[2023-03-17 23:43:20,542] [INFO] DFAST_QC pipeline started.
[2023-03-17 23:43:20,545] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 23:43:20,545] [INFO] DQC Reference Directory: /var/lib/cwl/stg57a2ab59-68c5-4063-b36b-8608fb77c8f3/dqc_reference
[2023-03-17 23:43:21,639] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 23:43:21,639] [INFO] Task started: Prodigal
[2023-03-17 23:43:21,639] [INFO] Running command: cat /var/lib/cwl/stg1650d086-40b3-4968-a29c-80260825b503/OceanDNA-b25452.fa | prodigal -d OceanDNA-b25452/cds.fna -a OceanDNA-b25452/protein.faa -g 11 -q > /dev/null
[2023-03-17 23:43:24,271] [INFO] Task succeeded: Prodigal
[2023-03-17 23:43:24,271] [INFO] Task started: HMMsearch
[2023-03-17 23:43:24,271] [INFO] Running command: hmmsearch --tblout OceanDNA-b25452/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg57a2ab59-68c5-4063-b36b-8608fb77c8f3/dqc_reference/reference_markers.hmm OceanDNA-b25452/protein.faa > /dev/null
[2023-03-17 23:43:24,387] [INFO] Task succeeded: HMMsearch
[2023-03-17 23:43:24,387] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg1650d086-40b3-4968-a29c-80260825b503/OceanDNA-b25452.fa]
[2023-03-17 23:43:24,395] [INFO] Query marker FASTA was written to OceanDNA-b25452/markers.fasta
[2023-03-17 23:43:24,397] [INFO] Task started: Blastn
[2023-03-17 23:43:24,397] [INFO] Running command: blastn -query OceanDNA-b25452/markers.fasta -db /var/lib/cwl/stg57a2ab59-68c5-4063-b36b-8608fb77c8f3/dqc_reference/reference_markers.fasta -out OceanDNA-b25452/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 23:43:24,965] [INFO] Task succeeded: Blastn
[2023-03-17 23:43:24,968] [INFO] Selected 10 target genomes.
[2023-03-17 23:43:24,968] [INFO] Target genome list was writen to OceanDNA-b25452/target_genomes.txt
[2023-03-17 23:43:25,003] [INFO] Task started: fastANI
[2023-03-17 23:43:25,003] [INFO] Running command: fastANI --query /var/lib/cwl/stg1650d086-40b3-4968-a29c-80260825b503/OceanDNA-b25452.fa --refList OceanDNA-b25452/target_genomes.txt --output OceanDNA-b25452/fastani_result.tsv --threads 1
[2023-03-17 23:43:29,921] [INFO] Task succeeded: fastANI
[2023-03-17 23:43:29,921] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg57a2ab59-68c5-4063-b36b-8608fb77c8f3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 23:43:29,921] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg57a2ab59-68c5-4063-b36b-8608fb77c8f3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 23:43:29,922] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 23:43:29,922] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 23:43:29,922] [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 23:43:29,922] [INFO] DFAST Taxonomy check result was written to OceanDNA-b25452/tc_result.tsv
[2023-03-17 23:43:29,922] [INFO] ===== Taxonomy check completed =====
[2023-03-17 23:43:29,922] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 23:43:29,922] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg57a2ab59-68c5-4063-b36b-8608fb77c8f3/dqc_reference/checkm_data
[2023-03-17 23:43:29,972] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 23:43:29,973] [INFO] Task started: CheckM
[2023-03-17 23:43:29,974] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b25452/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b25452/checkm_input OceanDNA-b25452/checkm_result
[2023-03-17 23:43:45,927] [INFO] Task succeeded: CheckM
[2023-03-17 23:43:45,927] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 67.23%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 23:43:45,931] [INFO] ===== Completeness check finished =====
[2023-03-17 23:43:45,931] [INFO] ===== Start GTDB Search =====
[2023-03-17 23:43:45,932] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b25452/markers.fasta)
[2023-03-17 23:43:45,933] [INFO] Task started: Blastn
[2023-03-17 23:43:45,933] [INFO] Running command: blastn -query OceanDNA-b25452/markers.fasta -db /var/lib/cwl/stg57a2ab59-68c5-4063-b36b-8608fb77c8f3/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b25452/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 23:43:46,918] [INFO] Task succeeded: Blastn
[2023-03-17 23:43:46,999] [INFO] Selected 12 target genomes.
[2023-03-17 23:43:46,999] [INFO] Target genome list was writen to OceanDNA-b25452/target_genomes_gtdb.txt
[2023-03-17 23:43:47,008] [INFO] Task started: fastANI
[2023-03-17 23:43:47,008] [INFO] Running command: fastANI --query /var/lib/cwl/stg1650d086-40b3-4968-a29c-80260825b503/OceanDNA-b25452.fa --refList OceanDNA-b25452/target_genomes_gtdb.txt --output OceanDNA-b25452/fastani_result_gtdb.tsv --threads 1
[2023-03-17 23:43:48,994] [INFO] Task succeeded: fastANI
[2023-03-17 23:43:49,001] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 23:43:49,001] [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_004213215.1	s__AG-414-E02 sp004213215	82.4191	79	121	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	82.342	57	121	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_902607625.1	s__AG-414-E02 sp902607625	81.8716	75	121	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	80.9081	66	121	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	80.5437	60	121	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	80.077	61	121	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	78.7549	54	121	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	78.742	70	121	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	78.47	54	121	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	78.0479	61	121	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	-
--------------------------------------------------------------------------------
[2023-03-17 23:43:49,001] [INFO] GTDB search result was written to OceanDNA-b25452/result_gtdb.tsv
[2023-03-17 23:43:49,002] [INFO] ===== GTDB Search completed =====
[2023-03-17 23:43:49,003] [INFO] DFAST_QC result json was written to OceanDNA-b25452/dqc_result.json
[2023-03-17 23:43:49,003] [INFO] DFAST_QC completed!
[2023-03-17 23:43:49,003] [INFO] Total running time: 0h0m28s