[2023-03-18 10:12:10,261] [INFO] DFAST_QC pipeline started.
[2023-03-18 10:12:10,261] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 10:12:10,261] [INFO] DQC Reference Directory: /var/lib/cwl/stg5de9bace-0683-4399-8030-9925a9f393c2/dqc_reference
[2023-03-18 10:12:11,374] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 10:12:11,374] [INFO] Task started: Prodigal
[2023-03-18 10:12:11,374] [INFO] Running command: cat /var/lib/cwl/stg4642de82-c836-4b68-b9d3-c1927218cd45/OceanDNA-b25448.fa | prodigal -d OceanDNA-b25448/cds.fna -a OceanDNA-b25448/protein.faa -g 11 -q > /dev/null
[2023-03-18 10:12:14,586] [INFO] Task succeeded: Prodigal
[2023-03-18 10:12:14,587] [INFO] Task started: HMMsearch
[2023-03-18 10:12:14,587] [INFO] Running command: hmmsearch --tblout OceanDNA-b25448/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5de9bace-0683-4399-8030-9925a9f393c2/dqc_reference/reference_markers.hmm OceanDNA-b25448/protein.faa > /dev/null
[2023-03-18 10:12:14,710] [INFO] Task succeeded: HMMsearch
[2023-03-18 10:12:14,711] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg4642de82-c836-4b68-b9d3-c1927218cd45/OceanDNA-b25448.fa]
[2023-03-18 10:12:14,724] [INFO] Query marker FASTA was written to OceanDNA-b25448/markers.fasta
[2023-03-18 10:12:14,725] [INFO] Task started: Blastn
[2023-03-18 10:12:14,725] [INFO] Running command: blastn -query OceanDNA-b25448/markers.fasta -db /var/lib/cwl/stg5de9bace-0683-4399-8030-9925a9f393c2/dqc_reference/reference_markers.fasta -out OceanDNA-b25448/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 10:12:15,160] [INFO] Task succeeded: Blastn
[2023-03-18 10:12:15,163] [INFO] Selected 11 target genomes.
[2023-03-18 10:12:15,163] [INFO] Target genome list was writen to OceanDNA-b25448/target_genomes.txt
[2023-03-18 10:12:15,171] [INFO] Task started: fastANI
[2023-03-18 10:12:15,171] [INFO] Running command: fastANI --query /var/lib/cwl/stg4642de82-c836-4b68-b9d3-c1927218cd45/OceanDNA-b25448.fa --refList OceanDNA-b25448/target_genomes.txt --output OceanDNA-b25448/fastani_result.tsv --threads 1
[2023-03-18 10:12:17,936] [INFO] Task succeeded: fastANI
[2023-03-18 10:12:17,936] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5de9bace-0683-4399-8030-9925a9f393c2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 10:12:17,937] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5de9bace-0683-4399-8030-9925a9f393c2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 10:12:17,937] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 10:12:17,937] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 10:12:17,937] [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
--------------------------------------------------------------------------------
[2023-03-18 10:12:17,939] [INFO] DFAST Taxonomy check result was written to OceanDNA-b25448/tc_result.tsv
[2023-03-18 10:12:17,939] [INFO] ===== Taxonomy check completed =====
[2023-03-18 10:12:17,939] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 10:12:17,939] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5de9bace-0683-4399-8030-9925a9f393c2/dqc_reference/checkm_data
[2023-03-18 10:12:17,942] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 10:12:17,997] [INFO] Task started: CheckM
[2023-03-18 10:12:17,997] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b25448/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b25448/checkm_input OceanDNA-b25448/checkm_result
[2023-03-18 10:12:32,782] [INFO] Task succeeded: CheckM
[2023-03-18 10:12:32,782] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 73.15%
Contamintation: 1.22%
Strain heterogeneity: 33.33%
--------------------------------------------------------------------------------
[2023-03-18 10:12:32,789] [INFO] ===== Completeness check finished =====
[2023-03-18 10:12:32,789] [INFO] ===== Start GTDB Search =====
[2023-03-18 10:12:32,790] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b25448/markers.fasta)
[2023-03-18 10:12:32,791] [INFO] Task started: Blastn
[2023-03-18 10:12:32,791] [INFO] Running command: blastn -query OceanDNA-b25448/markers.fasta -db /var/lib/cwl/stg5de9bace-0683-4399-8030-9925a9f393c2/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b25448/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 10:12:33,221] [INFO] Task succeeded: Blastn
[2023-03-18 10:12:33,224] [INFO] Selected 17 target genomes.
[2023-03-18 10:12:33,224] [INFO] Target genome list was writen to OceanDNA-b25448/target_genomes_gtdb.txt
[2023-03-18 10:12:33,242] [INFO] Task started: fastANI
[2023-03-18 10:12:33,242] [INFO] Running command: fastANI --query /var/lib/cwl/stg4642de82-c836-4b68-b9d3-c1927218cd45/OceanDNA-b25448.fa --refList OceanDNA-b25448/target_genomes_gtdb.txt --output OceanDNA-b25448/fastani_result_gtdb.tsv --threads 1
[2023-03-18 10:12:35,935] [INFO] Task succeeded: fastANI
[2023-03-18 10:12:35,943] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 10:12:35,943] [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_902607625.1	s__AG-414-E02 sp902607625	82.5768	84	133	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__AG-414-E02	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902607585.1	s__AG-414-E02 sp902607585	82.0407	58	133	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__AG-414-E02	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016764285.1	s__AG-414-E02 sp016764285	81.9637	82	133	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__AG-414-E02	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902588335.1	s__AG-414-E02 sp902588335	80.5817	75	133	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__AG-414-E02	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902607735.1	s__AG-414-E02 sp902607735	80.1012	67	133	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__AG-414-E02	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004213215.1	s__AG-414-E02 sp004213215	79.9784	79	133	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__AG-414-E02	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902561465.1	s__AG-414-E02 sp902561465	79.9237	59	133	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__AG-414-E02	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902589505.1	s__AG-414-E02 sp902589505	79.3948	74	133	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__AG-414-E02	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902607525.1	s__AG-414-E02 sp902607525	79.3114	50	133	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__AG-414-E02	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902606835.1	s__AG-414-E02 sp902606835	79.1747	83	133	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__AG-414-E02	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902568465.1	s__AG-414-E02 sp902568465	78.5163	55	133	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__AG-414-E02	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902590395.1	s__AG-414-E02 sp902590395	78.4922	62	133	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__AG-414-E02	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902589795.1	s__AG-414-E02 sp902589795	78.3676	51	133	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__AG-414-E02	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 10:12:35,945] [INFO] GTDB search result was written to OceanDNA-b25448/result_gtdb.tsv
[2023-03-18 10:12:35,946] [INFO] ===== GTDB Search completed =====
[2023-03-18 10:12:35,948] [INFO] DFAST_QC result json was written to OceanDNA-b25448/dqc_result.json
[2023-03-18 10:12:35,949] [INFO] DFAST_QC completed!
[2023-03-18 10:12:35,949] [INFO] Total running time: 0h0m26s