[2023-03-18 20:59:43,923] [INFO] DFAST_QC pipeline started.
[2023-03-18 20:59:43,923] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 20:59:43,923] [INFO] DQC Reference Directory: /var/lib/cwl/stg8b94d46b-6d90-4cc0-b762-a6d151dbc0f9/dqc_reference
[2023-03-18 20:59:45,685] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 20:59:45,685] [INFO] Task started: Prodigal
[2023-03-18 20:59:45,686] [INFO] Running command: cat /var/lib/cwl/stg714fd688-ce7e-4ffc-a57b-4b8250e72166/OceanDNA-b11517.fa | prodigal -d OceanDNA-b11517/cds.fna -a OceanDNA-b11517/protein.faa -g 11 -q > /dev/null
[2023-03-18 21:00:03,266] [INFO] Task succeeded: Prodigal
[2023-03-18 21:00:03,266] [INFO] Task started: HMMsearch
[2023-03-18 21:00:03,266] [INFO] Running command: hmmsearch --tblout OceanDNA-b11517/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8b94d46b-6d90-4cc0-b762-a6d151dbc0f9/dqc_reference/reference_markers.hmm OceanDNA-b11517/protein.faa > /dev/null
[2023-03-18 21:00:03,482] [INFO] Task succeeded: HMMsearch
[2023-03-18 21:00:03,483] [INFO] Found 6/6 markers.
[2023-03-18 21:00:03,504] [INFO] Query marker FASTA was written to OceanDNA-b11517/markers.fasta
[2023-03-18 21:00:03,505] [INFO] Task started: Blastn
[2023-03-18 21:00:03,505] [INFO] Running command: blastn -query OceanDNA-b11517/markers.fasta -db /var/lib/cwl/stg8b94d46b-6d90-4cc0-b762-a6d151dbc0f9/dqc_reference/reference_markers.fasta -out OceanDNA-b11517/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 21:00:04,092] [INFO] Task succeeded: Blastn
[2023-03-18 21:00:04,093] [INFO] Selected 23 target genomes.
[2023-03-18 21:00:04,093] [INFO] Target genome list was writen to OceanDNA-b11517/target_genomes.txt
[2023-03-18 21:00:04,105] [INFO] Task started: fastANI
[2023-03-18 21:00:04,105] [INFO] Running command: fastANI --query /var/lib/cwl/stg714fd688-ce7e-4ffc-a57b-4b8250e72166/OceanDNA-b11517.fa --refList OceanDNA-b11517/target_genomes.txt --output OceanDNA-b11517/fastani_result.tsv --threads 1
[2023-03-18 21:00:19,270] [INFO] Task succeeded: fastANI
[2023-03-18 21:00:19,270] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8b94d46b-6d90-4cc0-b762-a6d151dbc0f9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 21:00:19,271] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8b94d46b-6d90-4cc0-b762-a6d151dbc0f9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 21:00:19,271] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 21:00:19,271] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 21:00:19,271] [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
--------------------------------------------------------------------------------
[2023-03-18 21:00:19,271] [INFO] DFAST Taxonomy check result was written to OceanDNA-b11517/tc_result.tsv
[2023-03-18 21:00:19,271] [INFO] ===== Taxonomy check completed =====
[2023-03-18 21:00:19,271] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 21:00:19,272] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8b94d46b-6d90-4cc0-b762-a6d151dbc0f9/dqc_reference/checkm_data
[2023-03-18 21:00:19,274] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 21:00:19,299] [INFO] Task started: CheckM
[2023-03-18 21:00:19,299] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b11517/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b11517/checkm_input OceanDNA-b11517/checkm_result
[2023-03-18 21:01:05,567] [INFO] Task succeeded: CheckM
[2023-03-18 21:01:05,568] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 72.73%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 21:01:05,607] [INFO] ===== Completeness check finished =====
[2023-03-18 21:01:05,608] [INFO] ===== Start GTDB Search =====
[2023-03-18 21:01:05,608] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b11517/markers.fasta)
[2023-03-18 21:01:05,609] [INFO] Task started: Blastn
[2023-03-18 21:01:05,609] [INFO] Running command: blastn -query OceanDNA-b11517/markers.fasta -db /var/lib/cwl/stg8b94d46b-6d90-4cc0-b762-a6d151dbc0f9/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b11517/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 21:01:06,553] [INFO] Task succeeded: Blastn
[2023-03-18 21:01:06,558] [INFO] Selected 24 target genomes.
[2023-03-18 21:01:06,558] [INFO] Target genome list was writen to OceanDNA-b11517/target_genomes_gtdb.txt
[2023-03-18 21:01:06,596] [INFO] Task started: fastANI
[2023-03-18 21:01:06,596] [INFO] Running command: fastANI --query /var/lib/cwl/stg714fd688-ce7e-4ffc-a57b-4b8250e72166/OceanDNA-b11517.fa --refList OceanDNA-b11517/target_genomes_gtdb.txt --output OceanDNA-b11517/fastani_result_gtdb.tsv --threads 1
[2023-03-18 21:01:18,975] [INFO] Task succeeded: fastANI
[2023-03-18 21:01:18,978] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 21:01:18,978] [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_002717515.1	s__GCA-002722245 sp002717515	99.8501	788	895	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	conclusive
GCA_002720635.1	s__GCA-002722245 sp002720635	80.8244	364	895	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_002722245.1	s__GCA-002722245 sp002722245	79.9752	203	895	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	-
--------------------------------------------------------------------------------
[2023-03-18 21:01:18,981] [INFO] GTDB search result was written to OceanDNA-b11517/result_gtdb.tsv
[2023-03-18 21:01:18,981] [INFO] ===== GTDB Search completed =====
[2023-03-18 21:01:18,982] [INFO] DFAST_QC result json was written to OceanDNA-b11517/dqc_result.json
[2023-03-18 21:01:18,982] [INFO] DFAST_QC completed!
[2023-03-18 21:01:18,982] [INFO] Total running time: 0h1m35s