[2023-03-15 14:29:06,020] [INFO] DFAST_QC pipeline started.
[2023-03-15 14:29:06,020] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 14:29:06,020] [INFO] DQC Reference Directory: /var/lib/cwl/stgb205ec41-c27f-42e0-95a9-d77070ba2035/dqc_reference
[2023-03-15 14:29:07,112] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 14:29:07,112] [INFO] Task started: Prodigal
[2023-03-15 14:29:07,112] [INFO] Running command: cat /var/lib/cwl/stg07aceabd-1a2a-416f-9a5c-64fabb677536/OceanDNA-b8896.fa | prodigal -d OceanDNA-b8896/cds.fna -a OceanDNA-b8896/protein.faa -g 11 -q > /dev/null
[2023-03-15 14:29:11,823] [INFO] Task succeeded: Prodigal
[2023-03-15 14:29:11,823] [INFO] Task started: HMMsearch
[2023-03-15 14:29:11,823] [INFO] Running command: hmmsearch --tblout OceanDNA-b8896/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb205ec41-c27f-42e0-95a9-d77070ba2035/dqc_reference/reference_markers.hmm OceanDNA-b8896/protein.faa > /dev/null
[2023-03-15 14:29:11,982] [INFO] Task succeeded: HMMsearch
[2023-03-15 14:29:11,982] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg07aceabd-1a2a-416f-9a5c-64fabb677536/OceanDNA-b8896.fa]
[2023-03-15 14:29:11,990] [INFO] Query marker FASTA was written to OceanDNA-b8896/markers.fasta
[2023-03-15 14:29:11,992] [INFO] Task started: Blastn
[2023-03-15 14:29:11,992] [INFO] Running command: blastn -query OceanDNA-b8896/markers.fasta -db /var/lib/cwl/stgb205ec41-c27f-42e0-95a9-d77070ba2035/dqc_reference/reference_markers.fasta -out OceanDNA-b8896/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 14:29:12,569] [INFO] Task succeeded: Blastn
[2023-03-15 14:29:12,570] [INFO] Selected 26 target genomes.
[2023-03-15 14:29:12,570] [INFO] Target genome list was writen to OceanDNA-b8896/target_genomes.txt
[2023-03-15 14:29:12,620] [INFO] Task started: fastANI
[2023-03-15 14:29:12,621] [INFO] Running command: fastANI --query /var/lib/cwl/stg07aceabd-1a2a-416f-9a5c-64fabb677536/OceanDNA-b8896.fa --refList OceanDNA-b8896/target_genomes.txt --output OceanDNA-b8896/fastani_result.tsv --threads 1
[2023-03-15 14:29:25,445] [INFO] Task succeeded: fastANI
[2023-03-15 14:29:25,445] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb205ec41-c27f-42e0-95a9-d77070ba2035/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 14:29:25,446] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb205ec41-c27f-42e0-95a9-d77070ba2035/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 14:29:25,446] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 14:29:25,446] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 14:29:25,446] [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 14:29:25,446] [INFO] DFAST Taxonomy check result was written to OceanDNA-b8896/tc_result.tsv
[2023-03-15 14:29:25,446] [INFO] ===== Taxonomy check completed =====
[2023-03-15 14:29:25,446] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 14:29:25,446] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb205ec41-c27f-42e0-95a9-d77070ba2035/dqc_reference/checkm_data
[2023-03-15 14:29:25,449] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 14:29:25,452] [INFO] Task started: CheckM
[2023-03-15 14:29:25,452] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b8896/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b8896/checkm_input OceanDNA-b8896/checkm_result
[2023-03-15 14:29:45,685] [INFO] Task succeeded: CheckM
[2023-03-15 14:29:45,686] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 68.86%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 14:29:45,687] [INFO] ===== Completeness check finished =====
[2023-03-15 14:29:45,688] [INFO] ===== Start GTDB Search =====
[2023-03-15 14:29:45,688] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b8896/markers.fasta)
[2023-03-15 14:29:45,689] [INFO] Task started: Blastn
[2023-03-15 14:29:45,689] [INFO] Running command: blastn -query OceanDNA-b8896/markers.fasta -db /var/lib/cwl/stgb205ec41-c27f-42e0-95a9-d77070ba2035/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b8896/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 14:29:46,709] [INFO] Task succeeded: Blastn
[2023-03-15 14:29:46,710] [INFO] Selected 11 target genomes.
[2023-03-15 14:29:46,710] [INFO] Target genome list was writen to OceanDNA-b8896/target_genomes_gtdb.txt
[2023-03-15 14:29:46,794] [INFO] Task started: fastANI
[2023-03-15 14:29:46,794] [INFO] Running command: fastANI --query /var/lib/cwl/stg07aceabd-1a2a-416f-9a5c-64fabb677536/OceanDNA-b8896.fa --refList OceanDNA-b8896/target_genomes_gtdb.txt --output OceanDNA-b8896/fastani_result_gtdb.tsv --threads 1
[2023-03-15 14:29:48,861] [INFO] Task succeeded: fastANI
[2023-03-15 14:29:48,868] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 14:29:48,868] [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_902574335.1	s__MED-G14 sp902574335	81.1492	86	204	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G14	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902595555.1	s__MED-G14 sp902595555	81.0348	165	204	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G14	95.0	96.27	95.29	0.86	0.83	8	-
GCA_902622575.1	s__MED-G14 sp902622575	79.6608	128	204	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G14	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003331885.1	s__MED-G14 sp003331885	78.7633	82	204	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G14	95.0	96.85	96.85	0.80	0.80	2	-
GCA_902546095.1	s__MED-G14 sp902546095	78.5431	88	204	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G14	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902515405.1	s__MED-G14 sp902515405	78.5352	82	204	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G14	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902597545.1	s__MED-G14 sp902597545	78.4206	115	204	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G14	95.0	96.96	95.61	0.87	0.83	5	-
GCA_902535165.1	s__MED-G14 sp902535165	78.2003	103	204	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G14	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902606555.1	s__MED-G14 sp902606555	78.0886	66	204	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G14	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902610105.1	s__MED-G14 sp902610105	77.5665	50	204	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G14	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 14:29:48,868] [INFO] GTDB search result was written to OceanDNA-b8896/result_gtdb.tsv
[2023-03-15 14:29:48,868] [INFO] ===== GTDB Search completed =====
[2023-03-15 14:29:48,869] [INFO] DFAST_QC result json was written to OceanDNA-b8896/dqc_result.json
[2023-03-15 14:29:48,869] [INFO] DFAST_QC completed!
[2023-03-15 14:29:48,869] [INFO] Total running time: 0h0m43s