[2023-03-17 03:50:13,772] [INFO] DFAST_QC pipeline started.
[2023-03-17 03:50:13,772] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 03:50:13,772] [INFO] DQC Reference Directory: /var/lib/cwl/stgd84575d5-9585-4905-b5b4-68aad020d79d/dqc_reference
[2023-03-17 03:50:15,139] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 03:50:15,140] [INFO] Task started: Prodigal
[2023-03-17 03:50:15,140] [INFO] Running command: cat /var/lib/cwl/stg0cf577c6-8674-48d0-b9ae-abb9c06ec474/OceanDNA-b28106.fa | prodigal -d OceanDNA-b28106/cds.fna -a OceanDNA-b28106/protein.faa -g 11 -q > /dev/null
[2023-03-17 03:50:26,997] [INFO] Task succeeded: Prodigal
[2023-03-17 03:50:26,998] [INFO] Task started: HMMsearch
[2023-03-17 03:50:26,998] [INFO] Running command: hmmsearch --tblout OceanDNA-b28106/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd84575d5-9585-4905-b5b4-68aad020d79d/dqc_reference/reference_markers.hmm OceanDNA-b28106/protein.faa > /dev/null
[2023-03-17 03:50:27,165] [INFO] Task succeeded: HMMsearch
[2023-03-17 03:50:27,165] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg0cf577c6-8674-48d0-b9ae-abb9c06ec474/OceanDNA-b28106.fa]
[2023-03-17 03:50:27,186] [INFO] Query marker FASTA was written to OceanDNA-b28106/markers.fasta
[2023-03-17 03:50:27,186] [INFO] Task started: Blastn
[2023-03-17 03:50:27,186] [INFO] Running command: blastn -query OceanDNA-b28106/markers.fasta -db /var/lib/cwl/stgd84575d5-9585-4905-b5b4-68aad020d79d/dqc_reference/reference_markers.fasta -out OceanDNA-b28106/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 03:50:27,748] [INFO] Task succeeded: Blastn
[2023-03-17 03:50:27,749] [INFO] Selected 28 target genomes.
[2023-03-17 03:50:27,749] [INFO] Target genome list was writen to OceanDNA-b28106/target_genomes.txt
[2023-03-17 03:50:27,763] [INFO] Task started: fastANI
[2023-03-17 03:50:27,763] [INFO] Running command: fastANI --query /var/lib/cwl/stg0cf577c6-8674-48d0-b9ae-abb9c06ec474/OceanDNA-b28106.fa --refList OceanDNA-b28106/target_genomes.txt --output OceanDNA-b28106/fastani_result.tsv --threads 1
[2023-03-17 03:50:43,431] [INFO] Task succeeded: fastANI
[2023-03-17 03:50:43,431] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd84575d5-9585-4905-b5b4-68aad020d79d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 03:50:43,431] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd84575d5-9585-4905-b5b4-68aad020d79d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 03:50:43,434] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 03:50:43,435] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 03:50:43,435] [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
Kangsaoukella pontilimi	strain=GH1-50	GCA_009830125.1	2691042	2691042	type	True	76.3756	55	552	95	below_threshold
Ruegeria pomeroyi	strain=DSS-3	GCA_000011965.2	89184	89184	suspected-type	True	76.0381	50	552	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 03:50:43,435] [INFO] DFAST Taxonomy check result was written to OceanDNA-b28106/tc_result.tsv
[2023-03-17 03:50:43,435] [INFO] ===== Taxonomy check completed =====
[2023-03-17 03:50:43,435] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 03:50:43,435] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd84575d5-9585-4905-b5b4-68aad020d79d/dqc_reference/checkm_data
[2023-03-17 03:50:43,436] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 03:50:43,440] [INFO] Task started: CheckM
[2023-03-17 03:50:43,441] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b28106/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b28106/checkm_input OceanDNA-b28106/checkm_result
[2023-03-17 03:51:17,697] [INFO] Task succeeded: CheckM
[2023-03-17 03:51:17,698] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 48.44%
Contamintation: 0.52%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-17 03:51:17,700] [INFO] ===== Completeness check finished =====
[2023-03-17 03:51:17,701] [INFO] ===== Start GTDB Search =====
[2023-03-17 03:51:17,701] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b28106/markers.fasta)
[2023-03-17 03:51:17,701] [INFO] Task started: Blastn
[2023-03-17 03:51:17,701] [INFO] Running command: blastn -query OceanDNA-b28106/markers.fasta -db /var/lib/cwl/stgd84575d5-9585-4905-b5b4-68aad020d79d/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b28106/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 03:51:18,521] [INFO] Task succeeded: Blastn
[2023-03-17 03:51:18,521] [INFO] Selected 28 target genomes.
[2023-03-17 03:51:18,522] [INFO] Target genome list was writen to OceanDNA-b28106/target_genomes_gtdb.txt
[2023-03-17 03:51:18,754] [INFO] Task started: fastANI
[2023-03-17 03:51:18,754] [INFO] Running command: fastANI --query /var/lib/cwl/stg0cf577c6-8674-48d0-b9ae-abb9c06ec474/OceanDNA-b28106.fa --refList OceanDNA-b28106/target_genomes_gtdb.txt --output OceanDNA-b28106/fastani_result_gtdb.tsv --threads 1
[2023-03-17 03:51:34,666] [INFO] Task succeeded: fastANI
[2023-03-17 03:51:34,668] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 03:51:34,669] [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_013003245.1	s__JABDJX01 sp013003245	76.2625	51	552	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JABDJX01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013002465.1	s__JABDJO01 sp013002465	76.1642	59	552	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JABDJO01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 03:51:34,669] [INFO] GTDB search result was written to OceanDNA-b28106/result_gtdb.tsv
[2023-03-17 03:51:34,669] [INFO] ===== GTDB Search completed =====
[2023-03-17 03:51:34,669] [INFO] DFAST_QC result json was written to OceanDNA-b28106/dqc_result.json
[2023-03-17 03:51:34,670] [INFO] DFAST_QC completed!
[2023-03-17 03:51:34,670] [INFO] Total running time: 0h1m21s