[2023-03-15 11:20:29,269] [INFO] DFAST_QC pipeline started.
[2023-03-15 11:20:29,269] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 11:20:29,269] [INFO] DQC Reference Directory: /var/lib/cwl/stg35035fa6-4b59-498c-a0d7-82e3a1ad33f9/dqc_reference
[2023-03-15 11:20:30,437] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 11:20:30,437] [INFO] Task started: Prodigal
[2023-03-15 11:20:30,437] [INFO] Running command: cat /var/lib/cwl/stg21253506-d28a-4680-a7f4-8bc45ed6252e/OceanDNA-b21055.fa | prodigal -d OceanDNA-b21055/cds.fna -a OceanDNA-b21055/protein.faa -g 11 -q > /dev/null
[2023-03-15 11:20:45,357] [INFO] Task succeeded: Prodigal
[2023-03-15 11:20:45,358] [INFO] Task started: HMMsearch
[2023-03-15 11:20:45,358] [INFO] Running command: hmmsearch --tblout OceanDNA-b21055/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg35035fa6-4b59-498c-a0d7-82e3a1ad33f9/dqc_reference/reference_markers.hmm OceanDNA-b21055/protein.faa > /dev/null
[2023-03-15 11:20:45,586] [INFO] Task succeeded: HMMsearch
[2023-03-15 11:20:45,587] [INFO] Found 6/6 markers.
[2023-03-15 11:20:45,613] [INFO] Query marker FASTA was written to OceanDNA-b21055/markers.fasta
[2023-03-15 11:20:45,614] [INFO] Task started: Blastn
[2023-03-15 11:20:45,614] [INFO] Running command: blastn -query OceanDNA-b21055/markers.fasta -db /var/lib/cwl/stg35035fa6-4b59-498c-a0d7-82e3a1ad33f9/dqc_reference/reference_markers.fasta -out OceanDNA-b21055/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 11:20:46,197] [INFO] Task succeeded: Blastn
[2023-03-15 11:20:46,199] [INFO] Selected 19 target genomes.
[2023-03-15 11:20:46,199] [INFO] Target genome list was writen to OceanDNA-b21055/target_genomes.txt
[2023-03-15 11:20:46,213] [INFO] Task started: fastANI
[2023-03-15 11:20:46,213] [INFO] Running command: fastANI --query /var/lib/cwl/stg21253506-d28a-4680-a7f4-8bc45ed6252e/OceanDNA-b21055.fa --refList OceanDNA-b21055/target_genomes.txt --output OceanDNA-b21055/fastani_result.tsv --threads 1
[2023-03-15 11:20:58,727] [INFO] Task succeeded: fastANI
[2023-03-15 11:20:58,727] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg35035fa6-4b59-498c-a0d7-82e3a1ad33f9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 11:20:58,727] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg35035fa6-4b59-498c-a0d7-82e3a1ad33f9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 11:20:58,727] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 11:20:58,727] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 11:20:58,727] [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 11:20:58,728] [INFO] DFAST Taxonomy check result was written to OceanDNA-b21055/tc_result.tsv
[2023-03-15 11:20:58,729] [INFO] ===== Taxonomy check completed =====
[2023-03-15 11:20:58,729] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 11:20:58,729] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg35035fa6-4b59-498c-a0d7-82e3a1ad33f9/dqc_reference/checkm_data
[2023-03-15 11:20:58,731] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 11:20:58,738] [INFO] Task started: CheckM
[2023-03-15 11:20:58,738] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b21055/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b21055/checkm_input OceanDNA-b21055/checkm_result
[2023-03-15 11:21:39,101] [INFO] Task succeeded: CheckM
[2023-03-15 11:21:39,101] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 11:21:39,141] [INFO] ===== Completeness check finished =====
[2023-03-15 11:21:39,141] [INFO] ===== Start GTDB Search =====
[2023-03-15 11:21:39,142] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b21055/markers.fasta)
[2023-03-15 11:21:39,143] [INFO] Task started: Blastn
[2023-03-15 11:21:39,143] [INFO] Running command: blastn -query OceanDNA-b21055/markers.fasta -db /var/lib/cwl/stg35035fa6-4b59-498c-a0d7-82e3a1ad33f9/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b21055/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 11:21:40,113] [INFO] Task succeeded: Blastn
[2023-03-15 11:21:40,116] [INFO] Selected 29 target genomes.
[2023-03-15 11:21:40,117] [INFO] Target genome list was writen to OceanDNA-b21055/target_genomes_gtdb.txt
[2023-03-15 11:21:40,139] [INFO] Task started: fastANI
[2023-03-15 11:21:40,139] [INFO] Running command: fastANI --query /var/lib/cwl/stg21253506-d28a-4680-a7f4-8bc45ed6252e/OceanDNA-b21055.fa --refList OceanDNA-b21055/target_genomes_gtdb.txt --output OceanDNA-b21055/fastani_result_gtdb.tsv --threads 1
[2023-03-15 11:21:53,351] [INFO] Task succeeded: fastANI
[2023-03-15 11:21:53,354] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 11:21:53,354] [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_002787235.1	s__Nitrohelix sp002787235	77.1584	239	845	d__Bacteria;p__Nitrospinota;c__Nitrospinia;o__Nitrospinales;f__Nitrospinaceae;g__Nitrohelix	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015698305.1	s__Nitrohelix vancouverensis	76.1958	62	845	d__Bacteria;p__Nitrospinota;c__Nitrospinia;o__Nitrospinales;f__Nitrospinaceae;g__Nitrohelix	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 11:21:53,356] [INFO] GTDB search result was written to OceanDNA-b21055/result_gtdb.tsv
[2023-03-15 11:21:53,359] [INFO] ===== GTDB Search completed =====
[2023-03-15 11:21:53,362] [INFO] DFAST_QC result json was written to OceanDNA-b21055/dqc_result.json
[2023-03-15 11:21:53,362] [INFO] DFAST_QC completed!
[2023-03-15 11:21:53,362] [INFO] Total running time: 0h1m24s