[2023-03-19 00:01:03,310] [INFO] DFAST_QC pipeline started.
[2023-03-19 00:01:03,310] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 00:01:03,310] [INFO] DQC Reference Directory: /var/lib/cwl/stg26cdf96a-6c84-4647-9cb9-6e8d0605c83d/dqc_reference
[2023-03-19 00:01:04,554] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 00:01:04,555] [INFO] Task started: Prodigal
[2023-03-19 00:01:04,555] [INFO] Running command: cat /var/lib/cwl/stgc863f1dd-9160-460a-aef4-40e626a8063d/OceanDNA-b23131.fa | prodigal -d OceanDNA-b23131/cds.fna -a OceanDNA-b23131/protein.faa -g 11 -q > /dev/null
[2023-03-19 00:01:19,364] [INFO] Task succeeded: Prodigal
[2023-03-19 00:01:19,364] [INFO] Task started: HMMsearch
[2023-03-19 00:01:19,364] [INFO] Running command: hmmsearch --tblout OceanDNA-b23131/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg26cdf96a-6c84-4647-9cb9-6e8d0605c83d/dqc_reference/reference_markers.hmm OceanDNA-b23131/protein.faa > /dev/null
[2023-03-19 00:01:19,593] [INFO] Task succeeded: HMMsearch
[2023-03-19 00:01:19,593] [INFO] Found 6/6 markers.
[2023-03-19 00:01:19,620] [INFO] Query marker FASTA was written to OceanDNA-b23131/markers.fasta
[2023-03-19 00:01:19,620] [INFO] Task started: Blastn
[2023-03-19 00:01:19,620] [INFO] Running command: blastn -query OceanDNA-b23131/markers.fasta -db /var/lib/cwl/stg26cdf96a-6c84-4647-9cb9-6e8d0605c83d/dqc_reference/reference_markers.fasta -out OceanDNA-b23131/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 00:01:20,129] [INFO] Task succeeded: Blastn
[2023-03-19 00:01:20,130] [INFO] Selected 13 target genomes.
[2023-03-19 00:01:20,130] [INFO] Target genome list was writen to OceanDNA-b23131/target_genomes.txt
[2023-03-19 00:01:20,138] [INFO] Task started: fastANI
[2023-03-19 00:01:20,138] [INFO] Running command: fastANI --query /var/lib/cwl/stgc863f1dd-9160-460a-aef4-40e626a8063d/OceanDNA-b23131.fa --refList OceanDNA-b23131/target_genomes.txt --output OceanDNA-b23131/fastani_result.tsv --threads 1
[2023-03-19 00:01:27,781] [INFO] Task succeeded: fastANI
[2023-03-19 00:01:27,782] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg26cdf96a-6c84-4647-9cb9-6e8d0605c83d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 00:01:27,782] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg26cdf96a-6c84-4647-9cb9-6e8d0605c83d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 00:01:27,782] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 00:01:27,782] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 00:01:27,782] [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
--------------------------------------------------------------------------------
[2023-03-19 00:01:27,782] [INFO] DFAST Taxonomy check result was written to OceanDNA-b23131/tc_result.tsv
[2023-03-19 00:01:27,782] [INFO] ===== Taxonomy check completed =====
[2023-03-19 00:01:27,783] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 00:01:27,783] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg26cdf96a-6c84-4647-9cb9-6e8d0605c83d/dqc_reference/checkm_data
[2023-03-19 00:01:27,785] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 00:01:27,789] [INFO] Task started: CheckM
[2023-03-19 00:01:27,790] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b23131/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b23131/checkm_input OceanDNA-b23131/checkm_result
[2023-03-19 00:02:08,050] [INFO] Task succeeded: CheckM
[2023-03-19 00:02:08,051] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.46%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 00:02:08,053] [INFO] ===== Completeness check finished =====
[2023-03-19 00:02:08,053] [INFO] ===== Start GTDB Search =====
[2023-03-19 00:02:08,053] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b23131/markers.fasta)
[2023-03-19 00:02:08,053] [INFO] Task started: Blastn
[2023-03-19 00:02:08,053] [INFO] Running command: blastn -query OceanDNA-b23131/markers.fasta -db /var/lib/cwl/stg26cdf96a-6c84-4647-9cb9-6e8d0605c83d/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b23131/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 00:02:08,769] [INFO] Task succeeded: Blastn
[2023-03-19 00:02:08,770] [INFO] Selected 14 target genomes.
[2023-03-19 00:02:08,770] [INFO] Target genome list was writen to OceanDNA-b23131/target_genomes_gtdb.txt
[2023-03-19 00:02:08,786] [INFO] Task started: fastANI
[2023-03-19 00:02:08,786] [INFO] Running command: fastANI --query /var/lib/cwl/stgc863f1dd-9160-460a-aef4-40e626a8063d/OceanDNA-b23131.fa --refList OceanDNA-b23131/target_genomes_gtdb.txt --output OceanDNA-b23131/fastani_result_gtdb.tsv --threads 1
[2023-03-19 00:02:15,074] [INFO] Task succeeded: fastANI
[2023-03-19 00:02:15,078] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-19 00:02:15,078] [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_016776905.1	s__UBA12191 sp003540375	99.588	780	811	d__Bacteria;p__Planctomycetota;c__UBA8108;o__UBA1146;f__UBA1146;g__UBA12191	95.0	99.70	99.58	0.97	0.97	4	conclusive
GCA_009937185.1	s__UBA12191 sp009937185	94.4881	659	811	d__Bacteria;p__Planctomycetota;c__UBA8108;o__UBA1146;f__UBA1146;g__UBA12191	95.0	98.71	96.87	0.90	0.89	5	-
GCA_013911165.1	s__UBA12191 sp013911165	77.8182	125	811	d__Bacteria;p__Planctomycetota;c__UBA8108;o__UBA1146;f__UBA1146;g__UBA12191	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012269595.1	s__UBA12191 sp012269595	77.6262	128	811	d__Bacteria;p__Planctomycetota;c__UBA8108;o__UBA1146;f__UBA1146;g__UBA12191	95.0	99.68	99.68	0.96	0.96	2	-
GCA_002691835.1	s__UBA12191 sp002691835	77.523	83	811	d__Bacteria;p__Planctomycetota;c__UBA8108;o__UBA1146;f__UBA1146;g__UBA12191	95.0	100.00	100.00	0.93	0.93	2	-
GCA_002167285.1	s__UBA12191 sp002167285	77.2756	117	811	d__Bacteria;p__Planctomycetota;c__UBA8108;o__UBA1146;f__UBA1146;g__UBA12191	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 00:02:15,078] [INFO] GTDB search result was written to OceanDNA-b23131/result_gtdb.tsv
[2023-03-19 00:02:15,078] [INFO] ===== GTDB Search completed =====
[2023-03-19 00:02:15,079] [INFO] DFAST_QC result json was written to OceanDNA-b23131/dqc_result.json
[2023-03-19 00:02:15,079] [INFO] DFAST_QC completed!
[2023-03-19 00:02:15,079] [INFO] Total running time: 0h1m12s