[2023-03-15 23:07:04,516] [INFO] DFAST_QC pipeline started.
[2023-03-15 23:07:04,516] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 23:07:04,516] [INFO] DQC Reference Directory: /var/lib/cwl/stg7681e022-e3eb-4173-ab8d-d0b6b5d74f3f/dqc_reference
[2023-03-15 23:07:05,594] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 23:07:05,594] [INFO] Task started: Prodigal
[2023-03-15 23:07:05,594] [INFO] Running command: cat /var/lib/cwl/stg56008b4f-aa09-42bc-9890-d848abc9c73a/OceanDNA-b7198.fa | prodigal -d OceanDNA-b7198/cds.fna -a OceanDNA-b7198/protein.faa -g 11 -q > /dev/null
[2023-03-15 23:07:24,582] [INFO] Task succeeded: Prodigal
[2023-03-15 23:07:24,582] [INFO] Task started: HMMsearch
[2023-03-15 23:07:24,582] [INFO] Running command: hmmsearch --tblout OceanDNA-b7198/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7681e022-e3eb-4173-ab8d-d0b6b5d74f3f/dqc_reference/reference_markers.hmm OceanDNA-b7198/protein.faa > /dev/null
[2023-03-15 23:07:24,782] [INFO] Task succeeded: HMMsearch
[2023-03-15 23:07:24,783] [INFO] Found 6/6 markers.
[2023-03-15 23:07:24,802] [INFO] Query marker FASTA was written to OceanDNA-b7198/markers.fasta
[2023-03-15 23:07:24,802] [INFO] Task started: Blastn
[2023-03-15 23:07:24,802] [INFO] Running command: blastn -query OceanDNA-b7198/markers.fasta -db /var/lib/cwl/stg7681e022-e3eb-4173-ab8d-d0b6b5d74f3f/dqc_reference/reference_markers.fasta -out OceanDNA-b7198/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 23:07:25,370] [INFO] Task succeeded: Blastn
[2023-03-15 23:07:25,370] [INFO] Selected 27 target genomes.
[2023-03-15 23:07:25,371] [INFO] Target genome list was writen to OceanDNA-b7198/target_genomes.txt
[2023-03-15 23:07:25,412] [INFO] Task started: fastANI
[2023-03-15 23:07:25,412] [INFO] Running command: fastANI --query /var/lib/cwl/stg56008b4f-aa09-42bc-9890-d848abc9c73a/OceanDNA-b7198.fa --refList OceanDNA-b7198/target_genomes.txt --output OceanDNA-b7198/fastani_result.tsv --threads 1
[2023-03-15 23:07:40,049] [INFO] Task succeeded: fastANI
[2023-03-15 23:07:40,049] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7681e022-e3eb-4173-ab8d-d0b6b5d74f3f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 23:07:40,050] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7681e022-e3eb-4173-ab8d-d0b6b5d74f3f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 23:07:40,053] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 23:07:40,053] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 23:07:40,053] [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
Pukyongia salina	strain=RR4-38	GCA_002966125.1	2094025	2094025	type	True	75.5946	51	836	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 23:07:40,053] [INFO] DFAST Taxonomy check result was written to OceanDNA-b7198/tc_result.tsv
[2023-03-15 23:07:40,053] [INFO] ===== Taxonomy check completed =====
[2023-03-15 23:07:40,053] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 23:07:40,053] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7681e022-e3eb-4173-ab8d-d0b6b5d74f3f/dqc_reference/checkm_data
[2023-03-15 23:07:40,054] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 23:07:40,058] [INFO] Task started: CheckM
[2023-03-15 23:07:40,058] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b7198/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b7198/checkm_input OceanDNA-b7198/checkm_result
[2023-03-15 23:08:30,126] [INFO] Task succeeded: CheckM
[2023-03-15 23:08:30,127] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 73.96%
Contamintation: 2.08%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-15 23:08:30,151] [INFO] ===== Completeness check finished =====
[2023-03-15 23:08:30,151] [INFO] ===== Start GTDB Search =====
[2023-03-15 23:08:30,151] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b7198/markers.fasta)
[2023-03-15 23:08:30,152] [INFO] Task started: Blastn
[2023-03-15 23:08:30,152] [INFO] Running command: blastn -query OceanDNA-b7198/markers.fasta -db /var/lib/cwl/stg7681e022-e3eb-4173-ab8d-d0b6b5d74f3f/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b7198/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 23:08:30,916] [INFO] Task succeeded: Blastn
[2023-03-15 23:08:30,923] [INFO] Selected 23 target genomes.
[2023-03-15 23:08:30,923] [INFO] Target genome list was writen to OceanDNA-b7198/target_genomes_gtdb.txt
[2023-03-15 23:08:30,939] [INFO] Task started: fastANI
[2023-03-15 23:08:30,939] [INFO] Running command: fastANI --query /var/lib/cwl/stg56008b4f-aa09-42bc-9890-d848abc9c73a/OceanDNA-b7198.fa --refList OceanDNA-b7198/target_genomes_gtdb.txt --output OceanDNA-b7198/fastani_result_gtdb.tsv --threads 1
[2023-03-15 23:08:42,934] [INFO] Task succeeded: fastANI
[2023-03-15 23:08:42,937] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 23:08:42,938] [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
GCF_002163875.1	s__Gilvibacter sp002163875	78.3935	321	836	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gilvibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013214815.1	s__Gilvibacter sp013214815	78.1566	283	836	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gilvibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009827225.1	s__SMXJ01 sp009827225	76.0499	52	836	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__SMXJ01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 23:08:42,940] [INFO] GTDB search result was written to OceanDNA-b7198/result_gtdb.tsv
[2023-03-15 23:08:42,945] [INFO] ===== GTDB Search completed =====
[2023-03-15 23:08:42,949] [INFO] DFAST_QC result json was written to OceanDNA-b7198/dqc_result.json
[2023-03-15 23:08:42,950] [INFO] DFAST_QC completed!
[2023-03-15 23:08:42,950] [INFO] Total running time: 0h1m38s