[2023-03-15 08:11:05,955] [INFO] DFAST_QC pipeline started.
[2023-03-15 08:11:05,955] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 08:11:05,955] [INFO] DQC Reference Directory: /var/lib/cwl/stge5668eed-0c12-4515-a479-9c164d94dbcc/dqc_reference
[2023-03-15 08:11:07,061] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 08:11:07,061] [INFO] Task started: Prodigal
[2023-03-15 08:11:07,062] [INFO] Running command: cat /var/lib/cwl/stge393551b-ab07-4d0a-9153-b43476ebe48f/OceanDNA-b28327.fa | prodigal -d OceanDNA-b28327/cds.fna -a OceanDNA-b28327/protein.faa -g 11 -q > /dev/null
[2023-03-15 08:11:12,779] [INFO] Task succeeded: Prodigal
[2023-03-15 08:11:12,779] [INFO] Task started: HMMsearch
[2023-03-15 08:11:12,779] [INFO] Running command: hmmsearch --tblout OceanDNA-b28327/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge5668eed-0c12-4515-a479-9c164d94dbcc/dqc_reference/reference_markers.hmm OceanDNA-b28327/protein.faa > /dev/null
[2023-03-15 08:11:12,935] [INFO] Task succeeded: HMMsearch
[2023-03-15 08:11:12,936] [WARNING] Found 4/6 markers. [/var/lib/cwl/stge393551b-ab07-4d0a-9153-b43476ebe48f/OceanDNA-b28327.fa]
[2023-03-15 08:11:12,971] [INFO] Query marker FASTA was written to OceanDNA-b28327/markers.fasta
[2023-03-15 08:11:12,972] [INFO] Task started: Blastn
[2023-03-15 08:11:12,972] [INFO] Running command: blastn -query OceanDNA-b28327/markers.fasta -db /var/lib/cwl/stge5668eed-0c12-4515-a479-9c164d94dbcc/dqc_reference/reference_markers.fasta -out OceanDNA-b28327/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 08:11:13,512] [INFO] Task succeeded: Blastn
[2023-03-15 08:11:13,519] [INFO] Selected 18 target genomes.
[2023-03-15 08:11:13,520] [INFO] Target genome list was writen to OceanDNA-b28327/target_genomes.txt
[2023-03-15 08:11:13,532] [INFO] Task started: fastANI
[2023-03-15 08:11:13,532] [INFO] Running command: fastANI --query /var/lib/cwl/stge393551b-ab07-4d0a-9153-b43476ebe48f/OceanDNA-b28327.fa --refList OceanDNA-b28327/target_genomes.txt --output OceanDNA-b28327/fastani_result.tsv --threads 1
[2023-03-15 08:11:21,193] [INFO] Task succeeded: fastANI
[2023-03-15 08:11:21,194] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge5668eed-0c12-4515-a479-9c164d94dbcc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 08:11:21,194] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge5668eed-0c12-4515-a479-9c164d94dbcc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 08:11:21,194] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 08:11:21,194] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 08:11:21,194] [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
--------------------------------------------------------------------------------
[2023-03-15 08:11:21,194] [INFO] DFAST Taxonomy check result was written to OceanDNA-b28327/tc_result.tsv
[2023-03-15 08:11:21,194] [INFO] ===== Taxonomy check completed =====
[2023-03-15 08:11:21,195] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 08:11:21,195] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge5668eed-0c12-4515-a479-9c164d94dbcc/dqc_reference/checkm_data
[2023-03-15 08:11:21,198] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 08:11:21,201] [INFO] Task started: CheckM
[2023-03-15 08:11:21,201] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b28327/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b28327/checkm_input OceanDNA-b28327/checkm_result
[2023-03-15 08:11:41,369] [INFO] Task succeeded: CheckM
[2023-03-15 08:11:41,369] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 56.25%
Contamintation: 2.08%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-15 08:11:41,489] [INFO] ===== Completeness check finished =====
[2023-03-15 08:11:41,489] [INFO] ===== Start GTDB Search =====
[2023-03-15 08:11:41,489] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b28327/markers.fasta)
[2023-03-15 08:11:41,490] [INFO] Task started: Blastn
[2023-03-15 08:11:41,490] [INFO] Running command: blastn -query OceanDNA-b28327/markers.fasta -db /var/lib/cwl/stge5668eed-0c12-4515-a479-9c164d94dbcc/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b28327/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 08:11:42,375] [INFO] Task succeeded: Blastn
[2023-03-15 08:11:42,391] [INFO] Selected 27 target genomes.
[2023-03-15 08:11:42,391] [INFO] Target genome list was writen to OceanDNA-b28327/target_genomes_gtdb.txt
[2023-03-15 08:11:42,412] [INFO] Task started: fastANI
[2023-03-15 08:11:42,412] [INFO] Running command: fastANI --query /var/lib/cwl/stge393551b-ab07-4d0a-9153-b43476ebe48f/OceanDNA-b28327.fa --refList OceanDNA-b28327/target_genomes_gtdb.txt --output OceanDNA-b28327/fastani_result_gtdb.tsv --threads 1
[2023-03-15 08:11:52,681] [INFO] Task succeeded: fastANI
[2023-03-15 08:11:52,683] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 08:11:52,683] [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_902533625.1	s__CACKLF01 sp002725175	95.8718	252	336	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__CACKLF01	95.0	96.00	95.41	0.67	0.59	4	conclusive
--------------------------------------------------------------------------------
[2023-03-15 08:11:52,688] [INFO] GTDB search result was written to OceanDNA-b28327/result_gtdb.tsv
[2023-03-15 08:11:52,696] [INFO] ===== GTDB Search completed =====
[2023-03-15 08:11:52,705] [INFO] DFAST_QC result json was written to OceanDNA-b28327/dqc_result.json
[2023-03-15 08:11:52,705] [INFO] DFAST_QC completed!
[2023-03-15 08:11:52,705] [INFO] Total running time: 0h0m47s