[2023-03-17 13:01:52,508] [INFO] DFAST_QC pipeline started.
[2023-03-17 13:01:52,509] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 13:01:52,509] [INFO] DQC Reference Directory: /var/lib/cwl/stg17ec474c-bf12-496f-a223-8550af886514/dqc_reference
[2023-03-17 13:01:55,107] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 13:01:55,107] [INFO] Task started: Prodigal
[2023-03-17 13:01:55,107] [INFO] Running command: cat /var/lib/cwl/stg4634e80d-5717-484a-9521-937504b93760/OceanDNA-b42087.fa | prodigal -d OceanDNA-b42087/cds.fna -a OceanDNA-b42087/protein.faa -g 11 -q > /dev/null
[2023-03-17 13:01:59,980] [INFO] Task succeeded: Prodigal
[2023-03-17 13:01:59,980] [INFO] Task started: HMMsearch
[2023-03-17 13:01:59,980] [INFO] Running command: hmmsearch --tblout OceanDNA-b42087/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg17ec474c-bf12-496f-a223-8550af886514/dqc_reference/reference_markers.hmm OceanDNA-b42087/protein.faa > /dev/null
[2023-03-17 13:02:00,175] [INFO] Task succeeded: HMMsearch
[2023-03-17 13:02:00,176] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg4634e80d-5717-484a-9521-937504b93760/OceanDNA-b42087.fa]
[2023-03-17 13:02:00,185] [INFO] Query marker FASTA was written to OceanDNA-b42087/markers.fasta
[2023-03-17 13:02:00,187] [INFO] Task started: Blastn
[2023-03-17 13:02:00,187] [INFO] Running command: blastn -query OceanDNA-b42087/markers.fasta -db /var/lib/cwl/stg17ec474c-bf12-496f-a223-8550af886514/dqc_reference/reference_markers.fasta -out OceanDNA-b42087/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 13:02:02,811] [INFO] Task succeeded: Blastn
[2023-03-17 13:02:02,812] [INFO] Selected 15 target genomes.
[2023-03-17 13:02:02,812] [INFO] Target genome list was writen to OceanDNA-b42087/target_genomes.txt
[2023-03-17 13:02:02,822] [INFO] Task started: fastANI
[2023-03-17 13:02:02,822] [INFO] Running command: fastANI --query /var/lib/cwl/stg4634e80d-5717-484a-9521-937504b93760/OceanDNA-b42087.fa --refList OceanDNA-b42087/target_genomes.txt --output OceanDNA-b42087/fastani_result.tsv --threads 1
[2023-03-17 13:02:10,575] [INFO] Task succeeded: fastANI
[2023-03-17 13:02:10,576] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg17ec474c-bf12-496f-a223-8550af886514/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 13:02:10,576] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg17ec474c-bf12-496f-a223-8550af886514/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 13:02:10,576] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 13:02:10,576] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 13:02:10,576] [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
--------------------------------------------------------------------------------
[2023-03-17 13:02:10,576] [INFO] DFAST Taxonomy check result was written to OceanDNA-b42087/tc_result.tsv
[2023-03-17 13:02:10,577] [INFO] ===== Taxonomy check completed =====
[2023-03-17 13:02:10,577] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 13:02:10,577] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg17ec474c-bf12-496f-a223-8550af886514/dqc_reference/checkm_data
[2023-03-17 13:02:10,579] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 13:02:10,582] [INFO] Task started: CheckM
[2023-03-17 13:02:10,582] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b42087/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b42087/checkm_input OceanDNA-b42087/checkm_result
[2023-03-17 13:02:34,424] [INFO] Task succeeded: CheckM
[2023-03-17 13:02:34,425] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 62.46%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 13:02:34,426] [INFO] ===== Completeness check finished =====
[2023-03-17 13:02:34,426] [INFO] ===== Start GTDB Search =====
[2023-03-17 13:02:34,427] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b42087/markers.fasta)
[2023-03-17 13:02:34,428] [INFO] Task started: Blastn
[2023-03-17 13:02:34,428] [INFO] Running command: blastn -query OceanDNA-b42087/markers.fasta -db /var/lib/cwl/stg17ec474c-bf12-496f-a223-8550af886514/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b42087/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 13:02:35,704] [INFO] Task succeeded: Blastn
[2023-03-17 13:02:35,705] [INFO] Selected 22 target genomes.
[2023-03-17 13:02:35,705] [INFO] Target genome list was writen to OceanDNA-b42087/target_genomes_gtdb.txt
[2023-03-17 13:02:36,335] [INFO] Task started: fastANI
[2023-03-17 13:02:36,336] [INFO] Running command: fastANI --query /var/lib/cwl/stg4634e80d-5717-484a-9521-937504b93760/OceanDNA-b42087.fa --refList OceanDNA-b42087/target_genomes_gtdb.txt --output OceanDNA-b42087/fastani_result_gtdb.tsv --threads 1
[2023-03-17 13:02:42,671] [INFO] Task succeeded: fastANI
[2023-03-17 13:02:42,679] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 13:02:42,679] [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_003331545.1	s__D2472 sp003331545	99.1626	197	289	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__D2472	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_003283765.1	s__D2472 sp003283765	79.5572	137	289	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__D2472	95.0	100.00	100.00	0.99	0.99	2	-
GCA_902512655.1	s__D2472 sp902512655	79.4797	103	289	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__D2472	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902596165.1	s__D2472 sp902596165	79.2381	157	289	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__D2472	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902515775.1	s__D2472 sp902515775	79.1786	150	289	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__D2472	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902593675.1	s__D2472 sp902593675	78.9439	165	289	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__D2472	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902511425.1	s__D2472 sp902511425	78.7583	116	289	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__D2472	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902541245.1	s__D2472 sp902541245	78.7314	106	289	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__D2472	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902595065.1	s__D2472 sp902595065	78.7073	166	289	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__D2472	95.0	98.09	97.88	0.94	0.91	4	-
GCA_016779285.1	s__D2472 sp016779285	78.5994	87	289	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__D2472	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000307935.1	s__D2472 sp000307935	78.5557	134	289	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__D2472	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902515455.1	s__D2472 sp902515455	78.4153	112	289	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__D2472	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902623685.1	s__D2472 sp902623685	78.3116	144	289	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__D2472	95.0	99.90	99.90	0.83	0.83	2	-
GCA_002358345.1	s__D2472 sp002358345	76.8664	71	289	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__D2472	95.0	99.61	97.74	0.92	0.85	27	-
--------------------------------------------------------------------------------
[2023-03-17 13:02:42,680] [INFO] GTDB search result was written to OceanDNA-b42087/result_gtdb.tsv
[2023-03-17 13:02:42,680] [INFO] ===== GTDB Search completed =====
[2023-03-17 13:02:42,681] [INFO] DFAST_QC result json was written to OceanDNA-b42087/dqc_result.json
[2023-03-17 13:02:42,681] [INFO] DFAST_QC completed!
[2023-03-17 13:02:42,681] [INFO] Total running time: 0h0m50s