[2023-03-15 17:05:43,620] [INFO] DFAST_QC pipeline started.
[2023-03-15 17:05:43,620] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 17:05:43,620] [INFO] DQC Reference Directory: /var/lib/cwl/stg6884e0a5-3c24-482a-bd13-39e18277ea47/dqc_reference
[2023-03-15 17:05:45,975] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 17:05:45,976] [INFO] Task started: Prodigal
[2023-03-15 17:05:45,976] [INFO] Running command: cat /var/lib/cwl/stg6765efe4-7e3e-45f0-b270-c124bc9449ec/OceanDNA-b3834.fa | prodigal -d OceanDNA-b3834/cds.fna -a OceanDNA-b3834/protein.faa -g 11 -q > /dev/null
[2023-03-15 17:06:00,618] [INFO] Task succeeded: Prodigal
[2023-03-15 17:06:00,618] [INFO] Task started: HMMsearch
[2023-03-15 17:06:00,618] [INFO] Running command: hmmsearch --tblout OceanDNA-b3834/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6884e0a5-3c24-482a-bd13-39e18277ea47/dqc_reference/reference_markers.hmm OceanDNA-b3834/protein.faa > /dev/null
[2023-03-15 17:06:00,805] [INFO] Task succeeded: HMMsearch
[2023-03-15 17:06:00,805] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg6765efe4-7e3e-45f0-b270-c124bc9449ec/OceanDNA-b3834.fa]
[2023-03-15 17:06:00,821] [INFO] Query marker FASTA was written to OceanDNA-b3834/markers.fasta
[2023-03-15 17:06:00,822] [INFO] Task started: Blastn
[2023-03-15 17:06:00,823] [INFO] Running command: blastn -query OceanDNA-b3834/markers.fasta -db /var/lib/cwl/stg6884e0a5-3c24-482a-bd13-39e18277ea47/dqc_reference/reference_markers.fasta -out OceanDNA-b3834/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 17:06:01,392] [INFO] Task succeeded: Blastn
[2023-03-15 17:06:01,394] [INFO] Selected 20 target genomes.
[2023-03-15 17:06:01,394] [INFO] Target genome list was writen to OceanDNA-b3834/target_genomes.txt
[2023-03-15 17:06:01,406] [INFO] Task started: fastANI
[2023-03-15 17:06:01,406] [INFO] Running command: fastANI --query /var/lib/cwl/stg6765efe4-7e3e-45f0-b270-c124bc9449ec/OceanDNA-b3834.fa --refList OceanDNA-b3834/target_genomes.txt --output OceanDNA-b3834/fastani_result.tsv --threads 1
[2023-03-15 17:06:15,404] [INFO] Task succeeded: fastANI
[2023-03-15 17:06:15,404] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6884e0a5-3c24-482a-bd13-39e18277ea47/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 17:06:15,405] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6884e0a5-3c24-482a-bd13-39e18277ea47/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 17:06:15,405] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 17:06:15,405] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 17:06:15,405] [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 17:06:15,405] [INFO] DFAST Taxonomy check result was written to OceanDNA-b3834/tc_result.tsv
[2023-03-15 17:06:15,406] [INFO] ===== Taxonomy check completed =====
[2023-03-15 17:06:15,406] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 17:06:15,406] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6884e0a5-3c24-482a-bd13-39e18277ea47/dqc_reference/checkm_data
[2023-03-15 17:06:15,409] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 17:06:15,464] [INFO] Task started: CheckM
[2023-03-15 17:06:15,464] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b3834/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b3834/checkm_input OceanDNA-b3834/checkm_result
[2023-03-15 17:06:55,793] [INFO] Task succeeded: CheckM
[2023-03-15 17:06:55,794] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.17%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 17:06:55,821] [INFO] ===== Completeness check finished =====
[2023-03-15 17:06:55,821] [INFO] ===== Start GTDB Search =====
[2023-03-15 17:06:55,821] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b3834/markers.fasta)
[2023-03-15 17:06:55,822] [INFO] Task started: Blastn
[2023-03-15 17:06:55,822] [INFO] Running command: blastn -query OceanDNA-b3834/markers.fasta -db /var/lib/cwl/stg6884e0a5-3c24-482a-bd13-39e18277ea47/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b3834/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 17:06:56,711] [INFO] Task succeeded: Blastn
[2023-03-15 17:06:56,714] [INFO] Selected 19 target genomes.
[2023-03-15 17:06:56,714] [INFO] Target genome list was writen to OceanDNA-b3834/target_genomes_gtdb.txt
[2023-03-15 17:06:56,737] [INFO] Task started: fastANI
[2023-03-15 17:06:56,737] [INFO] Running command: fastANI --query /var/lib/cwl/stg6765efe4-7e3e-45f0-b270-c124bc9449ec/OceanDNA-b3834.fa --refList OceanDNA-b3834/target_genomes_gtdb.txt --output OceanDNA-b3834/fastani_result_gtdb.tsv --threads 1
[2023-03-15 17:07:08,020] [INFO] Task succeeded: fastANI
[2023-03-15 17:07:08,023] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 17:07:08,023] [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_017853115.1	s__JAFMKE01 sp017853115	93.8678	496	677	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__UBA8649;g__JAFMKE01	95.0	99.30	99.30	0.86	0.86	2	-
GCA_016777395.1	s__JAFMKE01 sp016777395	76.6669	77	677	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__UBA8649;g__JAFMKE01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 17:07:08,024] [INFO] GTDB search result was written to OceanDNA-b3834/result_gtdb.tsv
[2023-03-15 17:07:08,024] [INFO] ===== GTDB Search completed =====
[2023-03-15 17:07:08,025] [INFO] DFAST_QC result json was written to OceanDNA-b3834/dqc_result.json
[2023-03-15 17:07:08,026] [INFO] DFAST_QC completed!
[2023-03-15 17:07:08,026] [INFO] Total running time: 0h1m24s