[2023-03-18 05:35:37,307] [INFO] DFAST_QC pipeline started.
[2023-03-18 05:35:37,309] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 05:35:37,309] [INFO] DQC Reference Directory: /var/lib/cwl/stg940b46f0-c0af-4d27-bf35-8d04bdcafcc9/dqc_reference
[2023-03-18 05:35:38,971] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 05:35:38,971] [INFO] Task started: Prodigal
[2023-03-18 05:35:38,971] [INFO] Running command: cat /var/lib/cwl/stg9fac2abe-f463-4a76-ade1-5497a0899e12/OceanDNA-b42122.fa | prodigal -d OceanDNA-b42122/cds.fna -a OceanDNA-b42122/protein.faa -g 11 -q > /dev/null
[2023-03-18 05:35:45,283] [INFO] Task succeeded: Prodigal
[2023-03-18 05:35:45,283] [INFO] Task started: HMMsearch
[2023-03-18 05:35:45,283] [INFO] Running command: hmmsearch --tblout OceanDNA-b42122/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg940b46f0-c0af-4d27-bf35-8d04bdcafcc9/dqc_reference/reference_markers.hmm OceanDNA-b42122/protein.faa > /dev/null
[2023-03-18 05:35:45,445] [INFO] Task succeeded: HMMsearch
[2023-03-18 05:35:45,446] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg9fac2abe-f463-4a76-ade1-5497a0899e12/OceanDNA-b42122.fa]
[2023-03-18 05:35:45,461] [INFO] Query marker FASTA was written to OceanDNA-b42122/markers.fasta
[2023-03-18 05:35:45,462] [INFO] Task started: Blastn
[2023-03-18 05:35:45,462] [INFO] Running command: blastn -query OceanDNA-b42122/markers.fasta -db /var/lib/cwl/stg940b46f0-c0af-4d27-bf35-8d04bdcafcc9/dqc_reference/reference_markers.fasta -out OceanDNA-b42122/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 05:35:45,993] [INFO] Task succeeded: Blastn
[2023-03-18 05:35:45,996] [INFO] Selected 13 target genomes.
[2023-03-18 05:35:45,996] [INFO] Target genome list was writen to OceanDNA-b42122/target_genomes.txt
[2023-03-18 05:35:46,005] [INFO] Task started: fastANI
[2023-03-18 05:35:46,005] [INFO] Running command: fastANI --query /var/lib/cwl/stg9fac2abe-f463-4a76-ade1-5497a0899e12/OceanDNA-b42122.fa --refList OceanDNA-b42122/target_genomes.txt --output OceanDNA-b42122/fastani_result.tsv --threads 1
[2023-03-18 05:35:50,167] [INFO] Task succeeded: fastANI
[2023-03-18 05:35:50,168] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg940b46f0-c0af-4d27-bf35-8d04bdcafcc9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 05:35:50,168] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg940b46f0-c0af-4d27-bf35-8d04bdcafcc9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 05:35:50,168] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 05:35:50,168] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 05:35:50,168] [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 05:35:50,171] [INFO] DFAST Taxonomy check result was written to OceanDNA-b42122/tc_result.tsv
[2023-03-18 05:35:50,175] [INFO] ===== Taxonomy check completed =====
[2023-03-18 05:35:50,176] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 05:35:50,176] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg940b46f0-c0af-4d27-bf35-8d04bdcafcc9/dqc_reference/checkm_data
[2023-03-18 05:35:50,179] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 05:35:50,184] [INFO] Task started: CheckM
[2023-03-18 05:35:50,184] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b42122/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b42122/checkm_input OceanDNA-b42122/checkm_result
[2023-03-18 05:36:11,881] [INFO] Task succeeded: CheckM
[2023-03-18 05:36:11,881] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 51.56%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 05:36:11,916] [INFO] ===== Completeness check finished =====
[2023-03-18 05:36:11,917] [INFO] ===== Start GTDB Search =====
[2023-03-18 05:36:11,917] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b42122/markers.fasta)
[2023-03-18 05:36:11,918] [INFO] Task started: Blastn
[2023-03-18 05:36:11,918] [INFO] Running command: blastn -query OceanDNA-b42122/markers.fasta -db /var/lib/cwl/stg940b46f0-c0af-4d27-bf35-8d04bdcafcc9/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b42122/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 05:36:12,755] [INFO] Task succeeded: Blastn
[2023-03-18 05:36:12,761] [INFO] Selected 14 target genomes.
[2023-03-18 05:36:12,761] [INFO] Target genome list was writen to OceanDNA-b42122/target_genomes_gtdb.txt
[2023-03-18 05:36:12,776] [INFO] Task started: fastANI
[2023-03-18 05:36:12,776] [INFO] Running command: fastANI --query /var/lib/cwl/stg9fac2abe-f463-4a76-ade1-5497a0899e12/OceanDNA-b42122.fa --refList OceanDNA-b42122/target_genomes_gtdb.txt --output OceanDNA-b42122/fastani_result_gtdb.tsv --threads 1
[2023-03-18 05:36:16,785] [INFO] Task succeeded: fastANI
[2023-03-18 05:36:16,793] [INFO] Found 14 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 05:36:16,794] [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_902511575.1	s__D2472 sp902511575	91.8597	322	402	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	87.9465	254	402	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__D2472	95.0	100.00	100.00	0.99	0.99	2	-
GCA_902509555.1	s__D2472 sp902509555	87.8087	220	402	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	86.0046	314	402	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	84.208	204	402	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	83.8543	329	402	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	83.8041	231	402	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	83.5844	287	402	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	83.4823	228	402	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__D2472	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003284215.1	s__D2472 sp003284215	83.431	271	402	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__D2472	95.0	98.26	97.20	0.81	0.71	5	-
GCA_016779505.1	s__D2472 sp016779505	83.0531	212	402	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__D2472	95.0	98.99	98.50	0.76	0.70	3	-
GCA_902595065.1	s__D2472 sp902595065	82.7481	314	402	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__D2472	95.0	98.09	97.88	0.94	0.91	4	-
GCA_000307935.1	s__D2472 sp000307935	81.7663	234	402	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__D2472	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902608115.1	s__D2472 sp902608115	76.9644	107	402	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__D2472	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 05:36:16,796] [INFO] GTDB search result was written to OceanDNA-b42122/result_gtdb.tsv
[2023-03-18 05:36:16,800] [INFO] ===== GTDB Search completed =====
[2023-03-18 05:36:16,803] [INFO] DFAST_QC result json was written to OceanDNA-b42122/dqc_result.json
[2023-03-18 05:36:16,803] [INFO] DFAST_QC completed!
[2023-03-18 05:36:16,803] [INFO] Total running time: 0h0m39s