[2023-03-15 08:09:45,333] [INFO] DFAST_QC pipeline started.
[2023-03-15 08:09:45,334] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 08:09:45,334] [INFO] DQC Reference Directory: /var/lib/cwl/stg815f5db1-f94e-4563-9969-df71348a288e/dqc_reference
[2023-03-15 08:09:46,483] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 08:09:46,484] [INFO] Task started: Prodigal
[2023-03-15 08:09:46,484] [INFO] Running command: cat /var/lib/cwl/stg970bfd20-8982-41e4-98c7-86b01e2bd85b/OceanDNA-b104.fa | prodigal -d OceanDNA-b104/cds.fna -a OceanDNA-b104/protein.faa -g 11 -q > /dev/null
[2023-03-15 08:10:02,651] [INFO] Task succeeded: Prodigal
[2023-03-15 08:10:02,651] [INFO] Task started: HMMsearch
[2023-03-15 08:10:02,652] [INFO] Running command: hmmsearch --tblout OceanDNA-b104/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg815f5db1-f94e-4563-9969-df71348a288e/dqc_reference/reference_markers.hmm OceanDNA-b104/protein.faa > /dev/null
[2023-03-15 08:10:03,004] [INFO] Task succeeded: HMMsearch
[2023-03-15 08:10:03,004] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg970bfd20-8982-41e4-98c7-86b01e2bd85b/OceanDNA-b104.fa]
[2023-03-15 08:10:03,024] [INFO] Query marker FASTA was written to OceanDNA-b104/markers.fasta
[2023-03-15 08:10:03,025] [INFO] Task started: Blastn
[2023-03-15 08:10:03,025] [INFO] Running command: blastn -query OceanDNA-b104/markers.fasta -db /var/lib/cwl/stg815f5db1-f94e-4563-9969-df71348a288e/dqc_reference/reference_markers.fasta -out OceanDNA-b104/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 08:10:03,538] [INFO] Task succeeded: Blastn
[2023-03-15 08:10:03,539] [INFO] Selected 12 target genomes.
[2023-03-15 08:10:03,539] [INFO] Target genome list was writen to OceanDNA-b104/target_genomes.txt
[2023-03-15 08:10:03,553] [INFO] Task started: fastANI
[2023-03-15 08:10:03,553] [INFO] Running command: fastANI --query /var/lib/cwl/stg970bfd20-8982-41e4-98c7-86b01e2bd85b/OceanDNA-b104.fa --refList OceanDNA-b104/target_genomes.txt --output OceanDNA-b104/fastani_result.tsv --threads 1
[2023-03-15 08:10:12,302] [INFO] Task succeeded: fastANI
[2023-03-15 08:10:12,302] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg815f5db1-f94e-4563-9969-df71348a288e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 08:10:12,302] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg815f5db1-f94e-4563-9969-df71348a288e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 08:10:12,303] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 08:10:12,303] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 08:10:12,303] [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 08:10:12,303] [INFO] DFAST Taxonomy check result was written to OceanDNA-b104/tc_result.tsv
[2023-03-15 08:10:12,303] [INFO] ===== Taxonomy check completed =====
[2023-03-15 08:10:12,303] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 08:10:12,303] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg815f5db1-f94e-4563-9969-df71348a288e/dqc_reference/checkm_data
[2023-03-15 08:10:12,306] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 08:10:12,311] [INFO] Task started: CheckM
[2023-03-15 08:10:12,311] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b104/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b104/checkm_input OceanDNA-b104/checkm_result
[2023-03-15 08:10:54,857] [INFO] Task succeeded: CheckM
[2023-03-15 08:10:54,858] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.46%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 08:10:54,861] [INFO] ===== Completeness check finished =====
[2023-03-15 08:10:54,861] [INFO] ===== Start GTDB Search =====
[2023-03-15 08:10:54,861] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b104/markers.fasta)
[2023-03-15 08:10:54,862] [INFO] Task started: Blastn
[2023-03-15 08:10:54,862] [INFO] Running command: blastn -query OceanDNA-b104/markers.fasta -db /var/lib/cwl/stg815f5db1-f94e-4563-9969-df71348a288e/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b104/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 08:10:55,521] [INFO] Task succeeded: Blastn
[2023-03-15 08:10:55,522] [INFO] Selected 19 target genomes.
[2023-03-15 08:10:55,522] [INFO] Target genome list was writen to OceanDNA-b104/target_genomes_gtdb.txt
[2023-03-15 08:10:55,539] [INFO] Task started: fastANI
[2023-03-15 08:10:55,540] [INFO] Running command: fastANI --query /var/lib/cwl/stg970bfd20-8982-41e4-98c7-86b01e2bd85b/OceanDNA-b104.fa --refList OceanDNA-b104/target_genomes_gtdb.txt --output OceanDNA-b104/fastani_result_gtdb.tsv --threads 1
[2023-03-15 08:11:05,793] [INFO] Task succeeded: fastANI
[2023-03-15 08:11:05,795] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 08:11:05,795] [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_002731215.1	s__UBA890 sp002731215	99.7502	316	873	d__Bacteria;p__Acidobacteriota;c__UBA890;o__UBA890;f__UBA890;g__UBA890	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002722645.1	s__UBA890 sp002722645	90.4103	664	873	d__Bacteria;p__Acidobacteriota;c__UBA890;o__UBA890;f__UBA890;g__UBA890	95.0	97.90	97.61	0.78	0.75	3	-
--------------------------------------------------------------------------------
[2023-03-15 08:11:05,795] [INFO] GTDB search result was written to OceanDNA-b104/result_gtdb.tsv
[2023-03-15 08:11:05,796] [INFO] ===== GTDB Search completed =====
[2023-03-15 08:11:05,796] [INFO] DFAST_QC result json was written to OceanDNA-b104/dqc_result.json
[2023-03-15 08:11:05,796] [INFO] DFAST_QC completed!
[2023-03-15 08:11:05,796] [INFO] Total running time: 0h1m20s