[2023-03-17 10:48:45,527] [INFO] DFAST_QC pipeline started.
[2023-03-17 10:48:45,528] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 10:48:45,528] [INFO] DQC Reference Directory: /var/lib/cwl/stg5ad5fda3-05d0-4656-81f9-c7dbe92a8b66/dqc_reference
[2023-03-17 10:48:46,693] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 10:48:46,694] [INFO] Task started: Prodigal
[2023-03-17 10:48:46,694] [INFO] Running command: cat /var/lib/cwl/stg6ad77db8-1eac-4dba-80f7-3a16b9a337fa/OceanDNA-b11564.fa | prodigal -d OceanDNA-b11564/cds.fna -a OceanDNA-b11564/protein.faa -g 11 -q > /dev/null
[2023-03-17 10:48:50,822] [INFO] Task succeeded: Prodigal
[2023-03-17 10:48:50,823] [INFO] Task started: HMMsearch
[2023-03-17 10:48:50,823] [INFO] Running command: hmmsearch --tblout OceanDNA-b11564/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5ad5fda3-05d0-4656-81f9-c7dbe92a8b66/dqc_reference/reference_markers.hmm OceanDNA-b11564/protein.faa > /dev/null
[2023-03-17 10:48:50,997] [INFO] Task succeeded: HMMsearch
[2023-03-17 10:48:50,998] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg6ad77db8-1eac-4dba-80f7-3a16b9a337fa/OceanDNA-b11564.fa]
[2023-03-17 10:48:51,007] [INFO] Query marker FASTA was written to OceanDNA-b11564/markers.fasta
[2023-03-17 10:48:51,007] [INFO] Task started: Blastn
[2023-03-17 10:48:51,007] [INFO] Running command: blastn -query OceanDNA-b11564/markers.fasta -db /var/lib/cwl/stg5ad5fda3-05d0-4656-81f9-c7dbe92a8b66/dqc_reference/reference_markers.fasta -out OceanDNA-b11564/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 10:48:51,511] [INFO] Task succeeded: Blastn
[2023-03-17 10:48:51,512] [INFO] Selected 18 target genomes.
[2023-03-17 10:48:51,513] [INFO] Target genome list was writen to OceanDNA-b11564/target_genomes.txt
[2023-03-17 10:48:51,526] [INFO] Task started: fastANI
[2023-03-17 10:48:51,526] [INFO] Running command: fastANI --query /var/lib/cwl/stg6ad77db8-1eac-4dba-80f7-3a16b9a337fa/OceanDNA-b11564.fa --refList OceanDNA-b11564/target_genomes.txt --output OceanDNA-b11564/fastani_result.tsv --threads 1
[2023-03-17 10:49:01,747] [INFO] Task succeeded: fastANI
[2023-03-17 10:49:01,747] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5ad5fda3-05d0-4656-81f9-c7dbe92a8b66/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 10:49:01,747] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5ad5fda3-05d0-4656-81f9-c7dbe92a8b66/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 10:49:01,748] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 10:49:01,748] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 10:49:01,748] [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
--------------------------------------------------------------------------------
[2023-03-17 10:49:01,748] [INFO] DFAST Taxonomy check result was written to OceanDNA-b11564/tc_result.tsv
[2023-03-17 10:49:01,749] [INFO] ===== Taxonomy check completed =====
[2023-03-17 10:49:01,749] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 10:49:01,749] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5ad5fda3-05d0-4656-81f9-c7dbe92a8b66/dqc_reference/checkm_data
[2023-03-17 10:49:01,752] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 10:49:01,762] [INFO] Task started: CheckM
[2023-03-17 10:49:01,762] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b11564/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b11564/checkm_input OceanDNA-b11564/checkm_result
[2023-03-17 10:49:18,846] [INFO] Task succeeded: CheckM
[2023-03-17 10:49:18,847] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 61.58%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-17 10:49:18,849] [INFO] ===== Completeness check finished =====
[2023-03-17 10:49:18,849] [INFO] ===== Start GTDB Search =====
[2023-03-17 10:49:18,849] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b11564/markers.fasta)
[2023-03-17 10:49:18,850] [INFO] Task started: Blastn
[2023-03-17 10:49:18,850] [INFO] Running command: blastn -query OceanDNA-b11564/markers.fasta -db /var/lib/cwl/stg5ad5fda3-05d0-4656-81f9-c7dbe92a8b66/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b11564/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 10:49:19,696] [INFO] Task succeeded: Blastn
[2023-03-17 10:49:19,697] [INFO] Selected 20 target genomes.
[2023-03-17 10:49:19,697] [INFO] Target genome list was writen to OceanDNA-b11564/target_genomes_gtdb.txt
[2023-03-17 10:49:20,099] [INFO] Task started: fastANI
[2023-03-17 10:49:20,099] [INFO] Running command: fastANI --query /var/lib/cwl/stg6ad77db8-1eac-4dba-80f7-3a16b9a337fa/OceanDNA-b11564.fa --refList OceanDNA-b11564/target_genomes_gtdb.txt --output OceanDNA-b11564/fastani_result_gtdb.tsv --threads 1
[2023-03-17 10:49:26,782] [INFO] Task succeeded: fastANI
[2023-03-17 10:49:26,785] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 10:49:26,785] [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_002722215.1	s__SP256 sp002722215	92.2722	125	139	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__TMED113;g__SP256	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002713285.1	s__SP256 sp002713285	78.3257	74	139	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__TMED113;g__SP256	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002714185.1	s__SP256 sp002714185	77.7078	53	139	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__TMED113;g__SP256	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 10:49:26,785] [INFO] GTDB search result was written to OceanDNA-b11564/result_gtdb.tsv
[2023-03-17 10:49:26,785] [INFO] ===== GTDB Search completed =====
[2023-03-17 10:49:26,786] [INFO] DFAST_QC result json was written to OceanDNA-b11564/dqc_result.json
[2023-03-17 10:49:26,786] [INFO] DFAST_QC completed!
[2023-03-17 10:49:26,786] [INFO] Total running time: 0h0m41s