[2023-03-15 05:00:03,410] [INFO] DFAST_QC pipeline started.
[2023-03-15 05:00:03,410] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 05:00:03,411] [INFO] DQC Reference Directory: /var/lib/cwl/stg8afaced6-d9f0-4f78-899d-3f463eb2a76d/dqc_reference
[2023-03-15 05:00:04,516] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 05:00:04,516] [INFO] Task started: Prodigal
[2023-03-15 05:00:04,516] [INFO] Running command: cat /var/lib/cwl/stgf116dbb1-1569-4971-8e70-b5c157a6bae1/OceanDNA-b12488.fa | prodigal -d OceanDNA-b12488/cds.fna -a OceanDNA-b12488/protein.faa -g 11 -q > /dev/null
[2023-03-15 05:00:21,613] [INFO] Task succeeded: Prodigal
[2023-03-15 05:00:21,613] [INFO] Task started: HMMsearch
[2023-03-15 05:00:21,613] [INFO] Running command: hmmsearch --tblout OceanDNA-b12488/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8afaced6-d9f0-4f78-899d-3f463eb2a76d/dqc_reference/reference_markers.hmm OceanDNA-b12488/protein.faa > /dev/null
[2023-03-15 05:00:21,838] [INFO] Task succeeded: HMMsearch
[2023-03-15 05:00:21,838] [INFO] Found 6/6 markers.
[2023-03-15 05:00:21,866] [INFO] Query marker FASTA was written to OceanDNA-b12488/markers.fasta
[2023-03-15 05:00:21,866] [INFO] Task started: Blastn
[2023-03-15 05:00:21,866] [INFO] Running command: blastn -query OceanDNA-b12488/markers.fasta -db /var/lib/cwl/stg8afaced6-d9f0-4f78-899d-3f463eb2a76d/dqc_reference/reference_markers.fasta -out OceanDNA-b12488/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 05:00:22,391] [INFO] Task succeeded: Blastn
[2023-03-15 05:00:22,395] [INFO] Selected 25 target genomes.
[2023-03-15 05:00:22,395] [INFO] Target genome list was writen to OceanDNA-b12488/target_genomes.txt
[2023-03-15 05:00:22,409] [INFO] Task started: fastANI
[2023-03-15 05:00:22,409] [INFO] Running command: fastANI --query /var/lib/cwl/stgf116dbb1-1569-4971-8e70-b5c157a6bae1/OceanDNA-b12488.fa --refList OceanDNA-b12488/target_genomes.txt --output OceanDNA-b12488/fastani_result.tsv --threads 1
[2023-03-15 05:00:35,639] [INFO] Task succeeded: fastANI
[2023-03-15 05:00:35,640] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8afaced6-d9f0-4f78-899d-3f463eb2a76d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 05:00:35,640] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8afaced6-d9f0-4f78-899d-3f463eb2a76d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 05:00:35,640] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 05:00:35,640] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 05:00:35,640] [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 05:00:35,644] [INFO] DFAST Taxonomy check result was written to OceanDNA-b12488/tc_result.tsv
[2023-03-15 05:00:35,648] [INFO] ===== Taxonomy check completed =====
[2023-03-15 05:00:35,649] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 05:00:35,649] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8afaced6-d9f0-4f78-899d-3f463eb2a76d/dqc_reference/checkm_data
[2023-03-15 05:00:35,652] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 05:00:35,693] [INFO] Task started: CheckM
[2023-03-15 05:00:35,693] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b12488/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b12488/checkm_input OceanDNA-b12488/checkm_result
[2023-03-15 05:01:21,465] [INFO] Task succeeded: CheckM
[2023-03-15 05:01:21,466] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 78.82%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 05:01:21,490] [INFO] ===== Completeness check finished =====
[2023-03-15 05:01:21,491] [INFO] ===== Start GTDB Search =====
[2023-03-15 05:01:21,491] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b12488/markers.fasta)
[2023-03-15 05:01:21,492] [INFO] Task started: Blastn
[2023-03-15 05:01:21,492] [INFO] Running command: blastn -query OceanDNA-b12488/markers.fasta -db /var/lib/cwl/stg8afaced6-d9f0-4f78-899d-3f463eb2a76d/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b12488/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 05:01:22,205] [INFO] Task succeeded: Blastn
[2023-03-15 05:01:22,212] [INFO] Selected 23 target genomes.
[2023-03-15 05:01:22,212] [INFO] Target genome list was writen to OceanDNA-b12488/target_genomes_gtdb.txt
[2023-03-15 05:01:22,270] [INFO] Task started: fastANI
[2023-03-15 05:01:22,270] [INFO] Running command: fastANI --query /var/lib/cwl/stgf116dbb1-1569-4971-8e70-b5c157a6bae1/OceanDNA-b12488.fa --refList OceanDNA-b12488/target_genomes_gtdb.txt --output OceanDNA-b12488/fastani_result_gtdb.tsv --threads 1
[2023-03-15 05:01:34,291] [INFO] Task succeeded: fastANI
[2023-03-15 05:01:34,294] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 05:01:34,294] [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_905480225.1	s__UBA10066 sp905480225	99.2607	670	804	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UBA10066;g__UBA10066	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_018663635.1	s__UBA10066 sp018663635	88.8503	592	804	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UBA10066;g__UBA10066	95.0	99.16	98.96	0.84	0.82	4	-
GCA_003448535.1	s__UBA10066 sp003448535	76.3025	70	804	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UBA10066;g__UBA10066	95.0	97.80	97.80	0.81	0.81	2	-
--------------------------------------------------------------------------------
[2023-03-15 05:01:34,298] [INFO] GTDB search result was written to OceanDNA-b12488/result_gtdb.tsv
[2023-03-15 05:01:34,301] [INFO] ===== GTDB Search completed =====
[2023-03-15 05:01:34,304] [INFO] DFAST_QC result json was written to OceanDNA-b12488/dqc_result.json
[2023-03-15 05:01:34,305] [INFO] DFAST_QC completed!
[2023-03-15 05:01:34,305] [INFO] Total running time: 0h1m31s