[2023-03-16 02:38:04,965] [INFO] DFAST_QC pipeline started.
[2023-03-16 02:38:04,965] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 02:38:04,965] [INFO] DQC Reference Directory: /var/lib/cwl/stg6aebc0f8-625f-4faa-bec7-5b94d56b0fb3/dqc_reference
[2023-03-16 02:38:06,216] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 02:38:06,216] [INFO] Task started: Prodigal
[2023-03-16 02:38:06,216] [INFO] Running command: cat /var/lib/cwl/stga60204e0-74d9-42d8-9821-d3db5b614239/OceanDNA-b45255.fa | prodigal -d OceanDNA-b45255/cds.fna -a OceanDNA-b45255/protein.faa -g 11 -q > /dev/null
[2023-03-16 02:38:25,674] [INFO] Task succeeded: Prodigal
[2023-03-16 02:38:25,675] [INFO] Task started: HMMsearch
[2023-03-16 02:38:25,675] [INFO] Running command: hmmsearch --tblout OceanDNA-b45255/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6aebc0f8-625f-4faa-bec7-5b94d56b0fb3/dqc_reference/reference_markers.hmm OceanDNA-b45255/protein.faa > /dev/null
[2023-03-16 02:38:25,852] [INFO] Task succeeded: HMMsearch
[2023-03-16 02:38:25,853] [WARNING] Found 5/6 markers. [/var/lib/cwl/stga60204e0-74d9-42d8-9821-d3db5b614239/OceanDNA-b45255.fa]
[2023-03-16 02:38:25,873] [INFO] Query marker FASTA was written to OceanDNA-b45255/markers.fasta
[2023-03-16 02:38:25,873] [INFO] Task started: Blastn
[2023-03-16 02:38:25,873] [INFO] Running command: blastn -query OceanDNA-b45255/markers.fasta -db /var/lib/cwl/stg6aebc0f8-625f-4faa-bec7-5b94d56b0fb3/dqc_reference/reference_markers.fasta -out OceanDNA-b45255/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 02:38:26,414] [INFO] Task succeeded: Blastn
[2023-03-16 02:38:26,415] [INFO] Selected 20 target genomes.
[2023-03-16 02:38:26,415] [INFO] Target genome list was writen to OceanDNA-b45255/target_genomes.txt
[2023-03-16 02:38:26,427] [INFO] Task started: fastANI
[2023-03-16 02:38:26,427] [INFO] Running command: fastANI --query /var/lib/cwl/stga60204e0-74d9-42d8-9821-d3db5b614239/OceanDNA-b45255.fa --refList OceanDNA-b45255/target_genomes.txt --output OceanDNA-b45255/fastani_result.tsv --threads 1
[2023-03-16 02:38:42,060] [INFO] Task succeeded: fastANI
[2023-03-16 02:38:42,060] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6aebc0f8-625f-4faa-bec7-5b94d56b0fb3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 02:38:42,061] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6aebc0f8-625f-4faa-bec7-5b94d56b0fb3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 02:38:42,064] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 02:38:42,064] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 02:38:42,064] [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
Azospirillum oleiclasticum	strain=RWY-5-1-1	GCA_013423485.1	2735135	2735135	type	True	74.667	59	595	95	below_threshold
Nonomuraea jiangxiensis	strain=CGMCC 4.6533	GCA_900099965.1	633440	633440	type	True	74.5839	51	595	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 02:38:42,064] [INFO] DFAST Taxonomy check result was written to OceanDNA-b45255/tc_result.tsv
[2023-03-16 02:38:42,064] [INFO] ===== Taxonomy check completed =====
[2023-03-16 02:38:42,064] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 02:38:42,064] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6aebc0f8-625f-4faa-bec7-5b94d56b0fb3/dqc_reference/checkm_data
[2023-03-16 02:38:42,065] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 02:38:42,070] [INFO] Task started: CheckM
[2023-03-16 02:38:42,070] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b45255/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b45255/checkm_input OceanDNA-b45255/checkm_result
[2023-03-16 02:39:31,681] [INFO] Task succeeded: CheckM
[2023-03-16 02:39:31,681] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.38%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 02:39:31,684] [INFO] ===== Completeness check finished =====
[2023-03-16 02:39:31,684] [INFO] ===== Start GTDB Search =====
[2023-03-16 02:39:31,684] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b45255/markers.fasta)
[2023-03-16 02:39:31,684] [INFO] Task started: Blastn
[2023-03-16 02:39:31,684] [INFO] Running command: blastn -query OceanDNA-b45255/markers.fasta -db /var/lib/cwl/stg6aebc0f8-625f-4faa-bec7-5b94d56b0fb3/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b45255/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 02:39:32,439] [INFO] Task succeeded: Blastn
[2023-03-16 02:39:32,439] [INFO] Selected 23 target genomes.
[2023-03-16 02:39:32,440] [INFO] Target genome list was writen to OceanDNA-b45255/target_genomes_gtdb.txt
[2023-03-16 02:39:33,013] [INFO] Task started: fastANI
[2023-03-16 02:39:33,014] [INFO] Running command: fastANI --query /var/lib/cwl/stga60204e0-74d9-42d8-9821-d3db5b614239/OceanDNA-b45255.fa --refList OceanDNA-b45255/target_genomes_gtdb.txt --output OceanDNA-b45255/fastani_result_gtdb.tsv --threads 1
[2023-03-16 02:39:45,750] [INFO] Task succeeded: fastANI
[2023-03-16 02:39:45,753] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 02:39:45,753] [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_002238925.1	s__Bin103 sp002238925	76.6096	124	595	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__SZUA-6;f__Bin103;g__Bin103	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013423485.1	s__Azospirillum oleiclasticum	74.6723	58	595	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	100.00	100.00	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2023-03-16 02:39:45,753] [INFO] GTDB search result was written to OceanDNA-b45255/result_gtdb.tsv
[2023-03-16 02:39:45,753] [INFO] ===== GTDB Search completed =====
[2023-03-16 02:39:45,753] [INFO] DFAST_QC result json was written to OceanDNA-b45255/dqc_result.json
[2023-03-16 02:39:45,754] [INFO] DFAST_QC completed!
[2023-03-16 02:39:45,754] [INFO] Total running time: 0h1m41s