[2023-03-15 09:48:16,564] [INFO] DFAST_QC pipeline started.
[2023-03-15 09:48:16,564] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 09:48:16,564] [INFO] DQC Reference Directory: /var/lib/cwl/stg5f155d84-3af0-48df-8064-031aa6465181/dqc_reference
[2023-03-15 09:48:18,228] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 09:48:18,228] [INFO] Task started: Prodigal
[2023-03-15 09:48:18,228] [INFO] Running command: cat /var/lib/cwl/stgeaf55e69-5a49-4aec-8d6f-412d0d4263f5/OceanDNA-b8777.fa | prodigal -d OceanDNA-b8777/cds.fna -a OceanDNA-b8777/protein.faa -g 11 -q > /dev/null
[2023-03-15 09:48:24,411] [INFO] Task succeeded: Prodigal
[2023-03-15 09:48:24,412] [INFO] Task started: HMMsearch
[2023-03-15 09:48:24,412] [INFO] Running command: hmmsearch --tblout OceanDNA-b8777/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5f155d84-3af0-48df-8064-031aa6465181/dqc_reference/reference_markers.hmm OceanDNA-b8777/protein.faa > /dev/null
[2023-03-15 09:48:24,596] [INFO] Task succeeded: HMMsearch
[2023-03-15 09:48:24,597] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgeaf55e69-5a49-4aec-8d6f-412d0d4263f5/OceanDNA-b8777.fa]
[2023-03-15 09:48:24,604] [INFO] Query marker FASTA was written to OceanDNA-b8777/markers.fasta
[2023-03-15 09:48:24,604] [INFO] Task started: Blastn
[2023-03-15 09:48:24,604] [INFO] Running command: blastn -query OceanDNA-b8777/markers.fasta -db /var/lib/cwl/stg5f155d84-3af0-48df-8064-031aa6465181/dqc_reference/reference_markers.fasta -out OceanDNA-b8777/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 09:48:25,112] [INFO] Task succeeded: Blastn
[2023-03-15 09:48:25,112] [INFO] Selected 21 target genomes.
[2023-03-15 09:48:25,113] [INFO] Target genome list was writen to OceanDNA-b8777/target_genomes.txt
[2023-03-15 09:48:25,123] [INFO] Task started: fastANI
[2023-03-15 09:48:25,123] [INFO] Running command: fastANI --query /var/lib/cwl/stgeaf55e69-5a49-4aec-8d6f-412d0d4263f5/OceanDNA-b8777.fa --refList OceanDNA-b8777/target_genomes.txt --output OceanDNA-b8777/fastani_result.tsv --threads 1
[2023-03-15 09:48:36,667] [INFO] Task succeeded: fastANI
[2023-03-15 09:48:36,668] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5f155d84-3af0-48df-8064-031aa6465181/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 09:48:36,668] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5f155d84-3af0-48df-8064-031aa6465181/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 09:48:36,668] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 09:48:36,668] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 09:48:36,668] [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 09:48:36,668] [INFO] DFAST Taxonomy check result was written to OceanDNA-b8777/tc_result.tsv
[2023-03-15 09:48:36,669] [INFO] ===== Taxonomy check completed =====
[2023-03-15 09:48:36,669] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 09:48:36,669] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5f155d84-3af0-48df-8064-031aa6465181/dqc_reference/checkm_data
[2023-03-15 09:48:36,672] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 09:48:36,677] [INFO] Task started: CheckM
[2023-03-15 09:48:36,677] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b8777/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b8777/checkm_input OceanDNA-b8777/checkm_result
[2023-03-15 09:48:57,819] [INFO] Task succeeded: CheckM
[2023-03-15 09:48:57,819] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 66.67%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-15 09:48:57,820] [INFO] ===== Completeness check finished =====
[2023-03-15 09:48:57,821] [INFO] ===== Start GTDB Search =====
[2023-03-15 09:48:57,821] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b8777/markers.fasta)
[2023-03-15 09:48:57,821] [INFO] Task started: Blastn
[2023-03-15 09:48:57,821] [INFO] Running command: blastn -query OceanDNA-b8777/markers.fasta -db /var/lib/cwl/stg5f155d84-3af0-48df-8064-031aa6465181/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b8777/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 09:48:58,538] [INFO] Task succeeded: Blastn
[2023-03-15 09:48:58,539] [INFO] Selected 8 target genomes.
[2023-03-15 09:48:58,539] [INFO] Target genome list was writen to OceanDNA-b8777/target_genomes_gtdb.txt
[2023-03-15 09:48:58,785] [INFO] Task started: fastANI
[2023-03-15 09:48:58,785] [INFO] Running command: fastANI --query /var/lib/cwl/stgeaf55e69-5a49-4aec-8d6f-412d0d4263f5/OceanDNA-b8777.fa --refList OceanDNA-b8777/target_genomes_gtdb.txt --output OceanDNA-b8777/fastani_result_gtdb.tsv --threads 1
[2023-03-15 09:49:00,791] [INFO] Task succeeded: fastANI
[2023-03-15 09:49:00,797] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 09:49:00,797] [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_902614065.1	s__MED-G14 sp002697465	93.7502	283	313	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_902586095.1	s__MED-G14 sp902586095	91.4511	221	313	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_902544085.1	s__MED-G14 sp902544085	91.2104	266	313	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	88.1415	226	313	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_902526165.1	s__MED-G14 sp902526165	82.3837	220	313	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_902550325.1	s__MED-G14 sp902550325	82.2164	176	313	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_902609185.1	s__MED-G14 sp902609185	82.0504	163	313	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_003331875.1	s__MED-G14 sp003331875	81.6462	219	313	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 09:49:00,797] [INFO] GTDB search result was written to OceanDNA-b8777/result_gtdb.tsv
[2023-03-15 09:49:00,797] [INFO] ===== GTDB Search completed =====
[2023-03-15 09:49:00,798] [INFO] DFAST_QC result json was written to OceanDNA-b8777/dqc_result.json
[2023-03-15 09:49:00,798] [INFO] DFAST_QC completed!
[2023-03-15 09:49:00,798] [INFO] Total running time: 0h0m44s