[2023-03-15 23:15:05,777] [INFO] DFAST_QC pipeline started.
[2023-03-15 23:15:05,778] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 23:15:05,778] [INFO] DQC Reference Directory: /var/lib/cwl/stg4b57e32d-7141-4b17-8ce0-9500486195a1/dqc_reference
[2023-03-15 23:15:07,540] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 23:15:07,541] [INFO] Task started: Prodigal
[2023-03-15 23:15:07,541] [INFO] Running command: cat /var/lib/cwl/stgf8ba7ce1-9c90-4cf8-ab33-bd3f167baceb/OceanDNA-b20322.fa | prodigal -d OceanDNA-b20322/cds.fna -a OceanDNA-b20322/protein.faa -g 11 -q > /dev/null
[2023-03-15 23:15:16,399] [INFO] Task succeeded: Prodigal
[2023-03-15 23:15:16,400] [INFO] Task started: HMMsearch
[2023-03-15 23:15:16,400] [INFO] Running command: hmmsearch --tblout OceanDNA-b20322/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4b57e32d-7141-4b17-8ce0-9500486195a1/dqc_reference/reference_markers.hmm OceanDNA-b20322/protein.faa > /dev/null
[2023-03-15 23:15:16,563] [INFO] Task succeeded: HMMsearch
[2023-03-15 23:15:16,564] [INFO] Found 6/6 markers.
[2023-03-15 23:15:16,590] [INFO] Query marker FASTA was written to OceanDNA-b20322/markers.fasta
[2023-03-15 23:15:16,590] [INFO] Task started: Blastn
[2023-03-15 23:15:16,591] [INFO] Running command: blastn -query OceanDNA-b20322/markers.fasta -db /var/lib/cwl/stg4b57e32d-7141-4b17-8ce0-9500486195a1/dqc_reference/reference_markers.fasta -out OceanDNA-b20322/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 23:15:17,100] [INFO] Task succeeded: Blastn
[2023-03-15 23:15:17,102] [INFO] Selected 11 target genomes.
[2023-03-15 23:15:17,102] [INFO] Target genome list was writen to OceanDNA-b20322/target_genomes.txt
[2023-03-15 23:15:17,109] [INFO] Task started: fastANI
[2023-03-15 23:15:17,110] [INFO] Running command: fastANI --query /var/lib/cwl/stgf8ba7ce1-9c90-4cf8-ab33-bd3f167baceb/OceanDNA-b20322.fa --refList OceanDNA-b20322/target_genomes.txt --output OceanDNA-b20322/fastani_result.tsv --threads 1
[2023-03-15 23:15:21,991] [INFO] Task succeeded: fastANI
[2023-03-15 23:15:21,992] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4b57e32d-7141-4b17-8ce0-9500486195a1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 23:15:21,992] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4b57e32d-7141-4b17-8ce0-9500486195a1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 23:15:21,992] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 23:15:21,992] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 23:15:21,992] [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 23:15:21,993] [INFO] DFAST Taxonomy check result was written to OceanDNA-b20322/tc_result.tsv
[2023-03-15 23:15:21,995] [INFO] ===== Taxonomy check completed =====
[2023-03-15 23:15:21,995] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 23:15:21,995] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4b57e32d-7141-4b17-8ce0-9500486195a1/dqc_reference/checkm_data
[2023-03-15 23:15:21,999] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 23:15:22,002] [INFO] Task started: CheckM
[2023-03-15 23:15:22,002] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b20322/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b20322/checkm_input OceanDNA-b20322/checkm_result
[2023-03-15 23:15:49,194] [INFO] Task succeeded: CheckM
[2023-03-15 23:15:49,194] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 23:15:49,241] [INFO] ===== Completeness check finished =====
[2023-03-15 23:15:49,241] [INFO] ===== Start GTDB Search =====
[2023-03-15 23:15:49,241] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b20322/markers.fasta)
[2023-03-15 23:15:49,243] [INFO] Task started: Blastn
[2023-03-15 23:15:49,243] [INFO] Running command: blastn -query OceanDNA-b20322/markers.fasta -db /var/lib/cwl/stg4b57e32d-7141-4b17-8ce0-9500486195a1/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b20322/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 23:15:49,966] [INFO] Task succeeded: Blastn
[2023-03-15 23:15:49,982] [INFO] Selected 18 target genomes.
[2023-03-15 23:15:49,982] [INFO] Target genome list was writen to OceanDNA-b20322/target_genomes_gtdb.txt
[2023-03-15 23:15:50,029] [INFO] Task started: fastANI
[2023-03-15 23:15:50,029] [INFO] Running command: fastANI --query /var/lib/cwl/stgf8ba7ce1-9c90-4cf8-ab33-bd3f167baceb/OceanDNA-b20322.fa --refList OceanDNA-b20322/target_genomes_gtdb.txt --output OceanDNA-b20322/fastani_result_gtdb.tsv --threads 1
[2023-03-15 23:15:59,380] [INFO] Task succeeded: fastANI
[2023-03-15 23:15:59,383] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 23:15:59,383] [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_002471865.1	s__UBA2128 sp002471865	99.5661	378	511	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__UBA2128;g__UBA2128	95.0	99.17	96.76	0.86	0.75	6	conclusive
GCA_002402135.1	s__UBA2128 sp002402135	83.9867	375	511	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__UBA2128;g__UBA2128	95.0	98.48	98.38	0.92	0.90	5	-
--------------------------------------------------------------------------------
[2023-03-15 23:15:59,388] [INFO] GTDB search result was written to OceanDNA-b20322/result_gtdb.tsv
[2023-03-15 23:15:59,398] [INFO] ===== GTDB Search completed =====
[2023-03-15 23:15:59,404] [INFO] DFAST_QC result json was written to OceanDNA-b20322/dqc_result.json
[2023-03-15 23:15:59,404] [INFO] DFAST_QC completed!
[2023-03-15 23:15:59,404] [INFO] Total running time: 0h0m54s