[2023-03-18 09:15:00,471] [INFO] DFAST_QC pipeline started.
[2023-03-18 09:15:00,472] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 09:15:00,473] [INFO] DQC Reference Directory: /var/lib/cwl/stg7edc5807-7a17-4da7-a94e-12571f761433/dqc_reference
[2023-03-18 09:15:02,030] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 09:15:02,030] [INFO] Task started: Prodigal
[2023-03-18 09:15:02,030] [INFO] Running command: cat /var/lib/cwl/stga1f9dbf3-3b50-45c3-b19a-8941e09b3c18/OceanDNA-b42406.fa | prodigal -d OceanDNA-b42406/cds.fna -a OceanDNA-b42406/protein.faa -g 11 -q > /dev/null
[2023-03-18 09:15:06,197] [INFO] Task succeeded: Prodigal
[2023-03-18 09:15:06,198] [INFO] Task started: HMMsearch
[2023-03-18 09:15:06,198] [INFO] Running command: hmmsearch --tblout OceanDNA-b42406/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7edc5807-7a17-4da7-a94e-12571f761433/dqc_reference/reference_markers.hmm OceanDNA-b42406/protein.faa > /dev/null
[2023-03-18 09:15:06,365] [INFO] Task succeeded: HMMsearch
[2023-03-18 09:15:06,366] [INFO] Found 6/6 markers.
[2023-03-18 09:15:06,387] [INFO] Query marker FASTA was written to OceanDNA-b42406/markers.fasta
[2023-03-18 09:15:06,388] [INFO] Task started: Blastn
[2023-03-18 09:15:06,388] [INFO] Running command: blastn -query OceanDNA-b42406/markers.fasta -db /var/lib/cwl/stg7edc5807-7a17-4da7-a94e-12571f761433/dqc_reference/reference_markers.fasta -out OceanDNA-b42406/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 09:15:08,109] [INFO] Task succeeded: Blastn
[2023-03-18 09:15:08,115] [INFO] Selected 21 target genomes.
[2023-03-18 09:15:08,115] [INFO] Target genome list was writen to OceanDNA-b42406/target_genomes.txt
[2023-03-18 09:15:08,125] [INFO] Task started: fastANI
[2023-03-18 09:15:08,125] [INFO] Running command: fastANI --query /var/lib/cwl/stga1f9dbf3-3b50-45c3-b19a-8941e09b3c18/OceanDNA-b42406.fa --refList OceanDNA-b42406/target_genomes.txt --output OceanDNA-b42406/fastani_result.tsv --threads 1
[2023-03-18 09:15:16,571] [INFO] Task succeeded: fastANI
[2023-03-18 09:15:16,571] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7edc5807-7a17-4da7-a94e-12571f761433/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 09:15:16,571] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7edc5807-7a17-4da7-a94e-12571f761433/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 09:15:16,571] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 09:15:16,572] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 09:15:16,572] [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
--------------------------------------------------------------------------------
[2023-03-18 09:15:16,574] [INFO] DFAST Taxonomy check result was written to OceanDNA-b42406/tc_result.tsv
[2023-03-18 09:15:16,575] [INFO] ===== Taxonomy check completed =====
[2023-03-18 09:15:16,575] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 09:15:16,575] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7edc5807-7a17-4da7-a94e-12571f761433/dqc_reference/checkm_data
[2023-03-18 09:15:16,578] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 09:15:16,585] [INFO] Task started: CheckM
[2023-03-18 09:15:16,585] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b42406/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b42406/checkm_input OceanDNA-b42406/checkm_result
[2023-03-18 09:15:33,226] [INFO] Task succeeded: CheckM
[2023-03-18 09:15:33,226] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 54.17%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 09:15:33,267] [INFO] ===== Completeness check finished =====
[2023-03-18 09:15:33,267] [INFO] ===== Start GTDB Search =====
[2023-03-18 09:15:33,267] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b42406/markers.fasta)
[2023-03-18 09:15:33,268] [INFO] Task started: Blastn
[2023-03-18 09:15:33,268] [INFO] Running command: blastn -query OceanDNA-b42406/markers.fasta -db /var/lib/cwl/stg7edc5807-7a17-4da7-a94e-12571f761433/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b42406/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 09:15:34,155] [INFO] Task succeeded: Blastn
[2023-03-18 09:15:34,158] [INFO] Selected 13 target genomes.
[2023-03-18 09:15:34,158] [INFO] Target genome list was writen to OceanDNA-b42406/target_genomes_gtdb.txt
[2023-03-18 09:15:34,171] [INFO] Task started: fastANI
[2023-03-18 09:15:34,171] [INFO] Running command: fastANI --query /var/lib/cwl/stga1f9dbf3-3b50-45c3-b19a-8941e09b3c18/OceanDNA-b42406.fa --refList OceanDNA-b42406/target_genomes_gtdb.txt --output OceanDNA-b42406/fastani_result_gtdb.tsv --threads 1
[2023-03-18 09:15:36,934] [INFO] Task succeeded: fastANI
[2023-03-18 09:15:36,942] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 09:15:36,942] [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_902610905.1	s__SCGC-AAA076-P13 sp902610905	98.5391	208	271	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SCGC-AAA076-P13	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_902591565.1	s__SCGC-AAA076-P13 sp902591565	92.0367	203	271	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SCGC-AAA076-P13	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902591665.1	s__SCGC-AAA076-P13 sp902591665	88.5412	197	271	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SCGC-AAA076-P13	95.0	99.81	99.81	0.85	0.85	2	-
GCA_902635645.1	s__SCGC-AAA076-P13 sp902635645	88.4222	153	271	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SCGC-AAA076-P13	95.0	97.13	97.13	0.67	0.67	2	-
GCA_902558395.1	s__SCGC-AAA076-P13 sp902558395	88.2536	228	271	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SCGC-AAA076-P13	95.0	97.77	97.77	0.94	0.94	2	-
GCA_902556355.1	s__SCGC-AAA076-P13 sp902556355	88.2467	156	271	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SCGC-AAA076-P13	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902557705.1	s__SCGC-AAA076-P13 sp902557705	87.7246	185	271	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SCGC-AAA076-P13	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902558375.1	s__SCGC-AAA076-P13 sp902558375	86.7219	156	271	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SCGC-AAA076-P13	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000384935.1	s__SCGC-AAA076-P13 sp000384935	77.0975	108	271	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SCGC-AAA076-P13	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905478015.1	s__CAJQGY01 sp905478015	76.9402	56	271	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__CAJQGY01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905182885.1	s__SCGC-AAA076-P13 sp905182885	76.8199	91	271	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SCGC-AAA076-P13	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902563835.1	s__SAR86A sp902563835	76.7779	63	271	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002710265.1	s__SAR86A sp002710265	76.7111	54	271	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 09:15:36,942] [INFO] GTDB search result was written to OceanDNA-b42406/result_gtdb.tsv
[2023-03-18 09:15:36,943] [INFO] ===== GTDB Search completed =====
[2023-03-18 09:15:36,944] [INFO] DFAST_QC result json was written to OceanDNA-b42406/dqc_result.json
[2023-03-18 09:15:36,944] [INFO] DFAST_QC completed!
[2023-03-18 09:15:36,944] [INFO] Total running time: 0h0m36s