06-08 11:23:07,223] [INFO] Task started: Blastn
[2023-06-08 11:23:07,223] [INFO] Running command: blastn -query GCA_902526895.1_AG-337-K22_genomic.fna/markers.fasta -db /var/lib/cwl/stgc9b38de6-3846-4daa-be7a-fd77ccc594ea/dqc_reference/reference_markers_gtdb.fasta -out GCA_902526895.1_AG-337-K22_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 11:23:07,784] [INFO] Task succeeded: Blastn
[2023-06-08 11:23:07,789] [INFO] Selected 9 target genomes.
[2023-06-08 11:23:07,789] [INFO] Target genome list was writen to GCA_902526895.1_AG-337-K22_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 11:23:07,793] [INFO] Task started: fastANI
[2023-06-08 11:23:07,793] [INFO] Running command: fastANI --query /var/lib/cwl/stg46077187-0642-4268-9e54-f15953916190/GCA_902526895.1_AG-337-K22_genomic.fna.gz --refList GCA_902526895.1_AG-337-K22_genomic.fna/target_genomes_gtdb.txt --output GCA_902526895.1_AG-337-K22_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 11:23:09,498] [INFO] Task succeeded: fastANI
[2023-06-08 11:23:09,507] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 11:23:09,507] [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_002169625.2	s__SAR86A sp002169625	96.5306	126	185	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	98.57	98.54	0.85	0.74	4	conclusive
GCA_902517505.1	s__SAR86A sp902517505	79.579	91	185	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	97.73	97.59	0.82	0.80	3	-
GCA_902560315.1	s__SAR86A sp902560315	79.2508	87	185	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	95.47	95.47	0.82	0.82	2	-
GCA_902582355.1	s__SAR86A sp902582355	79.124	76	185	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	98.87	98.87	0.67	0.67	2	-
GCA_902556105.1	s__SAR86A sp902556105	78.8377	81	185	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902517425.1	s__SAR86A sp902517425	78.6211	57	185	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902559345.1	s__SAR86A sp902559345	78.3221	62	185	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902630885.1	s__SAR86A sp902630885	78.1777	90	185	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902558095.1	s__SAR86A sp902558095	77.8187	72	185	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-08 11:23:09,509] [INFO] GTDB search result was written to GCA_902526895.1_AG-337-K22_genomic.fna/result_gtdb.tsv
[2023-06-08 11:23:09,510] [INFO] ===== GTDB Search completed =====
[2023-06-08 11:23:09,513] [INFO] DFAST_QC result json was written to GCA_902526895.1_AG-337-K22_genomic.fna/dqc_result.json
[2023-06-08 11:23:09,513] [INFO] DFAST_QC completed!
[2023-06-08 11:23:09,513] [INFO] Total running time: 0h0m20s