[2023-03-15 13:58:53,817] [INFO] DFAST_QC pipeline started.
[2023-03-15 13:58:53,822] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 13:58:53,822] [INFO] DQC Reference Directory: /var/lib/cwl/stge0026013-77bb-4b4a-bb83-270bc2255c97/dqc_reference
[2023-03-15 13:58:56,130] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 13:58:56,131] [INFO] Task started: Prodigal
[2023-03-15 13:58:56,131] [INFO] Running command: cat /var/lib/cwl/stg6f990694-9988-4ba6-b7b6-3c7a24d45693/OceanDNA-b32498.fa | prodigal -d OceanDNA-b32498/cds.fna -a OceanDNA-b32498/protein.faa -g 11 -q > /dev/null
[2023-03-15 13:59:01,554] [INFO] Task succeeded: Prodigal
[2023-03-15 13:59:01,554] [INFO] Task started: HMMsearch
[2023-03-15 13:59:01,554] [INFO] Running command: hmmsearch --tblout OceanDNA-b32498/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge0026013-77bb-4b4a-bb83-270bc2255c97/dqc_reference/reference_markers.hmm OceanDNA-b32498/protein.faa > /dev/null
[2023-03-15 13:59:01,750] [INFO] Task succeeded: HMMsearch
[2023-03-15 13:59:01,751] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg6f990694-9988-4ba6-b7b6-3c7a24d45693/OceanDNA-b32498.fa]
[2023-03-15 13:59:01,766] [INFO] Query marker FASTA was written to OceanDNA-b32498/markers.fasta
[2023-03-15 13:59:01,768] [INFO] Task started: Blastn
[2023-03-15 13:59:01,768] [INFO] Running command: blastn -query OceanDNA-b32498/markers.fasta -db /var/lib/cwl/stge0026013-77bb-4b4a-bb83-270bc2255c97/dqc_reference/reference_markers.fasta -out OceanDNA-b32498/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 13:59:02,282] [INFO] Task succeeded: Blastn
[2023-03-15 13:59:02,283] [INFO] Selected 14 target genomes.
[2023-03-15 13:59:02,283] [INFO] Target genome list was writen to OceanDNA-b32498/target_genomes.txt
[2023-03-15 13:59:02,293] [INFO] Task started: fastANI
[2023-03-15 13:59:02,293] [INFO] Running command: fastANI --query /var/lib/cwl/stg6f990694-9988-4ba6-b7b6-3c7a24d45693/OceanDNA-b32498.fa --refList OceanDNA-b32498/target_genomes.txt --output OceanDNA-b32498/fastani_result.tsv --threads 1
[2023-03-15 13:59:06,954] [INFO] Task succeeded: fastANI
[2023-03-15 13:59:06,955] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge0026013-77bb-4b4a-bb83-270bc2255c97/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 13:59:06,955] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge0026013-77bb-4b4a-bb83-270bc2255c97/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 13:59:06,955] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 13:59:06,955] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 13:59:06,955] [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 13:59:06,955] [INFO] DFAST Taxonomy check result was written to OceanDNA-b32498/tc_result.tsv
[2023-03-15 13:59:06,955] [INFO] ===== Taxonomy check completed =====
[2023-03-15 13:59:06,955] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 13:59:06,955] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge0026013-77bb-4b4a-bb83-270bc2255c97/dqc_reference/checkm_data
[2023-03-15 13:59:06,966] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 13:59:06,980] [INFO] Task started: CheckM
[2023-03-15 13:59:06,980] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b32498/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b32498/checkm_input OceanDNA-b32498/checkm_result
[2023-03-15 13:59:29,045] [INFO] Task succeeded: CheckM
[2023-03-15 13:59:29,045] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.96%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 13:59:29,073] [INFO] ===== Completeness check finished =====
[2023-03-15 13:59:29,074] [INFO] ===== Start GTDB Search =====
[2023-03-15 13:59:29,074] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b32498/markers.fasta)
[2023-03-15 13:59:29,076] [INFO] Task started: Blastn
[2023-03-15 13:59:29,076] [INFO] Running command: blastn -query OceanDNA-b32498/markers.fasta -db /var/lib/cwl/stge0026013-77bb-4b4a-bb83-270bc2255c97/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b32498/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 13:59:29,812] [INFO] Task succeeded: Blastn
[2023-03-15 13:59:29,815] [INFO] Selected 9 target genomes.
[2023-03-15 13:59:29,815] [INFO] Target genome list was writen to OceanDNA-b32498/target_genomes_gtdb.txt
[2023-03-15 13:59:29,828] [INFO] Task started: fastANI
[2023-03-15 13:59:29,828] [INFO] Running command: fastANI --query /var/lib/cwl/stg6f990694-9988-4ba6-b7b6-3c7a24d45693/OceanDNA-b32498.fa --refList OceanDNA-b32498/target_genomes_gtdb.txt --output OceanDNA-b32498/fastani_result_gtdb.tsv --threads 1
[2023-03-15 13:59:32,393] [INFO] Task succeeded: fastANI
[2023-03-15 13:59:32,399] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 13:59:32,399] [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_002689325.1	s__GCA-002690875 sp002689325	99.8435	331	358	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__TMED127;f__TMED127;g__GCA-002690875	95.0	100.00	100.00	0.99	0.99	2	conclusive
GCA_002690875.1	s__GCA-002690875 sp002690875	85.3324	256	358	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__TMED127;f__TMED127;g__GCA-002690875	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002171275.2	s__GCA-2704625 sp002171275	84.7856	57	358	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__GCA-2704625	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902536485.1	s__GCA-002690875 sp902536485	84.7058	210	358	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__TMED127;f__TMED127;g__GCA-002690875	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902618535.1	s__GCA-002690875 sp902618535	84.6269	240	358	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__TMED127;f__TMED127;g__GCA-002690875	95.0	97.44	97.44	0.66	0.66	2	-
GCA_902537615.1	s__GCA-002690875 sp902537615	84.2935	255	358	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__TMED127;f__TMED127;g__GCA-002690875	95.0	96.75	96.75	0.77	0.77	2	-
GCA_002712255.1	s__MED-G10 sp002712255	76.0182	76	358	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__TMED127;f__TMED127;g__MED-G10	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002167825.1	s__TMED13 sp002167825	75.9996	52	358	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__TMED127;f__TMED127;g__TMED13	95.0	100.00	100.00	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2023-03-15 13:59:32,401] [INFO] GTDB search result was written to OceanDNA-b32498/result_gtdb.tsv
[2023-03-15 13:59:32,403] [INFO] ===== GTDB Search completed =====
[2023-03-15 13:59:32,404] [INFO] DFAST_QC result json was written to OceanDNA-b32498/dqc_result.json
[2023-03-15 13:59:32,404] [INFO] DFAST_QC completed!
[2023-03-15 13:59:32,404] [INFO] Total running time: 0h0m39s