[2023-03-18 05:27:36,797] [INFO] DFAST_QC pipeline started.
[2023-03-18 05:27:36,797] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 05:27:36,797] [INFO] DQC Reference Directory: /var/lib/cwl/stg2a737feb-c63a-46ec-90cf-a1c3adb7539a/dqc_reference
[2023-03-18 05:27:37,913] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 05:27:37,913] [INFO] Task started: Prodigal
[2023-03-18 05:27:37,914] [INFO] Running command: cat /var/lib/cwl/stg88a9becd-53b9-4503-b2d3-6e2ea4d8e775/OceanDNA-b38366.fa | prodigal -d OceanDNA-b38366/cds.fna -a OceanDNA-b38366/protein.faa -g 11 -q > /dev/null
[2023-03-18 05:27:49,270] [INFO] Task succeeded: Prodigal
[2023-03-18 05:27:49,270] [INFO] Task started: HMMsearch
[2023-03-18 05:27:49,270] [INFO] Running command: hmmsearch --tblout OceanDNA-b38366/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2a737feb-c63a-46ec-90cf-a1c3adb7539a/dqc_reference/reference_markers.hmm OceanDNA-b38366/protein.faa > /dev/null
[2023-03-18 05:27:49,452] [INFO] Task succeeded: HMMsearch
[2023-03-18 05:27:49,452] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg88a9becd-53b9-4503-b2d3-6e2ea4d8e775/OceanDNA-b38366.fa]
[2023-03-18 05:27:49,471] [INFO] Query marker FASTA was written to OceanDNA-b38366/markers.fasta
[2023-03-18 05:27:49,471] [INFO] Task started: Blastn
[2023-03-18 05:27:49,471] [INFO] Running command: blastn -query OceanDNA-b38366/markers.fasta -db /var/lib/cwl/stg2a737feb-c63a-46ec-90cf-a1c3adb7539a/dqc_reference/reference_markers.fasta -out OceanDNA-b38366/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 05:27:50,088] [INFO] Task succeeded: Blastn
[2023-03-18 05:27:50,089] [INFO] Selected 28 target genomes.
[2023-03-18 05:27:50,090] [INFO] Target genome list was writen to OceanDNA-b38366/target_genomes.txt
[2023-03-18 05:27:50,106] [INFO] Task started: fastANI
[2023-03-18 05:27:50,106] [INFO] Running command: fastANI --query /var/lib/cwl/stg88a9becd-53b9-4503-b2d3-6e2ea4d8e775/OceanDNA-b38366.fa --refList OceanDNA-b38366/target_genomes.txt --output OceanDNA-b38366/fastani_result.tsv --threads 1
[2023-03-18 05:28:07,698] [INFO] Task succeeded: fastANI
[2023-03-18 05:28:07,698] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2a737feb-c63a-46ec-90cf-a1c3adb7539a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 05:28:07,698] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2a737feb-c63a-46ec-90cf-a1c3adb7539a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 05:28:07,702] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 05:28:07,702] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 05:28:07,702] [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
Ketobacter alkanivorans	strain=GI5	GCA_002863865.1	1917421	1917421	type	True	77.0187	130	535	95	below_threshold
Alcanivorax gelatiniphagus	strain=MEBiC 08158	GCA_005938655.1	1194167	1194167	type	True	75.8211	64	535	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 05:28:07,703] [INFO] DFAST Taxonomy check result was written to OceanDNA-b38366/tc_result.tsv
[2023-03-18 05:28:07,703] [INFO] ===== Taxonomy check completed =====
[2023-03-18 05:28:07,703] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 05:28:07,703] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2a737feb-c63a-46ec-90cf-a1c3adb7539a/dqc_reference/checkm_data
[2023-03-18 05:28:07,704] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 05:28:07,708] [INFO] Task started: CheckM
[2023-03-18 05:28:07,708] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b38366/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b38366/checkm_input OceanDNA-b38366/checkm_result
[2023-03-18 05:28:40,779] [INFO] Task succeeded: CheckM
[2023-03-18 05:28:40,779] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 61.13%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 05:28:40,841] [INFO] ===== Completeness check finished =====
[2023-03-18 05:28:40,841] [INFO] ===== Start GTDB Search =====
[2023-03-18 05:28:40,841] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b38366/markers.fasta)
[2023-03-18 05:28:40,843] [INFO] Task started: Blastn
[2023-03-18 05:28:40,843] [INFO] Running command: blastn -query OceanDNA-b38366/markers.fasta -db /var/lib/cwl/stg2a737feb-c63a-46ec-90cf-a1c3adb7539a/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b38366/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 05:28:41,843] [INFO] Task succeeded: Blastn
[2023-03-18 05:28:41,843] [INFO] Selected 11 target genomes.
[2023-03-18 05:28:41,843] [INFO] Target genome list was writen to OceanDNA-b38366/target_genomes_gtdb.txt
[2023-03-18 05:28:41,857] [INFO] Task started: fastANI
[2023-03-18 05:28:41,857] [INFO] Running command: fastANI --query /var/lib/cwl/stg88a9becd-53b9-4503-b2d3-6e2ea4d8e775/OceanDNA-b38366.fa --refList OceanDNA-b38366/target_genomes_gtdb.txt --output OceanDNA-b38366/fastani_result_gtdb.tsv --threads 1
[2023-03-18 05:28:49,651] [INFO] Task succeeded: fastANI
[2023-03-18 05:28:49,655] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 05:28:49,655] [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_002701845.1	s__Ketobacter sp002701845	99.9693	531	535	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Ketobacteraceae;g__Ketobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_003671495.1	s__Ketobacter sp003671495	78.3487	236	535	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Ketobacteraceae;g__Ketobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002708905.1	s__Ketobacter sp002708905	77.9103	174	535	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Ketobacteraceae;g__Ketobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002471665.1	s__Ketobacter sp002471665	77.8854	202	535	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Ketobacteraceae;g__Ketobacter	95.0	99.82	99.43	0.96	0.93	14	-
GCA_013178375.1	s__Ch67 sp013178375	77.0423	137	535	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Ketobacteraceae;g__Ch67	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002863865.1	s__Ketobacter alkanivorans	77.0187	130	535	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Ketobacteraceae;g__Ketobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 05:28:49,656] [INFO] GTDB search result was written to OceanDNA-b38366/result_gtdb.tsv
[2023-03-18 05:28:49,656] [INFO] ===== GTDB Search completed =====
[2023-03-18 05:28:49,656] [INFO] DFAST_QC result json was written to OceanDNA-b38366/dqc_result.json
[2023-03-18 05:28:49,657] [INFO] DFAST_QC completed!
[2023-03-18 05:28:49,657] [INFO] Total running time: 0h1m13s