[2023-03-15 11:20:30,886] [INFO] DFAST_QC pipeline started.
[2023-03-15 11:20:30,887] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 11:20:30,887] [INFO] DQC Reference Directory: /var/lib/cwl/stg9f18c400-5bdc-4d63-ba56-5ab4126e2c05/dqc_reference
[2023-03-15 11:20:32,009] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 11:20:32,009] [INFO] Task started: Prodigal
[2023-03-15 11:20:32,009] [INFO] Running command: cat /var/lib/cwl/stg96ccc14d-40b3-4c23-bde1-58040340b972/OceanDNA-b17424.fa | prodigal -d OceanDNA-b17424/cds.fna -a OceanDNA-b17424/protein.faa -g 11 -q > /dev/null
[2023-03-15 11:20:43,771] [INFO] Task succeeded: Prodigal
[2023-03-15 11:20:43,771] [INFO] Task started: HMMsearch
[2023-03-15 11:20:43,771] [INFO] Running command: hmmsearch --tblout OceanDNA-b17424/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9f18c400-5bdc-4d63-ba56-5ab4126e2c05/dqc_reference/reference_markers.hmm OceanDNA-b17424/protein.faa > /dev/null
[2023-03-15 11:20:43,928] [INFO] Task succeeded: HMMsearch
[2023-03-15 11:20:43,929] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg96ccc14d-40b3-4c23-bde1-58040340b972/OceanDNA-b17424.fa]
[2023-03-15 11:20:43,955] [INFO] Query marker FASTA was written to OceanDNA-b17424/markers.fasta
[2023-03-15 11:20:43,956] [INFO] Task started: Blastn
[2023-03-15 11:20:43,956] [INFO] Running command: blastn -query OceanDNA-b17424/markers.fasta -db /var/lib/cwl/stg9f18c400-5bdc-4d63-ba56-5ab4126e2c05/dqc_reference/reference_markers.fasta -out OceanDNA-b17424/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 11:20:44,512] [INFO] Task succeeded: Blastn
[2023-03-15 11:20:44,518] [INFO] Selected 20 target genomes.
[2023-03-15 11:20:44,518] [INFO] Target genome list was writen to OceanDNA-b17424/target_genomes.txt
[2023-03-15 11:20:44,533] [INFO] Task started: fastANI
[2023-03-15 11:20:44,533] [INFO] Running command: fastANI --query /var/lib/cwl/stg96ccc14d-40b3-4c23-bde1-58040340b972/OceanDNA-b17424.fa --refList OceanDNA-b17424/target_genomes.txt --output OceanDNA-b17424/fastani_result.tsv --threads 1
[2023-03-15 11:20:58,682] [INFO] Task succeeded: fastANI
[2023-03-15 11:20:58,683] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9f18c400-5bdc-4d63-ba56-5ab4126e2c05/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 11:20:58,683] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9f18c400-5bdc-4d63-ba56-5ab4126e2c05/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 11:20:58,683] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 11:20:58,683] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 11:20:58,683] [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 11:20:58,685] [INFO] DFAST Taxonomy check result was written to OceanDNA-b17424/tc_result.tsv
[2023-03-15 11:20:58,685] [INFO] ===== Taxonomy check completed =====
[2023-03-15 11:20:58,685] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 11:20:58,686] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9f18c400-5bdc-4d63-ba56-5ab4126e2c05/dqc_reference/checkm_data
[2023-03-15 11:20:58,688] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 11:20:58,693] [INFO] Task started: CheckM
[2023-03-15 11:20:58,693] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b17424/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b17424/checkm_input OceanDNA-b17424/checkm_result
[2023-03-15 11:21:31,504] [INFO] Task succeeded: CheckM
[2023-03-15 11:21:31,505] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 49.48%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 11:21:31,510] [INFO] ===== Completeness check finished =====
[2023-03-15 11:21:31,510] [INFO] ===== Start GTDB Search =====
[2023-03-15 11:21:31,510] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b17424/markers.fasta)
[2023-03-15 11:21:31,511] [INFO] Task started: Blastn
[2023-03-15 11:21:31,511] [INFO] Running command: blastn -query OceanDNA-b17424/markers.fasta -db /var/lib/cwl/stg9f18c400-5bdc-4d63-ba56-5ab4126e2c05/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b17424/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 11:21:32,356] [INFO] Task succeeded: Blastn
[2023-03-15 11:21:32,366] [INFO] Selected 16 target genomes.
[2023-03-15 11:21:32,366] [INFO] Target genome list was writen to OceanDNA-b17424/target_genomes_gtdb.txt
[2023-03-15 11:21:32,382] [INFO] Task started: fastANI
[2023-03-15 11:21:32,383] [INFO] Running command: fastANI --query /var/lib/cwl/stg96ccc14d-40b3-4c23-bde1-58040340b972/OceanDNA-b17424.fa --refList OceanDNA-b17424/target_genomes_gtdb.txt --output OceanDNA-b17424/fastani_result_gtdb.tsv --threads 1
[2023-03-15 11:21:40,824] [INFO] Task succeeded: fastANI
[2023-03-15 11:21:40,826] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 11:21:40,827] [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_002712565.1	s__UBA822 sp002712565	81.1713	206	642	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Longimicrobiales;f__UBA6960;g__UBA822	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002731735.1	s__UBA822 sp002731735	81.1642	290	642	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Longimicrobiales;f__UBA6960;g__UBA822	95.0	97.30	96.95	0.68	0.67	5	-
--------------------------------------------------------------------------------
[2023-03-15 11:21:40,828] [INFO] GTDB search result was written to OceanDNA-b17424/result_gtdb.tsv
[2023-03-15 11:21:40,831] [INFO] ===== GTDB Search completed =====
[2023-03-15 11:21:40,833] [INFO] DFAST_QC result json was written to OceanDNA-b17424/dqc_result.json
[2023-03-15 11:21:40,833] [INFO] DFAST_QC completed!
[2023-03-15 11:21:40,833] [INFO] Total running time: 0h1m10s