[2023-03-15 22:44:22,143] [INFO] DFAST_QC pipeline started.
[2023-03-15 22:44:22,147] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 22:44:22,147] [INFO] DQC Reference Directory: /var/lib/cwl/stg2d1f05c6-46f9-4369-bef3-043d755613df/dqc_reference
[2023-03-15 22:44:23,252] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 22:44:23,252] [INFO] Task started: Prodigal
[2023-03-15 22:44:23,252] [INFO] Running command: cat /var/lib/cwl/stgcf9e9756-e2b2-4bf3-af36-da5939a92d46/OceanDNA-b11515.fa | prodigal -d OceanDNA-b11515/cds.fna -a OceanDNA-b11515/protein.faa -g 11 -q > /dev/null
[2023-03-15 22:44:34,348] [INFO] Task succeeded: Prodigal
[2023-03-15 22:44:34,348] [INFO] Task started: HMMsearch
[2023-03-15 22:44:34,348] [INFO] Running command: hmmsearch --tblout OceanDNA-b11515/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2d1f05c6-46f9-4369-bef3-043d755613df/dqc_reference/reference_markers.hmm OceanDNA-b11515/protein.faa > /dev/null
[2023-03-15 22:44:34,533] [INFO] Task succeeded: HMMsearch
[2023-03-15 22:44:34,534] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgcf9e9756-e2b2-4bf3-af36-da5939a92d46/OceanDNA-b11515.fa]
[2023-03-15 22:44:34,644] [INFO] Query marker FASTA was written to OceanDNA-b11515/markers.fasta
[2023-03-15 22:44:34,646] [INFO] Task started: Blastn
[2023-03-15 22:44:34,646] [INFO] Running command: blastn -query OceanDNA-b11515/markers.fasta -db /var/lib/cwl/stg2d1f05c6-46f9-4369-bef3-043d755613df/dqc_reference/reference_markers.fasta -out OceanDNA-b11515/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 22:44:35,213] [INFO] Task succeeded: Blastn
[2023-03-15 22:44:35,219] [INFO] Selected 20 target genomes.
[2023-03-15 22:44:35,219] [INFO] Target genome list was writen to OceanDNA-b11515/target_genomes.txt
[2023-03-15 22:44:35,230] [INFO] Task started: fastANI
[2023-03-15 22:44:35,230] [INFO] Running command: fastANI --query /var/lib/cwl/stgcf9e9756-e2b2-4bf3-af36-da5939a92d46/OceanDNA-b11515.fa --refList OceanDNA-b11515/target_genomes.txt --output OceanDNA-b11515/fastani_result.tsv --threads 1
[2023-03-15 22:44:46,279] [INFO] Task succeeded: fastANI
[2023-03-15 22:44:46,280] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2d1f05c6-46f9-4369-bef3-043d755613df/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 22:44:46,280] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2d1f05c6-46f9-4369-bef3-043d755613df/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 22:44:46,280] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 22:44:46,280] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 22:44:46,280] [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 22:44:46,285] [INFO] DFAST Taxonomy check result was written to OceanDNA-b11515/tc_result.tsv
[2023-03-15 22:44:46,290] [INFO] ===== Taxonomy check completed =====
[2023-03-15 22:44:46,290] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 22:44:46,290] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2d1f05c6-46f9-4369-bef3-043d755613df/dqc_reference/checkm_data
[2023-03-15 22:44:46,293] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 22:44:46,373] [INFO] Task started: CheckM
[2023-03-15 22:44:46,373] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b11515/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b11515/checkm_input OceanDNA-b11515/checkm_result
[2023-03-15 22:45:18,385] [INFO] Task succeeded: CheckM
[2023-03-15 22:45:18,385] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 53.70%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 22:45:18,566] [INFO] ===== Completeness check finished =====
[2023-03-15 22:45:18,566] [INFO] ===== Start GTDB Search =====
[2023-03-15 22:45:18,566] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b11515/markers.fasta)
[2023-03-15 22:45:18,567] [INFO] Task started: Blastn
[2023-03-15 22:45:18,567] [INFO] Running command: blastn -query OceanDNA-b11515/markers.fasta -db /var/lib/cwl/stg2d1f05c6-46f9-4369-bef3-043d755613df/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b11515/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 22:45:19,502] [INFO] Task succeeded: Blastn
[2023-03-15 22:45:19,554] [INFO] Selected 21 target genomes.
[2023-03-15 22:45:19,555] [INFO] Target genome list was writen to OceanDNA-b11515/target_genomes_gtdb.txt
[2023-03-15 22:45:19,803] [INFO] Task started: fastANI
[2023-03-15 22:45:19,803] [INFO] Running command: fastANI --query /var/lib/cwl/stgcf9e9756-e2b2-4bf3-af36-da5939a92d46/OceanDNA-b11515.fa --refList OceanDNA-b11515/target_genomes_gtdb.txt --output OceanDNA-b11515/fastani_result_gtdb.tsv --threads 1
[2023-03-15 22:45:31,374] [INFO] Task succeeded: fastANI
[2023-03-15 22:45:31,377] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 22:45:31,377] [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_002720635.1	s__GCA-002722245 sp002720635	81.5656	261	603	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__GCA-002722245;g__GCA-002722245	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002717515.1	s__GCA-002722245 sp002717515	78.4842	265	603	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__GCA-002722245;g__GCA-002722245	95.0	99.42	99.42	0.83	0.83	2	-
GCA_002722245.1	s__GCA-002722245 sp002722245	77.0607	118	603	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__GCA-002722245;g__GCA-002722245	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 22:45:31,395] [INFO] GTDB search result was written to OceanDNA-b11515/result_gtdb.tsv
[2023-03-15 22:45:31,425] [INFO] ===== GTDB Search completed =====
[2023-03-15 22:45:31,443] [INFO] DFAST_QC result json was written to OceanDNA-b11515/dqc_result.json
[2023-03-15 22:45:31,443] [INFO] DFAST_QC completed!
[2023-03-15 22:45:31,443] [INFO] Total running time: 0h1m9s