[2023-03-18 01:59:39,753] [INFO] DFAST_QC pipeline started.
[2023-03-18 01:59:39,755] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 01:59:39,755] [INFO] DQC Reference Directory: /var/lib/cwl/stg1bd7631f-1c24-4572-a599-162876d1d1b1/dqc_reference
[2023-03-18 01:59:40,985] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 01:59:40,986] [INFO] Task started: Prodigal
[2023-03-18 01:59:40,986] [INFO] Running command: cat /var/lib/cwl/stgfe970913-692c-4b06-b163-26121c60d772/OceanDNA-b23841.fa | prodigal -d OceanDNA-b23841/cds.fna -a OceanDNA-b23841/protein.faa -g 11 -q > /dev/null
[2023-03-18 01:59:50,247] [INFO] Task succeeded: Prodigal
[2023-03-18 01:59:50,247] [INFO] Task started: HMMsearch
[2023-03-18 01:59:50,247] [INFO] Running command: hmmsearch --tblout OceanDNA-b23841/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1bd7631f-1c24-4572-a599-162876d1d1b1/dqc_reference/reference_markers.hmm OceanDNA-b23841/protein.faa > /dev/null
[2023-03-18 01:59:50,427] [INFO] Task succeeded: HMMsearch
[2023-03-18 01:59:50,427] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgfe970913-692c-4b06-b163-26121c60d772/OceanDNA-b23841.fa]
[2023-03-18 01:59:50,462] [INFO] Query marker FASTA was written to OceanDNA-b23841/markers.fasta
[2023-03-18 01:59:50,462] [INFO] Task started: Blastn
[2023-03-18 01:59:50,462] [INFO] Running command: blastn -query OceanDNA-b23841/markers.fasta -db /var/lib/cwl/stg1bd7631f-1c24-4572-a599-162876d1d1b1/dqc_reference/reference_markers.fasta -out OceanDNA-b23841/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 01:59:50,998] [INFO] Task succeeded: Blastn
[2023-03-18 01:59:51,003] [INFO] Selected 25 target genomes.
[2023-03-18 01:59:51,003] [INFO] Target genome list was writen to OceanDNA-b23841/target_genomes.txt
[2023-03-18 01:59:51,020] [INFO] Task started: fastANI
[2023-03-18 01:59:51,020] [INFO] Running command: fastANI --query /var/lib/cwl/stgfe970913-692c-4b06-b163-26121c60d772/OceanDNA-b23841.fa --refList OceanDNA-b23841/target_genomes.txt --output OceanDNA-b23841/fastani_result.tsv --threads 1
[2023-03-18 02:00:04,010] [INFO] Task succeeded: fastANI
[2023-03-18 02:00:04,011] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1bd7631f-1c24-4572-a599-162876d1d1b1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 02:00:04,011] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1bd7631f-1c24-4572-a599-162876d1d1b1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 02:00:04,015] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 02:00:04,015] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 02:00:04,015] [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
Litorimonas taeanensis	strain=DSM 22008	GCA_003634015.1	568099	568099	type	True	76.4594	64	520	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 02:00:04,017] [INFO] DFAST Taxonomy check result was written to OceanDNA-b23841/tc_result.tsv
[2023-03-18 02:00:04,020] [INFO] ===== Taxonomy check completed =====
[2023-03-18 02:00:04,020] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 02:00:04,020] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1bd7631f-1c24-4572-a599-162876d1d1b1/dqc_reference/checkm_data
[2023-03-18 02:00:04,021] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 02:00:04,061] [INFO] Task started: CheckM
[2023-03-18 02:00:04,061] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b23841/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b23841/checkm_input OceanDNA-b23841/checkm_result
[2023-03-18 02:00:32,224] [INFO] Task succeeded: CheckM
[2023-03-18 02:00:32,225] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 37.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 02:00:32,289] [INFO] ===== Completeness check finished =====
[2023-03-18 02:00:32,289] [INFO] ===== Start GTDB Search =====
[2023-03-18 02:00:32,289] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b23841/markers.fasta)
[2023-03-18 02:00:32,290] [INFO] Task started: Blastn
[2023-03-18 02:00:32,290] [INFO] Running command: blastn -query OceanDNA-b23841/markers.fasta -db /var/lib/cwl/stg1bd7631f-1c24-4572-a599-162876d1d1b1/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b23841/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 02:00:33,085] [INFO] Task succeeded: Blastn
[2023-03-18 02:00:33,087] [INFO] Selected 26 target genomes.
[2023-03-18 02:00:33,087] [INFO] Target genome list was writen to OceanDNA-b23841/target_genomes_gtdb.txt
[2023-03-18 02:00:33,194] [INFO] Task started: fastANI
[2023-03-18 02:00:33,194] [INFO] Running command: fastANI --query /var/lib/cwl/stgfe970913-692c-4b06-b163-26121c60d772/OceanDNA-b23841.fa --refList OceanDNA-b23841/target_genomes_gtdb.txt --output OceanDNA-b23841/fastani_result_gtdb.tsv --threads 1
[2023-03-18 02:00:47,541] [INFO] Task succeeded: fastANI
[2023-03-18 02:00:47,543] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 02:00:47,543] [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_003634015.1	s__Litorimonas taeanensis	76.4594	64	520	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Litorimonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 02:00:47,545] [INFO] GTDB search result was written to OceanDNA-b23841/result_gtdb.tsv
[2023-03-18 02:00:47,549] [INFO] ===== GTDB Search completed =====
[2023-03-18 02:00:47,551] [INFO] DFAST_QC result json was written to OceanDNA-b23841/dqc_result.json
[2023-03-18 02:00:47,551] [INFO] DFAST_QC completed!
[2023-03-18 02:00:47,551] [INFO] Total running time: 0h1m8s