[2023-03-16 16:26:08,362] [INFO] DFAST_QC pipeline started.
[2023-03-16 16:26:08,363] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 16:26:08,363] [INFO] DQC Reference Directory: /var/lib/cwl/stg84905834-61ce-4b8d-98ca-ae0401698b6b/dqc_reference
[2023-03-16 16:26:10,859] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 16:26:10,860] [INFO] Task started: Prodigal
[2023-03-16 16:26:10,860] [INFO] Running command: cat /var/lib/cwl/stgba0c69a6-e0bc-4f40-9c5e-9f68925218c7/OceanDNA-b42294.fa | prodigal -d OceanDNA-b42294/cds.fna -a OceanDNA-b42294/protein.faa -g 11 -q > /dev/null
[2023-03-16 16:26:15,687] [INFO] Task succeeded: Prodigal
[2023-03-16 16:26:15,687] [INFO] Task started: HMMsearch
[2023-03-16 16:26:15,687] [INFO] Running command: hmmsearch --tblout OceanDNA-b42294/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg84905834-61ce-4b8d-98ca-ae0401698b6b/dqc_reference/reference_markers.hmm OceanDNA-b42294/protein.faa > /dev/null
[2023-03-16 16:26:15,848] [INFO] Task succeeded: HMMsearch
[2023-03-16 16:26:15,848] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgba0c69a6-e0bc-4f40-9c5e-9f68925218c7/OceanDNA-b42294.fa]
[2023-03-16 16:26:15,856] [INFO] Query marker FASTA was written to OceanDNA-b42294/markers.fasta
[2023-03-16 16:26:15,858] [INFO] Task started: Blastn
[2023-03-16 16:26:15,858] [INFO] Running command: blastn -query OceanDNA-b42294/markers.fasta -db /var/lib/cwl/stg84905834-61ce-4b8d-98ca-ae0401698b6b/dqc_reference/reference_markers.fasta -out OceanDNA-b42294/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 16:26:18,049] [INFO] Task succeeded: Blastn
[2023-03-16 16:26:18,049] [INFO] Selected 10 target genomes.
[2023-03-16 16:26:18,050] [INFO] Target genome list was writen to OceanDNA-b42294/target_genomes.txt
[2023-03-16 16:26:18,056] [INFO] Task started: fastANI
[2023-03-16 16:26:18,056] [INFO] Running command: fastANI --query /var/lib/cwl/stgba0c69a6-e0bc-4f40-9c5e-9f68925218c7/OceanDNA-b42294.fa --refList OceanDNA-b42294/target_genomes.txt --output OceanDNA-b42294/fastani_result.tsv --threads 1
[2023-03-16 16:26:24,180] [INFO] Task succeeded: fastANI
[2023-03-16 16:26:24,181] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg84905834-61ce-4b8d-98ca-ae0401698b6b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 16:26:24,181] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg84905834-61ce-4b8d-98ca-ae0401698b6b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 16:26:24,181] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 16:26:24,181] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 16:26:24,181] [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
--------------------------------------------------------------------------------
[2023-03-16 16:26:24,181] [INFO] DFAST Taxonomy check result was written to OceanDNA-b42294/tc_result.tsv
[2023-03-16 16:26:24,181] [INFO] ===== Taxonomy check completed =====
[2023-03-16 16:26:24,181] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 16:26:24,182] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg84905834-61ce-4b8d-98ca-ae0401698b6b/dqc_reference/checkm_data
[2023-03-16 16:26:24,185] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 16:26:24,187] [INFO] Task started: CheckM
[2023-03-16 16:26:24,187] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b42294/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b42294/checkm_input OceanDNA-b42294/checkm_result
[2023-03-16 16:26:50,600] [INFO] Task succeeded: CheckM
[2023-03-16 16:26:50,601] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 72.92%
Contamintation: 1.04%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-16 16:26:50,602] [INFO] ===== Completeness check finished =====
[2023-03-16 16:26:50,602] [INFO] ===== Start GTDB Search =====
[2023-03-16 16:26:50,603] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b42294/markers.fasta)
[2023-03-16 16:26:50,603] [INFO] Task started: Blastn
[2023-03-16 16:26:50,603] [INFO] Running command: blastn -query OceanDNA-b42294/markers.fasta -db /var/lib/cwl/stg84905834-61ce-4b8d-98ca-ae0401698b6b/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b42294/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 16:26:52,062] [INFO] Task succeeded: Blastn
[2023-03-16 16:26:52,063] [INFO] Selected 17 target genomes.
[2023-03-16 16:26:52,063] [INFO] Target genome list was writen to OceanDNA-b42294/target_genomes_gtdb.txt
[2023-03-16 16:26:52,313] [INFO] Task started: fastANI
[2023-03-16 16:26:52,313] [INFO] Running command: fastANI --query /var/lib/cwl/stgba0c69a6-e0bc-4f40-9c5e-9f68925218c7/OceanDNA-b42294.fa --refList OceanDNA-b42294/target_genomes_gtdb.txt --output OceanDNA-b42294/fastani_result_gtdb.tsv --threads 1
[2023-03-16 16:26:55,974] [INFO] Task succeeded: fastANI
[2023-03-16 16:26:55,984] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 16:26:55,984] [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_002169105.1	s__SAR86A sp002169105	99.5041	203	309	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_902559345.1	s__SAR86A sp902559345	80.0705	163	309	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	79.8593	177	309	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	79.5104	164	309	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	79.232	163	309	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	99.82	99.82	0.73	0.73	2	-
GCA_902558095.1	s__SAR86A sp902558095	79.2222	167	309	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902583575.1	s__SAR86A sp902583575	78.4768	143	309	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902551185.1	s__SAR86A sp902551185	78.2943	112	309	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	99.17	99.17	0.78	0.78	2	-
GCA_902556105.1	s__SAR86A sp902556105	78.2894	117	309	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	77.8267	130	309	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	96.06	95.32	0.86	0.86	4	-
GCA_902547295.1	s__SAR86A sp902547295	77.8096	99	309	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902612915.1	s__SAR86A sp902612915	77.7574	117	309	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	77.6662	129	309	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	97.32	97.27	0.90	0.89	3	-
GCA_002169625.2	s__SAR86A sp002169625	77.6596	105	309	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	98.57	98.54	0.85	0.74	4	-
GCA_902541175.1	s__SAR86A sp902541175	77.5736	144	309	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	97.65	95.31	0.89	0.85	3	-
GCA_000252525.1	s__SAR86A sp000252525	77.4069	122	309	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	96.49	95.25	0.88	0.84	16	-
GCA_002710265.1	s__SAR86A sp002710265	77.3061	100	309	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 16:26:55,984] [INFO] GTDB search result was written to OceanDNA-b42294/result_gtdb.tsv
[2023-03-16 16:26:55,984] [INFO] ===== GTDB Search completed =====
[2023-03-16 16:26:55,985] [INFO] DFAST_QC result json was written to OceanDNA-b42294/dqc_result.json
[2023-03-16 16:26:55,986] [INFO] DFAST_QC completed!
[2023-03-16 16:26:55,986] [INFO] Total running time: 0h0m48s