[2023-03-15 12:44:24,470] [INFO] DFAST_QC pipeline started.
[2023-03-15 12:44:24,470] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 12:44:24,470] [INFO] DQC Reference Directory: /var/lib/cwl/stgcf325c01-c9f3-4998-945d-0b3755350d52/dqc_reference
[2023-03-15 12:44:26,204] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 12:44:26,205] [INFO] Task started: Prodigal
[2023-03-15 12:44:26,206] [INFO] Running command: cat /var/lib/cwl/stge6ac4e35-d60a-4e77-817c-dd490edcd247/OceanDNA-b41843.fa | prodigal -d OceanDNA-b41843/cds.fna -a OceanDNA-b41843/protein.faa -g 11 -q > /dev/null
[2023-03-15 12:44:31,333] [INFO] Task succeeded: Prodigal
[2023-03-15 12:44:31,333] [INFO] Task started: HMMsearch
[2023-03-15 12:44:31,333] [INFO] Running command: hmmsearch --tblout OceanDNA-b41843/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcf325c01-c9f3-4998-945d-0b3755350d52/dqc_reference/reference_markers.hmm OceanDNA-b41843/protein.faa > /dev/null
[2023-03-15 12:44:31,504] [INFO] Task succeeded: HMMsearch
[2023-03-15 12:44:31,504] [WARNING] Found 5/6 markers. [/var/lib/cwl/stge6ac4e35-d60a-4e77-817c-dd490edcd247/OceanDNA-b41843.fa]
[2023-03-15 12:44:31,513] [INFO] Query marker FASTA was written to OceanDNA-b41843/markers.fasta
[2023-03-15 12:44:31,513] [INFO] Task started: Blastn
[2023-03-15 12:44:31,513] [INFO] Running command: blastn -query OceanDNA-b41843/markers.fasta -db /var/lib/cwl/stgcf325c01-c9f3-4998-945d-0b3755350d52/dqc_reference/reference_markers.fasta -out OceanDNA-b41843/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 12:44:32,074] [INFO] Task succeeded: Blastn
[2023-03-15 12:44:32,075] [INFO] Selected 15 target genomes.
[2023-03-15 12:44:32,075] [INFO] Target genome list was writen to OceanDNA-b41843/target_genomes.txt
[2023-03-15 12:44:32,087] [INFO] Task started: fastANI
[2023-03-15 12:44:32,087] [INFO] Running command: fastANI --query /var/lib/cwl/stge6ac4e35-d60a-4e77-817c-dd490edcd247/OceanDNA-b41843.fa --refList OceanDNA-b41843/target_genomes.txt --output OceanDNA-b41843/fastani_result.tsv --threads 1
[2023-03-15 12:44:37,461] [INFO] Task succeeded: fastANI
[2023-03-15 12:44:37,462] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcf325c01-c9f3-4998-945d-0b3755350d52/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 12:44:37,462] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcf325c01-c9f3-4998-945d-0b3755350d52/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 12:44:37,462] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 12:44:37,462] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 12:44:37,462] [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 12:44:37,462] [INFO] DFAST Taxonomy check result was written to OceanDNA-b41843/tc_result.tsv
[2023-03-15 12:44:37,462] [INFO] ===== Taxonomy check completed =====
[2023-03-15 12:44:37,463] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 12:44:37,463] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcf325c01-c9f3-4998-945d-0b3755350d52/dqc_reference/checkm_data
[2023-03-15 12:44:37,466] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 12:44:37,468] [INFO] Task started: CheckM
[2023-03-15 12:44:37,468] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b41843/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b41843/checkm_input OceanDNA-b41843/checkm_result
[2023-03-15 12:44:56,213] [INFO] Task succeeded: CheckM
[2023-03-15 12:44:56,214] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 54.17%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 12:44:56,215] [INFO] ===== Completeness check finished =====
[2023-03-15 12:44:56,216] [INFO] ===== Start GTDB Search =====
[2023-03-15 12:44:56,216] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b41843/markers.fasta)
[2023-03-15 12:44:56,216] [INFO] Task started: Blastn
[2023-03-15 12:44:56,216] [INFO] Running command: blastn -query OceanDNA-b41843/markers.fasta -db /var/lib/cwl/stgcf325c01-c9f3-4998-945d-0b3755350d52/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b41843/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 12:44:57,012] [INFO] Task succeeded: Blastn
[2023-03-15 12:44:57,013] [INFO] Selected 17 target genomes.
[2023-03-15 12:44:57,013] [INFO] Target genome list was writen to OceanDNA-b41843/target_genomes_gtdb.txt
[2023-03-15 12:44:57,082] [INFO] Task started: fastANI
[2023-03-15 12:44:57,082] [INFO] Running command: fastANI --query /var/lib/cwl/stge6ac4e35-d60a-4e77-817c-dd490edcd247/OceanDNA-b41843.fa --refList OceanDNA-b41843/target_genomes_gtdb.txt --output OceanDNA-b41843/fastani_result_gtdb.tsv --threads 1
[2023-03-15 12:45:01,037] [INFO] Task succeeded: fastANI
[2023-03-15 12:45:01,047] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 12:45:01,047] [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_902608115.1	s__D2472 sp902608115	98.8319	271	330	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_902593675.1	s__D2472 sp902593675	77.5672	115	330	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__D2472	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003283765.1	s__D2472 sp003283765	77.5183	80	330	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__D2472	95.0	100.00	100.00	0.99	0.99	2	-
GCA_003284215.1	s__D2472 sp003284215	77.4409	77	330	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__D2472	95.0	98.26	97.20	0.81	0.71	5	-
GCA_902602595.1	s__D2472 sp902602595	77.3391	100	330	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	77.3333	92	330	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__D2472	95.0	98.09	97.88	0.94	0.91	4	-
GCA_902512655.1	s__D2472 sp902512655	77.2779	70	330	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	77.1771	107	330	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__D2472	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902509555.1	s__D2472 sp902509555	77.1597	73	330	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	77.0689	70	330	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__D2472	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016779505.1	s__D2472 sp016779505	77.0626	77	330	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__D2472	95.0	98.99	98.50	0.76	0.70	3	-
GCA_016779285.1	s__D2472 sp016779285	77.0593	54	330	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	76.9739	83	330	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	76.8784	73	330	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__D2472	95.0	99.90	99.90	0.83	0.83	2	-
GCA_902599315.1	s__D2472 sp902599315	76.8651	79	330	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__D2472	95.0	97.18	96.37	0.89	0.86	3	-
GCA_902528215.1	s__D2472 sp902528215	76.6401	73	330	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 12:45:01,048] [INFO] GTDB search result was written to OceanDNA-b41843/result_gtdb.tsv
[2023-03-15 12:45:01,048] [INFO] ===== GTDB Search completed =====
[2023-03-15 12:45:01,049] [INFO] DFAST_QC result json was written to OceanDNA-b41843/dqc_result.json
[2023-03-15 12:45:01,049] [INFO] DFAST_QC completed!
[2023-03-15 12:45:01,049] [INFO] Total running time: 0h0m37s