[2023-03-15 04:04:36,563] [INFO] DFAST_QC pipeline started.
[2023-03-15 04:04:36,563] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 04:04:36,563] [INFO] DQC Reference Directory: /var/lib/cwl/stge98e888c-2bcc-4e08-bc10-d3794d9842a8/dqc_reference
[2023-03-15 04:04:39,814] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 04:04:39,815] [INFO] Task started: Prodigal
[2023-03-15 04:04:39,815] [INFO] Running command: cat /var/lib/cwl/stg7f8ecae6-e0c9-4b6d-ab83-6d71c7ba8b30/OceanDNA-b4784.fa | prodigal -d OceanDNA-b4784/cds.fna -a OceanDNA-b4784/protein.faa -g 11 -q > /dev/null
[2023-03-15 04:04:45,960] [INFO] Task succeeded: Prodigal
[2023-03-15 04:04:45,961] [INFO] Task started: HMMsearch
[2023-03-15 04:04:45,961] [INFO] Running command: hmmsearch --tblout OceanDNA-b4784/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge98e888c-2bcc-4e08-bc10-d3794d9842a8/dqc_reference/reference_markers.hmm OceanDNA-b4784/protein.faa > /dev/null
[2023-03-15 04:04:46,126] [INFO] Task succeeded: HMMsearch
[2023-03-15 04:04:46,127] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg7f8ecae6-e0c9-4b6d-ab83-6d71c7ba8b30/OceanDNA-b4784.fa]
[2023-03-15 04:04:46,139] [INFO] Query marker FASTA was written to OceanDNA-b4784/markers.fasta
[2023-03-15 04:04:46,140] [INFO] Task started: Blastn
[2023-03-15 04:04:46,140] [INFO] Running command: blastn -query OceanDNA-b4784/markers.fasta -db /var/lib/cwl/stge98e888c-2bcc-4e08-bc10-d3794d9842a8/dqc_reference/reference_markers.fasta -out OceanDNA-b4784/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 04:04:47,489] [INFO] Task succeeded: Blastn
[2023-03-15 04:04:47,490] [INFO] Selected 25 target genomes.
[2023-03-15 04:04:47,491] [INFO] Target genome list was writen to OceanDNA-b4784/target_genomes.txt
[2023-03-15 04:04:47,502] [INFO] Task started: fastANI
[2023-03-15 04:04:47,502] [INFO] Running command: fastANI --query /var/lib/cwl/stg7f8ecae6-e0c9-4b6d-ab83-6d71c7ba8b30/OceanDNA-b4784.fa --refList OceanDNA-b4784/target_genomes.txt --output OceanDNA-b4784/fastani_result.tsv --threads 1
[2023-03-15 04:05:02,054] [INFO] Task succeeded: fastANI
[2023-03-15 04:05:02,054] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge98e888c-2bcc-4e08-bc10-d3794d9842a8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 04:05:02,054] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge98e888c-2bcc-4e08-bc10-d3794d9842a8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 04:05:02,054] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 04:05:02,054] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 04:05:02,055] [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 04:05:02,056] [INFO] DFAST Taxonomy check result was written to OceanDNA-b4784/tc_result.tsv
[2023-03-15 04:05:02,058] [INFO] ===== Taxonomy check completed =====
[2023-03-15 04:05:02,058] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 04:05:02,058] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge98e888c-2bcc-4e08-bc10-d3794d9842a8/dqc_reference/checkm_data
[2023-03-15 04:05:02,061] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 04:05:02,071] [INFO] Task started: CheckM
[2023-03-15 04:05:02,071] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b4784/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b4784/checkm_input OceanDNA-b4784/checkm_result
[2023-03-15 04:05:23,058] [INFO] Task succeeded: CheckM
[2023-03-15 04:05:23,058] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 74.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 04:05:23,065] [INFO] ===== Completeness check finished =====
[2023-03-15 04:05:23,065] [INFO] ===== Start GTDB Search =====
[2023-03-15 04:05:23,065] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b4784/markers.fasta)
[2023-03-15 04:05:23,066] [INFO] Task started: Blastn
[2023-03-15 04:05:23,066] [INFO] Running command: blastn -query OceanDNA-b4784/markers.fasta -db /var/lib/cwl/stge98e888c-2bcc-4e08-bc10-d3794d9842a8/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b4784/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 04:05:23,794] [INFO] Task succeeded: Blastn
[2023-03-15 04:05:23,798] [INFO] Selected 26 target genomes.
[2023-03-15 04:05:23,798] [INFO] Target genome list was writen to OceanDNA-b4784/target_genomes_gtdb.txt
[2023-03-15 04:05:23,859] [INFO] Task started: fastANI
[2023-03-15 04:05:23,860] [INFO] Running command: fastANI --query /var/lib/cwl/stg7f8ecae6-e0c9-4b6d-ab83-6d71c7ba8b30/OceanDNA-b4784.fa --refList OceanDNA-b4784/target_genomes_gtdb.txt --output OceanDNA-b4784/fastani_result_gtdb.tsv --threads 1
[2023-03-15 04:05:32,446] [INFO] Task succeeded: fastANI
[2023-03-15 04:05:32,450] [INFO] Found 4 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 04:05:32,450] [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_012960835.1	s__DUAL01 sp012960835	77.2244	99	302	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__DUAL01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014381465.1	s__DUAL01 sp014381465	76.9251	100	302	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__DUAL01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905478185.1	s__UWMA-0277 sp905478185	76.431	64	302	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__UWMA-0277	95.0	96.67	96.67	0.88	0.88	2	-
GCA_905478555.1	s__GCA-002697625 sp905478555	75.6427	53	302	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__GCA-002697625	95.0	96.63	96.63	0.87	0.87	2	-
--------------------------------------------------------------------------------
[2023-03-15 04:05:32,452] [INFO] GTDB search result was written to OceanDNA-b4784/result_gtdb.tsv
[2023-03-15 04:05:32,453] [INFO] ===== GTDB Search completed =====
[2023-03-15 04:05:32,457] [INFO] DFAST_QC result json was written to OceanDNA-b4784/dqc_result.json
[2023-03-15 04:05:32,457] [INFO] DFAST_QC completed!
[2023-03-15 04:05:32,457] [INFO] Total running time: 0h0m56s