[2023-03-15 20:34:26,739] [INFO] DFAST_QC pipeline started.
[2023-03-15 20:34:26,739] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 20:34:26,739] [INFO] DQC Reference Directory: /var/lib/cwl/stg7b783847-31dc-481b-9fec-d1cb228e24f8/dqc_reference
[2023-03-15 20:34:28,459] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 20:34:28,460] [INFO] Task started: Prodigal
[2023-03-15 20:34:28,460] [INFO] Running command: cat /var/lib/cwl/stg39b86c4b-6c14-4ec3-a63a-5d886b572b6c/OceanDNA-b42068.fa | prodigal -d OceanDNA-b42068/cds.fna -a OceanDNA-b42068/protein.faa -g 11 -q > /dev/null
[2023-03-15 20:34:33,668] [INFO] Task succeeded: Prodigal
[2023-03-15 20:34:33,668] [INFO] Task started: HMMsearch
[2023-03-15 20:34:33,668] [INFO] Running command: hmmsearch --tblout OceanDNA-b42068/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7b783847-31dc-481b-9fec-d1cb228e24f8/dqc_reference/reference_markers.hmm OceanDNA-b42068/protein.faa > /dev/null
[2023-03-15 20:34:33,819] [INFO] Task succeeded: HMMsearch
[2023-03-15 20:34:33,819] [INFO] Found 6/6 markers.
[2023-03-15 20:34:33,829] [INFO] Query marker FASTA was written to OceanDNA-b42068/markers.fasta
[2023-03-15 20:34:33,829] [INFO] Task started: Blastn
[2023-03-15 20:34:33,829] [INFO] Running command: blastn -query OceanDNA-b42068/markers.fasta -db /var/lib/cwl/stg7b783847-31dc-481b-9fec-d1cb228e24f8/dqc_reference/reference_markers.fasta -out OceanDNA-b42068/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 20:34:34,326] [INFO] Task succeeded: Blastn
[2023-03-15 20:34:34,327] [INFO] Selected 15 target genomes.
[2023-03-15 20:34:34,327] [INFO] Target genome list was writen to OceanDNA-b42068/target_genomes.txt
[2023-03-15 20:34:34,335] [INFO] Task started: fastANI
[2023-03-15 20:34:34,335] [INFO] Running command: fastANI --query /var/lib/cwl/stg39b86c4b-6c14-4ec3-a63a-5d886b572b6c/OceanDNA-b42068.fa --refList OceanDNA-b42068/target_genomes.txt --output OceanDNA-b42068/fastani_result.tsv --threads 1
[2023-03-15 20:34:40,352] [INFO] Task succeeded: fastANI
[2023-03-15 20:34:40,353] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7b783847-31dc-481b-9fec-d1cb228e24f8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 20:34:40,353] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7b783847-31dc-481b-9fec-d1cb228e24f8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 20:34:40,353] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 20:34:40,353] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 20:34:40,353] [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
--------------------------------------------------------------------------------
[2023-03-15 20:34:40,353] [INFO] DFAST Taxonomy check result was written to OceanDNA-b42068/tc_result.tsv
[2023-03-15 20:34:40,354] [INFO] ===== Taxonomy check completed =====
[2023-03-15 20:34:40,354] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 20:34:40,354] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7b783847-31dc-481b-9fec-d1cb228e24f8/dqc_reference/checkm_data
[2023-03-15 20:34:40,356] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 20:34:40,360] [INFO] Task started: CheckM
[2023-03-15 20:34:40,360] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b42068/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b42068/checkm_input OceanDNA-b42068/checkm_result
[2023-03-15 20:34:59,433] [INFO] Task succeeded: CheckM
[2023-03-15 20:34:59,433] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 1.85%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-03-15 20:34:59,435] [INFO] ===== Completeness check finished =====
[2023-03-15 20:34:59,435] [INFO] ===== Start GTDB Search =====
[2023-03-15 20:34:59,435] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b42068/markers.fasta)
[2023-03-15 20:34:59,435] [INFO] Task started: Blastn
[2023-03-15 20:34:59,435] [INFO] Running command: blastn -query OceanDNA-b42068/markers.fasta -db /var/lib/cwl/stg7b783847-31dc-481b-9fec-d1cb228e24f8/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b42068/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 20:35:00,140] [INFO] Task succeeded: Blastn
[2023-03-15 20:35:00,141] [INFO] Selected 22 target genomes.
[2023-03-15 20:35:00,141] [INFO] Target genome list was writen to OceanDNA-b42068/target_genomes_gtdb.txt
[2023-03-15 20:35:00,887] [INFO] Task started: fastANI
[2023-03-15 20:35:00,887] [INFO] Running command: fastANI --query /var/lib/cwl/stg39b86c4b-6c14-4ec3-a63a-5d886b572b6c/OceanDNA-b42068.fa --refList OceanDNA-b42068/target_genomes_gtdb.txt --output OceanDNA-b42068/fastani_result_gtdb.tsv --threads 1
[2023-03-15 20:35:05,514] [INFO] Task succeeded: fastANI
[2023-03-15 20:35:05,523] [INFO] Found 15 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 20:35:05,523] [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_905181595.1	s__D2472 sp905181595	94.3767	284	296	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__D2472	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002358345.1	s__D2472 sp002358345	79.7831	146	296	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__D2472	95.0	99.61	97.74	0.92	0.85	27	-
GCA_002469975.1	s__D2472 sp002469975	79.7264	133	296	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__D2472	95.0	99.56	99.38	0.87	0.81	4	-
GCA_003284215.1	s__D2472 sp003284215	78.1856	96	296	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__D2472	95.0	98.26	97.20	0.81	0.71	5	-
GCA_003283765.1	s__D2472 sp003283765	78.0934	87	296	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__D2472	95.0	100.00	100.00	0.99	0.99	2	-
GCA_902511575.1	s__D2472 sp902511575	77.92	109	296	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	77.817	105	296	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__D2472	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902513515.1	s__D2472 sp902513515	77.7161	70	296	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	77.643	105	296	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	77.4987	64	296	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__D2472	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902602595.1	s__D2472 sp902602595	77.4881	89	296	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__D2472	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902512655.1	s__D2472 sp902512655	77.3723	74	296	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__D2472	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902627055.1	s__D2472 sp902627055	77.3299	79	296	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	77.1632	78	296	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__D2472	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902528215.1	s__D2472 sp902528215	77.1391	72	296	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__D2472	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 20:35:05,523] [INFO] GTDB search result was written to OceanDNA-b42068/result_gtdb.tsv
[2023-03-15 20:35:05,523] [INFO] ===== GTDB Search completed =====
[2023-03-15 20:35:05,524] [INFO] DFAST_QC result json was written to OceanDNA-b42068/dqc_result.json
[2023-03-15 20:35:05,524] [INFO] DFAST_QC completed!
[2023-03-15 20:35:05,524] [INFO] Total running time: 0h0m39s