[2023-03-15 11:10:12,323] [INFO] DFAST_QC pipeline started.
[2023-03-15 11:10:12,323] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 11:10:12,323] [INFO] DQC Reference Directory: /var/lib/cwl/stgff3d7658-30f7-4e27-842e-8496a8c18672/dqc_reference
[2023-03-15 11:10:13,388] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 11:10:13,389] [INFO] Task started: Prodigal
[2023-03-15 11:10:13,389] [INFO] Running command: cat /var/lib/cwl/stg68301ab0-bf12-4ccd-81e0-907bb6efb38c/OceanDNA-b8766.fa | prodigal -d OceanDNA-b8766/cds.fna -a OceanDNA-b8766/protein.faa -g 11 -q > /dev/null
[2023-03-15 11:10:20,123] [INFO] Task succeeded: Prodigal
[2023-03-15 11:10:20,123] [INFO] Task started: HMMsearch
[2023-03-15 11:10:20,123] [INFO] Running command: hmmsearch --tblout OceanDNA-b8766/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgff3d7658-30f7-4e27-842e-8496a8c18672/dqc_reference/reference_markers.hmm OceanDNA-b8766/protein.faa > /dev/null
[2023-03-15 11:10:20,300] [INFO] Task succeeded: HMMsearch
[2023-03-15 11:10:20,300] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg68301ab0-bf12-4ccd-81e0-907bb6efb38c/OceanDNA-b8766.fa]
[2023-03-15 11:10:20,357] [INFO] Query marker FASTA was written to OceanDNA-b8766/markers.fasta
[2023-03-15 11:10:20,357] [INFO] Task started: Blastn
[2023-03-15 11:10:20,357] [INFO] Running command: blastn -query OceanDNA-b8766/markers.fasta -db /var/lib/cwl/stgff3d7658-30f7-4e27-842e-8496a8c18672/dqc_reference/reference_markers.fasta -out OceanDNA-b8766/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 11:10:20,876] [INFO] Task succeeded: Blastn
[2023-03-15 11:10:20,896] [INFO] Selected 28 target genomes.
[2023-03-15 11:10:20,897] [INFO] Target genome list was writen to OceanDNA-b8766/target_genomes.txt
[2023-03-15 11:10:20,912] [INFO] Task started: fastANI
[2023-03-15 11:10:20,912] [INFO] Running command: fastANI --query /var/lib/cwl/stg68301ab0-bf12-4ccd-81e0-907bb6efb38c/OceanDNA-b8766.fa --refList OceanDNA-b8766/target_genomes.txt --output OceanDNA-b8766/fastani_result.tsv --threads 1
[2023-03-15 11:10:37,104] [INFO] Task succeeded: fastANI
[2023-03-15 11:10:37,104] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgff3d7658-30f7-4e27-842e-8496a8c18672/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 11:10:37,104] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgff3d7658-30f7-4e27-842e-8496a8c18672/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 11:10:37,104] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 11:10:37,104] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 11:10:37,104] [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 11:10:37,107] [INFO] DFAST Taxonomy check result was written to OceanDNA-b8766/tc_result.tsv
[2023-03-15 11:10:37,111] [INFO] ===== Taxonomy check completed =====
[2023-03-15 11:10:37,111] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 11:10:37,112] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgff3d7658-30f7-4e27-842e-8496a8c18672/dqc_reference/checkm_data
[2023-03-15 11:10:37,115] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 11:10:37,127] [INFO] Task started: CheckM
[2023-03-15 11:10:37,128] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b8766/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b8766/checkm_input OceanDNA-b8766/checkm_result
[2023-03-15 11:11:00,379] [INFO] Task succeeded: CheckM
[2023-03-15 11:11:00,379] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 11:11:00,383] [INFO] ===== Completeness check finished =====
[2023-03-15 11:11:00,384] [INFO] ===== Start GTDB Search =====
[2023-03-15 11:11:00,384] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b8766/markers.fasta)
[2023-03-15 11:11:00,385] [INFO] Task started: Blastn
[2023-03-15 11:11:00,385] [INFO] Running command: blastn -query OceanDNA-b8766/markers.fasta -db /var/lib/cwl/stgff3d7658-30f7-4e27-842e-8496a8c18672/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b8766/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 11:11:01,044] [INFO] Task succeeded: Blastn
[2023-03-15 11:11:01,045] [INFO] Selected 10 target genomes.
[2023-03-15 11:11:01,045] [INFO] Target genome list was writen to OceanDNA-b8766/target_genomes_gtdb.txt
[2023-03-15 11:11:01,055] [INFO] Task started: fastANI
[2023-03-15 11:11:01,056] [INFO] Running command: fastANI --query /var/lib/cwl/stg68301ab0-bf12-4ccd-81e0-907bb6efb38c/OceanDNA-b8766.fa --refList OceanDNA-b8766/target_genomes_gtdb.txt --output OceanDNA-b8766/fastani_result_gtdb.tsv --threads 1
[2023-03-15 11:11:03,449] [INFO] Task succeeded: fastANI
[2023-03-15 11:11:03,455] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 11:11:03,455] [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_003331875.1	s__MED-G14 sp003331875	99.4971	289	355	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G14	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_902550325.1	s__MED-G14 sp902550325	90.6163	215	355	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G14	95.0	95.73	95.39	0.65	0.57	4	-
GCA_902526165.1	s__MED-G14 sp902526165	90.3496	262	355	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G14	95.0	95.12	95.12	0.75	0.75	2	-
GCA_902609185.1	s__MED-G14 sp902609185	89.9119	188	355	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_902586095.1	s__MED-G14 sp902586095	82.7392	233	355	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_902614065.1	s__MED-G14 sp002697465	82.69	292	355	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G14	95.0	97.49	95.51	0.88	0.84	14	-
GCA_902544085.1	s__MED-G14 sp902544085	82.5861	288	355	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G14	95.0	99.92	99.92	0.94	0.94	2	-
GCA_902598295.1	s__MED-G14 sp902598295	82.3067	241	355	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_902520835.1	s__MED-G14 sp902520835	76.9651	89	355	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_002457715.1	s__MED-G14 sp002457715	76.7275	79	355	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G14	95.0	98.34	98.31	0.91	0.89	3	-
--------------------------------------------------------------------------------
[2023-03-15 11:11:03,455] [INFO] GTDB search result was written to OceanDNA-b8766/result_gtdb.tsv
[2023-03-15 11:11:03,455] [INFO] ===== GTDB Search completed =====
[2023-03-15 11:11:03,456] [INFO] DFAST_QC result json was written to OceanDNA-b8766/dqc_result.json
[2023-03-15 11:11:03,456] [INFO] DFAST_QC completed!
[2023-03-15 11:11:03,456] [INFO] Total running time: 0h0m51s