[2023-06-08 10:14:58,353] [INFO] DFAST_QC pipeline started.
[2023-06-08 10:14:58,358] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 10:14:58,359] [INFO] DQC Reference Directory: /var/lib/cwl/stga21f43a5-c017-4b1c-bb6f-aafb5efd007e/dqc_reference
[2023-06-08 10:14:59,592] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 10:14:59,593] [INFO] Task started: Prodigal
[2023-06-08 10:14:59,593] [INFO] Running command: gunzip -c /var/lib/cwl/stg13b61c82-d63a-41fe-a202-d91a5cbad4a2/GCA_902620155.1_AG-892-P18_genomic.fna.gz | prodigal -d GCA_902620155.1_AG-892-P18_genomic.fna/cds.fna -a GCA_902620155.1_AG-892-P18_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 10:15:01,523] [INFO] Task succeeded: Prodigal
[2023-06-08 10:15:01,523] [INFO] Task started: HMMsearch
[2023-06-08 10:15:01,523] [INFO] Running command: hmmsearch --tblout GCA_902620155.1_AG-892-P18_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga21f43a5-c017-4b1c-bb6f-aafb5efd007e/dqc_reference/reference_markers.hmm GCA_902620155.1_AG-892-P18_genomic.fna/protein.faa > /dev/null
[2023-06-08 10:15:01,680] [INFO] Task succeeded: HMMsearch
[2023-06-08 10:15:01,681] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg13b61c82-d63a-41fe-a202-d91a5cbad4a2/GCA_902620155.1_AG-892-P18_genomic.fna.gz]
[2023-06-08 10:15:01,692] [INFO] Query marker FASTA was written to GCA_902620155.1_AG-892-P18_genomic.fna/markers.fasta
[2023-06-08 10:15:01,692] [INFO] Task started: Blastn
[2023-06-08 10:15:01,692] [INFO] Running command: blastn -query GCA_902620155.1_AG-892-P18_genomic.fna/markers.fasta -db /var/lib/cwl/stga21f43a5-c017-4b1c-bb6f-aafb5efd007e/dqc_reference/reference_markers.fasta -out GCA_902620155.1_AG-892-P18_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 10:15:02,146] [INFO] Task succeeded: Blastn
[2023-06-08 10:15:02,151] [INFO] Selected 10 target genomes.
[2023-06-08 10:15:02,151] [INFO] Target genome list was writen to GCA_902620155.1_AG-892-P18_genomic.fna/target_genomes.txt
[2023-06-08 10:15:02,295] [INFO] Task started: fastANI
[2023-06-08 10:15:02,296] [INFO] Running command: fastANI --query /var/lib/cwl/stg13b61c82-d63a-41fe-a202-d91a5cbad4a2/GCA_902620155.1_AG-892-P18_genomic.fna.gz --refList GCA_902620155.1_AG-892-P18_genomic.fna/target_genomes.txt --output GCA_902620155.1_AG-892-P18_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 10:15:07,305] [INFO] Task succeeded: fastANI
[2023-06-08 10:15:07,306] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga21f43a5-c017-4b1c-bb6f-aafb5efd007e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 10:15:07,306] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga21f43a5-c017-4b1c-bb6f-aafb5efd007e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 10:15:07,308] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 10:15:07,308] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-08 10:15:07,308] [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 10:15:07,310] [INFO] DFAST Taxonomy check result was written to GCA_902620155.1_AG-892-P18_genomic.fna/tc_result.tsv
[2023-06-08 10:15:07,310] [INFO] ===== Taxonomy check completed =====
[2023-06-08 10:15:07,310] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 10:15:07,311] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga21f43a5-c017-4b1c-bb6f-aafb5efd007e/dqc_reference/checkm_data
[2023-06-08 10:15:07,314] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 10:15:07,324] [INFO] Task started: CheckM
[2023-06-08 10:15:07,324] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902620155.1_AG-892-P18_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902620155.1_AG-892-P18_genomic.fna/checkm_input GCA_902620155.1_AG-892-P18_genomic.fna/checkm_result
[2023-06-08 10:15:20,544] [INFO] Task succeeded: CheckM
[2023-06-08 10:15:20,545] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 10:15:20,561] [INFO] ===== Completeness check finished =====
[2023-06-08 10:15:20,562] [INFO] ===== Start GTDB Search =====
[2023-06-08 10:15:20,562] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902620155.1_AG-892-P18_genomic.fna/markers.fasta)
[2023-06-08 10:15:20,562] [INFO] Task started: Blastn
[2023-06-08 10:15:20,562] [INFO] Running command: blastn -query GCA_902620155.1_AG-892-P18_genomic.fna/markers.fasta -db /var/lib/cwl/stga21f43a5-c017-4b1c-bb6f-aafb5efd007e/dqc_reference/reference_markers_gtdb.fasta -out GCA_902620155.1_AG-892-P18_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 10:15:21,009] [INFO] Task succeeded: Blastn
[2023-06-08 10:15:21,012] [INFO] Selected 11 target genomes.
[2023-06-08 10:15:21,012] [INFO] Target genome list was writen to GCA_902620155.1_AG-892-P18_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 10:15:21,017] [INFO] Task started: fastANI
[2023-06-08 10:15:21,017] [INFO] Running command: fastANI --query /var/lib/cwl/stg13b61c82-d63a-41fe-a202-d91a5cbad4a2/GCA_902620155.1_AG-892-P18_genomic.fna.gz --refList GCA_902620155.1_AG-892-P18_genomic.fna/target_genomes_gtdb.txt --output GCA_902620155.1_AG-892-P18_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 10:15:22,894] [INFO] Task succeeded: fastANI
[2023-06-08 10:15:22,904] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 10:15:22,904] [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_902601705.1	s__Pelagibacter_A sp902601705	99.4484	211	223	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter_A	95.0	99.55	99.55	0.96	0.96	2	conclusive
GCA_902575095.1	s__Pelagibacter_A sp902575095	86.2121	158	223	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902615435.1	s__Pelagibacter_A sp902615435	85.6874	157	223	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902615715.1	s__Pelagibacter_A sp902615715	85.6781	166	223	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902595625.1	s__Pelagibacter_A sp902595625	85.0709	126	223	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003213555.1	s__Pelagibacter_A sp003213555	85.0097	102	223	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter_A	95.0	100.00	100.00	1.00	1.00	2	-
GCA_902623395.1	s__Pelagibacter_A sp902623395	84.2535	164	223	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902625125.1	s__Pelagibacter_A sp902625125	83.9441	113	223	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902572475.1	s__Pelagibacter_A sp902572475	82.6698	103	223	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902598735.1	s__Pelagibacter_A sp902598735	81.7566	139	223	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902569735.1	s__Pelagibacter_A sp902569735	79.3355	85	223	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter_A	95.0	95.22	95.22	0.72	0.72	2	-
--------------------------------------------------------------------------------
[2023-06-08 10:15:22,906] [INFO] GTDB search result was written to GCA_902620155.1_AG-892-P18_genomic.fna/result_gtdb.tsv
[2023-06-08 10:15:22,906] [INFO] ===== GTDB Search completed =====
[2023-06-08 10:15:22,908] [INFO] DFAST_QC result json was written to GCA_902620155.1_AG-892-P18_genomic.fna/dqc_result.json
[2023-06-08 10:15:22,908] [INFO] DFAST_QC completed!
[2023-06-08 10:15:22,908] [INFO] Total running time: 0h0m25s