[2023-03-16 22:05:57,088] [INFO] DFAST_QC pipeline started.
[2023-03-16 22:05:57,088] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 22:05:57,088] [INFO] DQC Reference Directory: /var/lib/cwl/stg1c42ce2a-e8b3-41f1-9993-91b8f8b42fa4/dqc_reference
[2023-03-16 22:05:58,247] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 22:05:58,248] [INFO] Task started: Prodigal
[2023-03-16 22:05:58,248] [INFO] Running command: cat /var/lib/cwl/stgb3025792-4d23-49eb-ad9e-320f62cd721c/OceanDNA-b42250.fa | prodigal -d OceanDNA-b42250/cds.fna -a OceanDNA-b42250/protein.faa -g 11 -q > /dev/null
[2023-03-16 22:06:02,280] [INFO] Task succeeded: Prodigal
[2023-03-16 22:06:02,280] [INFO] Task started: HMMsearch
[2023-03-16 22:06:02,280] [INFO] Running command: hmmsearch --tblout OceanDNA-b42250/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1c42ce2a-e8b3-41f1-9993-91b8f8b42fa4/dqc_reference/reference_markers.hmm OceanDNA-b42250/protein.faa > /dev/null
[2023-03-16 22:06:02,458] [INFO] Task succeeded: HMMsearch
[2023-03-16 22:06:02,459] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgb3025792-4d23-49eb-ad9e-320f62cd721c/OceanDNA-b42250.fa]
[2023-03-16 22:06:02,466] [INFO] Query marker FASTA was written to OceanDNA-b42250/markers.fasta
[2023-03-16 22:06:02,469] [INFO] Task started: Blastn
[2023-03-16 22:06:02,469] [INFO] Running command: blastn -query OceanDNA-b42250/markers.fasta -db /var/lib/cwl/stg1c42ce2a-e8b3-41f1-9993-91b8f8b42fa4/dqc_reference/reference_markers.fasta -out OceanDNA-b42250/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 22:06:03,448] [INFO] Task succeeded: Blastn
[2023-03-16 22:06:03,448] [INFO] Selected 4 target genomes.
[2023-03-16 22:06:03,449] [INFO] Target genome list was writen to OceanDNA-b42250/target_genomes.txt
[2023-03-16 22:06:03,452] [INFO] Task started: fastANI
[2023-03-16 22:06:03,452] [INFO] Running command: fastANI --query /var/lib/cwl/stgb3025792-4d23-49eb-ad9e-320f62cd721c/OceanDNA-b42250.fa --refList OceanDNA-b42250/target_genomes.txt --output OceanDNA-b42250/fastani_result.tsv --threads 1
[2023-03-16 22:06:05,482] [INFO] Task succeeded: fastANI
[2023-03-16 22:06:05,482] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1c42ce2a-e8b3-41f1-9993-91b8f8b42fa4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 22:06:05,483] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1c42ce2a-e8b3-41f1-9993-91b8f8b42fa4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 22:06:05,483] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 22:06:05,483] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 22:06:05,483] [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 22:06:05,483] [INFO] DFAST Taxonomy check result was written to OceanDNA-b42250/tc_result.tsv
[2023-03-16 22:06:05,483] [INFO] ===== Taxonomy check completed =====
[2023-03-16 22:06:05,483] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 22:06:05,483] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1c42ce2a-e8b3-41f1-9993-91b8f8b42fa4/dqc_reference/checkm_data
[2023-03-16 22:06:05,645] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 22:06:05,647] [INFO] Task started: CheckM
[2023-03-16 22:06:05,647] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b42250/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b42250/checkm_input OceanDNA-b42250/checkm_result
[2023-03-16 22:06:28,795] [INFO] Task succeeded: CheckM
[2023-03-16 22:06:28,795] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 37.50%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-16 22:06:28,797] [INFO] ===== Completeness check finished =====
[2023-03-16 22:06:28,797] [INFO] ===== Start GTDB Search =====
[2023-03-16 22:06:28,797] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b42250/markers.fasta)
[2023-03-16 22:06:28,799] [INFO] Task started: Blastn
[2023-03-16 22:06:28,799] [INFO] Running command: blastn -query OceanDNA-b42250/markers.fasta -db /var/lib/cwl/stg1c42ce2a-e8b3-41f1-9993-91b8f8b42fa4/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b42250/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 22:06:30,536] [INFO] Task succeeded: Blastn
[2023-03-16 22:06:30,536] [INFO] Selected 12 target genomes.
[2023-03-16 22:06:30,537] [INFO] Target genome list was writen to OceanDNA-b42250/target_genomes_gtdb.txt
[2023-03-16 22:06:30,933] [INFO] Task started: fastANI
[2023-03-16 22:06:30,934] [INFO] Running command: fastANI --query /var/lib/cwl/stgb3025792-4d23-49eb-ad9e-320f62cd721c/OceanDNA-b42250.fa --refList OceanDNA-b42250/target_genomes_gtdb.txt --output OceanDNA-b42250/fastani_result_gtdb.tsv --threads 1
[2023-03-16 22:06:33,639] [INFO] Task succeeded: fastANI
[2023-03-16 22:06:33,645] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 22:06:33,646] [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_003284215.1	s__D2472 sp003284215	98.1888	202	249	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__D2472	95.0	98.26	97.20	0.81	0.71	5	conclusive
GCA_003283765.1	s__D2472 sp003283765	83.6159	153	249	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	83.1592	134	249	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__D2472	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902511575.1	s__D2472 sp902511575	83.1506	181	249	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	83.0756	124	249	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	82.7231	136	249	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	82.4249	181	249	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	81.5905	198	249	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__D2472	95.0	98.09	97.88	0.94	0.91	4	-
GCA_016779505.1	s__D2472 sp016779505	81.564	137	249	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__D2472	95.0	98.99	98.50	0.76	0.70	3	-
GCA_902596165.1	s__D2472 sp902596165	81.5637	172	249	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	80.7129	139	249	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__D2472	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 22:06:33,646] [INFO] GTDB search result was written to OceanDNA-b42250/result_gtdb.tsv
[2023-03-16 22:06:33,646] [INFO] ===== GTDB Search completed =====
[2023-03-16 22:06:33,647] [INFO] DFAST_QC result json was written to OceanDNA-b42250/dqc_result.json
[2023-03-16 22:06:33,647] [INFO] DFAST_QC completed!
[2023-03-16 22:06:33,647] [INFO] Total running time: 0h0m37s