[2023-03-18 08:42:34,374] [INFO] DFAST_QC pipeline started.
[2023-03-18 08:42:34,374] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 08:42:34,374] [INFO] DQC Reference Directory: /var/lib/cwl/stg6d92cf7a-8de5-4281-8e3b-63b92f435bdb/dqc_reference
[2023-03-18 08:42:35,477] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 08:42:35,478] [INFO] Task started: Prodigal
[2023-03-18 08:42:35,478] [INFO] Running command: cat /var/lib/cwl/stg7b0b191d-8eb7-4e9a-9371-e65ac993fb3c/OceanDNA-b25393.fa | prodigal -d OceanDNA-b25393/cds.fna -a OceanDNA-b25393/protein.faa -g 11 -q > /dev/null
[2023-03-18 08:42:38,902] [INFO] Task succeeded: Prodigal
[2023-03-18 08:42:38,903] [INFO] Task started: HMMsearch
[2023-03-18 08:42:38,903] [INFO] Running command: hmmsearch --tblout OceanDNA-b25393/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6d92cf7a-8de5-4281-8e3b-63b92f435bdb/dqc_reference/reference_markers.hmm OceanDNA-b25393/protein.faa > /dev/null
[2023-03-18 08:42:39,021] [INFO] Task succeeded: HMMsearch
[2023-03-18 08:42:39,022] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg7b0b191d-8eb7-4e9a-9371-e65ac993fb3c/OceanDNA-b25393.fa]
[2023-03-18 08:42:39,035] [INFO] Query marker FASTA was written to OceanDNA-b25393/markers.fasta
[2023-03-18 08:42:39,036] [INFO] Task started: Blastn
[2023-03-18 08:42:39,036] [INFO] Running command: blastn -query OceanDNA-b25393/markers.fasta -db /var/lib/cwl/stg6d92cf7a-8de5-4281-8e3b-63b92f435bdb/dqc_reference/reference_markers.fasta -out OceanDNA-b25393/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 08:42:39,511] [INFO] Task succeeded: Blastn
[2023-03-18 08:42:39,513] [INFO] Selected 6 target genomes.
[2023-03-18 08:42:39,513] [INFO] Target genome list was writen to OceanDNA-b25393/target_genomes.txt
[2023-03-18 08:42:39,516] [INFO] Task started: fastANI
[2023-03-18 08:42:39,517] [INFO] Running command: fastANI --query /var/lib/cwl/stg7b0b191d-8eb7-4e9a-9371-e65ac993fb3c/OceanDNA-b25393.fa --refList OceanDNA-b25393/target_genomes.txt --output OceanDNA-b25393/fastani_result.tsv --threads 1
[2023-03-18 08:42:41,898] [INFO] Task succeeded: fastANI
[2023-03-18 08:42:41,898] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6d92cf7a-8de5-4281-8e3b-63b92f435bdb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 08:42:41,898] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6d92cf7a-8de5-4281-8e3b-63b92f435bdb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 08:42:41,899] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 08:42:41,899] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 08:42:41,899] [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
--------------------------------------------------------------------------------
[2023-03-18 08:42:41,900] [INFO] DFAST Taxonomy check result was written to OceanDNA-b25393/tc_result.tsv
[2023-03-18 08:42:41,902] [INFO] ===== Taxonomy check completed =====
[2023-03-18 08:42:41,902] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 08:42:41,902] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6d92cf7a-8de5-4281-8e3b-63b92f435bdb/dqc_reference/checkm_data
[2023-03-18 08:42:41,912] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 08:42:41,914] [INFO] Task started: CheckM
[2023-03-18 08:42:41,914] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b25393/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b25393/checkm_input OceanDNA-b25393/checkm_result
[2023-03-18 08:42:57,798] [INFO] Task succeeded: CheckM
[2023-03-18 08:42:57,798] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 63.79%
Contamintation: 7.29%
Strain heterogeneity: 16.67%
--------------------------------------------------------------------------------
[2023-03-18 08:42:57,821] [INFO] ===== Completeness check finished =====
[2023-03-18 08:42:57,821] [INFO] ===== Start GTDB Search =====
[2023-03-18 08:42:57,821] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b25393/markers.fasta)
[2023-03-18 08:42:57,823] [INFO] Task started: Blastn
[2023-03-18 08:42:57,823] [INFO] Running command: blastn -query OceanDNA-b25393/markers.fasta -db /var/lib/cwl/stg6d92cf7a-8de5-4281-8e3b-63b92f435bdb/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b25393/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 08:42:58,413] [INFO] Task succeeded: Blastn
[2023-03-18 08:42:58,414] [INFO] Selected 15 target genomes.
[2023-03-18 08:42:58,414] [INFO] Target genome list was writen to OceanDNA-b25393/target_genomes_gtdb.txt
[2023-03-18 08:42:58,430] [INFO] Task started: fastANI
[2023-03-18 08:42:58,431] [INFO] Running command: fastANI --query /var/lib/cwl/stg7b0b191d-8eb7-4e9a-9371-e65ac993fb3c/OceanDNA-b25393.fa --refList OceanDNA-b25393/target_genomes_gtdb.txt --output OceanDNA-b25393/fastani_result_gtdb.tsv --threads 1
[2023-03-18 08:43:01,059] [INFO] Task succeeded: fastANI
[2023-03-18 08:43:01,061] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 08:43:01,061] [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_000504625.1	s__AAA240-E13 sp000504625	78.0407	51	123	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__AAA240-E13	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 08:43:01,061] [INFO] GTDB search result was written to OceanDNA-b25393/result_gtdb.tsv
[2023-03-18 08:43:01,061] [INFO] ===== GTDB Search completed =====
[2023-03-18 08:43:01,062] [INFO] DFAST_QC result json was written to OceanDNA-b25393/dqc_result.json
[2023-03-18 08:43:01,062] [INFO] DFAST_QC completed!
[2023-03-18 08:43:01,062] [INFO] Total running time: 0h0m27s