[2023-03-18 01:59:39,748] [INFO] DFAST_QC pipeline started.
[2023-03-18 01:59:39,750] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 01:59:39,750] [INFO] DQC Reference Directory: /var/lib/cwl/stgf10b3083-9637-4b09-abfe-878474a6a658/dqc_reference
[2023-03-18 01:59:40,951] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 01:59:40,952] [INFO] Task started: Prodigal
[2023-03-18 01:59:40,952] [INFO] Running command: cat /var/lib/cwl/stg8b54d719-f3f7-4a9a-bdf7-82b54ffa1049/OceanDNA-b42293.fa | prodigal -d OceanDNA-b42293/cds.fna -a OceanDNA-b42293/protein.faa -g 11 -q > /dev/null
[2023-03-18 01:59:44,649] [INFO] Task succeeded: Prodigal
[2023-03-18 01:59:44,649] [INFO] Task started: HMMsearch
[2023-03-18 01:59:44,649] [INFO] Running command: hmmsearch --tblout OceanDNA-b42293/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf10b3083-9637-4b09-abfe-878474a6a658/dqc_reference/reference_markers.hmm OceanDNA-b42293/protein.faa > /dev/null
[2023-03-18 01:59:44,793] [INFO] Task succeeded: HMMsearch
[2023-03-18 01:59:44,794] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg8b54d719-f3f7-4a9a-bdf7-82b54ffa1049/OceanDNA-b42293.fa]
[2023-03-18 01:59:44,817] [INFO] Query marker FASTA was written to OceanDNA-b42293/markers.fasta
[2023-03-18 01:59:44,817] [INFO] Task started: Blastn
[2023-03-18 01:59:44,818] [INFO] Running command: blastn -query OceanDNA-b42293/markers.fasta -db /var/lib/cwl/stgf10b3083-9637-4b09-abfe-878474a6a658/dqc_reference/reference_markers.fasta -out OceanDNA-b42293/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 01:59:45,815] [INFO] Task succeeded: Blastn
[2023-03-18 01:59:45,826] [INFO] Selected 6 target genomes.
[2023-03-18 01:59:45,827] [INFO] Target genome list was writen to OceanDNA-b42293/target_genomes.txt
[2023-03-18 01:59:45,831] [INFO] Task started: fastANI
[2023-03-18 01:59:45,831] [INFO] Running command: fastANI --query /var/lib/cwl/stg8b54d719-f3f7-4a9a-bdf7-82b54ffa1049/OceanDNA-b42293.fa --refList OceanDNA-b42293/target_genomes.txt --output OceanDNA-b42293/fastani_result.tsv --threads 1
[2023-03-18 01:59:47,558] [INFO] Task succeeded: fastANI
[2023-03-18 01:59:47,559] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf10b3083-9637-4b09-abfe-878474a6a658/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 01:59:47,559] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf10b3083-9637-4b09-abfe-878474a6a658/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 01:59:47,559] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 01:59:47,559] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 01:59:47,560] [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 01:59:47,566] [INFO] DFAST Taxonomy check result was written to OceanDNA-b42293/tc_result.tsv
[2023-03-18 01:59:47,575] [INFO] ===== Taxonomy check completed =====
[2023-03-18 01:59:47,575] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 01:59:47,575] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf10b3083-9637-4b09-abfe-878474a6a658/dqc_reference/checkm_data
[2023-03-18 01:59:47,580] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 01:59:47,585] [INFO] Task started: CheckM
[2023-03-18 01:59:47,585] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b42293/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b42293/checkm_input OceanDNA-b42293/checkm_result
[2023-03-18 02:00:03,215] [INFO] Task succeeded: CheckM
[2023-03-18 02:00:03,215] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 66.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 02:00:03,248] [INFO] ===== Completeness check finished =====
[2023-03-18 02:00:03,248] [INFO] ===== Start GTDB Search =====
[2023-03-18 02:00:03,249] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b42293/markers.fasta)
[2023-03-18 02:00:03,250] [INFO] Task started: Blastn
[2023-03-18 02:00:03,250] [INFO] Running command: blastn -query OceanDNA-b42293/markers.fasta -db /var/lib/cwl/stgf10b3083-9637-4b09-abfe-878474a6a658/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b42293/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 02:00:03,958] [INFO] Task succeeded: Blastn
[2023-03-18 02:00:03,962] [INFO] Selected 17 target genomes.
[2023-03-18 02:00:03,962] [INFO] Target genome list was writen to OceanDNA-b42293/target_genomes_gtdb.txt
[2023-03-18 02:00:03,989] [INFO] Task started: fastANI
[2023-03-18 02:00:03,989] [INFO] Running command: fastANI --query /var/lib/cwl/stg8b54d719-f3f7-4a9a-bdf7-82b54ffa1049/OceanDNA-b42293.fa --refList OceanDNA-b42293/target_genomes_gtdb.txt --output OceanDNA-b42293/fastani_result_gtdb.tsv --threads 1
[2023-03-18 02:00:07,285] [INFO] Task succeeded: fastANI
[2023-03-18 02:00:07,294] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 02:00:07,294] [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_000252525.1	s__SAR86A sp000252525	97.5731	223	237	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	96.49	95.25	0.88	0.84	16	conclusive
GCA_902547295.1	s__SAR86A sp902547295	78.5392	79	237	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902617045.1	s__SAR86A sp902617045	78.4027	89	237	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	96.06	95.32	0.86	0.86	4	-
GCA_902612915.1	s__SAR86A sp902612915	78.3709	84	237	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	97.80	95.61	0.84	0.75	10	-
GCA_902591925.1	s__SAR86A sp902591925	78.1673	105	237	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	97.32	97.27	0.90	0.89	3	-
GCA_902632555.1	s__SAR86A sp902632555	77.9389	112	237	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902520495.1	s__SAR86A sp902520495	77.8585	80	237	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902520725.1	s__SAR86A sp902520725	77.7673	77	237	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	99.82	99.82	0.73	0.73	2	-
GCA_902583575.1	s__SAR86A sp902583575	77.6617	96	237	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	77.6235	105	237	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902563835.1	s__SAR86A sp902563835	77.6064	81	237	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902626385.1	s__SAR86A sp902626385	77.431	108	237	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	77.304	89	237	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	77.2709	61	237	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 02:00:07,295] [INFO] GTDB search result was written to OceanDNA-b42293/result_gtdb.tsv
[2023-03-18 02:00:07,296] [INFO] ===== GTDB Search completed =====
[2023-03-18 02:00:07,298] [INFO] DFAST_QC result json was written to OceanDNA-b42293/dqc_result.json
[2023-03-18 02:00:07,298] [INFO] DFAST_QC completed!
[2023-03-18 02:00:07,298] [INFO] Total running time: 0h0m28s