[2023-03-18 01:30:35,469] [INFO] DFAST_QC pipeline started.
[2023-03-18 01:30:35,469] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 01:30:35,469] [INFO] DQC Reference Directory: /var/lib/cwl/stg5004266a-dad2-42f1-9451-80ac42b2abfb/dqc_reference
[2023-03-18 01:30:36,568] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 01:30:36,568] [INFO] Task started: Prodigal
[2023-03-18 01:30:36,568] [INFO] Running command: cat /var/lib/cwl/stg0fd34783-0e1b-4661-99aa-f207edf1b6ad/OceanDNA-b42119.fa | prodigal -d OceanDNA-b42119/cds.fna -a OceanDNA-b42119/protein.faa -g 11 -q > /dev/null
[2023-03-18 01:30:41,792] [INFO] Task succeeded: Prodigal
[2023-03-18 01:30:41,792] [INFO] Task started: HMMsearch
[2023-03-18 01:30:41,793] [INFO] Running command: hmmsearch --tblout OceanDNA-b42119/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5004266a-dad2-42f1-9451-80ac42b2abfb/dqc_reference/reference_markers.hmm OceanDNA-b42119/protein.faa > /dev/null
[2023-03-18 01:30:41,946] [INFO] Task succeeded: HMMsearch
[2023-03-18 01:30:41,947] [INFO] Found 6/6 markers.
[2023-03-18 01:30:41,956] [INFO] Query marker FASTA was written to OceanDNA-b42119/markers.fasta
[2023-03-18 01:30:41,957] [INFO] Task started: Blastn
[2023-03-18 01:30:41,957] [INFO] Running command: blastn -query OceanDNA-b42119/markers.fasta -db /var/lib/cwl/stg5004266a-dad2-42f1-9451-80ac42b2abfb/dqc_reference/reference_markers.fasta -out OceanDNA-b42119/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 01:30:42,554] [INFO] Task succeeded: Blastn
[2023-03-18 01:30:42,554] [INFO] Selected 21 target genomes.
[2023-03-18 01:30:42,555] [INFO] Target genome list was writen to OceanDNA-b42119/target_genomes.txt
[2023-03-18 01:30:42,564] [INFO] Task started: fastANI
[2023-03-18 01:30:42,564] [INFO] Running command: fastANI --query /var/lib/cwl/stg0fd34783-0e1b-4661-99aa-f207edf1b6ad/OceanDNA-b42119.fa --refList OceanDNA-b42119/target_genomes.txt --output OceanDNA-b42119/fastani_result.tsv --threads 1
[2023-03-18 01:30:51,153] [INFO] Task succeeded: fastANI
[2023-03-18 01:30:51,153] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5004266a-dad2-42f1-9451-80ac42b2abfb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 01:30:51,154] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5004266a-dad2-42f1-9451-80ac42b2abfb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 01:30:51,154] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 01:30:51,154] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 01:30:51,154] [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 01:30:51,154] [INFO] DFAST Taxonomy check result was written to OceanDNA-b42119/tc_result.tsv
[2023-03-18 01:30:51,154] [INFO] ===== Taxonomy check completed =====
[2023-03-18 01:30:51,154] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 01:30:51,154] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5004266a-dad2-42f1-9451-80ac42b2abfb/dqc_reference/checkm_data
[2023-03-18 01:30:51,157] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 01:30:51,160] [INFO] Task started: CheckM
[2023-03-18 01:30:51,160] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b42119/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b42119/checkm_input OceanDNA-b42119/checkm_result
[2023-03-18 01:31:10,488] [INFO] Task succeeded: CheckM
[2023-03-18 01:31:10,488] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 86.11%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 01:31:10,490] [INFO] ===== Completeness check finished =====
[2023-03-18 01:31:10,490] [INFO] ===== Start GTDB Search =====
[2023-03-18 01:31:10,490] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b42119/markers.fasta)
[2023-03-18 01:31:10,491] [INFO] Task started: Blastn
[2023-03-18 01:31:10,491] [INFO] Running command: blastn -query OceanDNA-b42119/markers.fasta -db /var/lib/cwl/stg5004266a-dad2-42f1-9451-80ac42b2abfb/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b42119/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 01:31:11,403] [INFO] Task succeeded: Blastn
[2023-03-18 01:31:11,404] [INFO] Selected 14 target genomes.
[2023-03-18 01:31:11,404] [INFO] Target genome list was writen to OceanDNA-b42119/target_genomes_gtdb.txt
[2023-03-18 01:31:11,559] [INFO] Task started: fastANI
[2023-03-18 01:31:11,559] [INFO] Running command: fastANI --query /var/lib/cwl/stg0fd34783-0e1b-4661-99aa-f207edf1b6ad/OceanDNA-b42119.fa --refList OceanDNA-b42119/target_genomes_gtdb.txt --output OceanDNA-b42119/fastani_result_gtdb.tsv --threads 1
[2023-03-18 01:31:15,049] [INFO] Task succeeded: fastANI
[2023-03-18 01:31:15,057] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 01:31:15,057] [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_902596165.1	s__D2472 sp902596165	90.6811	274	336	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	90.0579	290	336	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	86.1477	286	336	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__D2472	95.0	98.09	97.88	0.94	0.91	4	-
GCA_902602595.1	s__D2472 sp902602595	86.0827	259	336	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	85.1568	178	336	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	85.0077	192	336	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	84.6867	252	336	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	84.6362	234	336	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__D2472	95.0	100.00	100.00	0.99	0.99	2	-
GCA_902513515.1	s__D2472 sp902513515	83.8664	191	336	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	83.0662	190	336	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	82.9722	184	336	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__D2472	95.0	98.99	98.50	0.76	0.70	3	-
GCA_000307935.1	s__D2472 sp000307935	81.9713	204	336	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	79.3948	167	336	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__D2472	95.0	99.90	99.90	0.83	0.83	2	-
--------------------------------------------------------------------------------
[2023-03-18 01:31:15,057] [INFO] GTDB search result was written to OceanDNA-b42119/result_gtdb.tsv
[2023-03-18 01:31:15,057] [INFO] ===== GTDB Search completed =====
[2023-03-18 01:31:15,058] [INFO] DFAST_QC result json was written to OceanDNA-b42119/dqc_result.json
[2023-03-18 01:31:15,058] [INFO] DFAST_QC completed!
[2023-03-18 01:31:15,058] [INFO] Total running time: 0h0m40s