[2023-03-14 11:14:12,735] [INFO] DFAST_QC pipeline started.
[2023-03-14 11:14:12,735] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 11:14:12,735] [INFO] DQC Reference Directory: /var/lib/cwl/stge33869f2-8e54-4369-8b32-52c79b1abf86/dqc_reference
[2023-03-14 11:14:14,201] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 11:14:14,202] [INFO] Task started: Prodigal
[2023-03-14 11:14:14,202] [INFO] Running command: cat /var/lib/cwl/stgc61028d9-d00f-440e-92b2-f6fa2e33128b/OceanDNA-b11595.fa | prodigal -d OceanDNA-b11595/cds.fna -a OceanDNA-b11595/protein.faa -g 11 -q > /dev/null
[2023-03-14 11:14:22,355] [INFO] Task succeeded: Prodigal
[2023-03-14 11:14:22,355] [INFO] Task started: HMMsearch
[2023-03-14 11:14:22,356] [INFO] Running command: hmmsearch --tblout OceanDNA-b11595/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge33869f2-8e54-4369-8b32-52c79b1abf86/dqc_reference/reference_markers.hmm OceanDNA-b11595/protein.faa > /dev/null
[2023-03-14 11:14:22,577] [INFO] Task succeeded: HMMsearch
[2023-03-14 11:14:22,578] [INFO] Found 6/6 markers.
[2023-03-14 11:14:22,589] [INFO] Query marker FASTA was written to OceanDNA-b11595/markers.fasta
[2023-03-14 11:14:22,592] [INFO] Task started: Blastn
[2023-03-14 11:14:22,592] [INFO] Running command: blastn -query OceanDNA-b11595/markers.fasta -db /var/lib/cwl/stge33869f2-8e54-4369-8b32-52c79b1abf86/dqc_reference/reference_markers.fasta -out OceanDNA-b11595/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 11:14:23,208] [INFO] Task succeeded: Blastn
[2023-03-14 11:14:23,209] [INFO] Selected 31 target genomes.
[2023-03-14 11:14:23,209] [INFO] Target genome list was writen to OceanDNA-b11595/target_genomes.txt
[2023-03-14 11:14:23,232] [INFO] Task started: fastANI
[2023-03-14 11:14:23,232] [INFO] Running command: fastANI --query /var/lib/cwl/stgc61028d9-d00f-440e-92b2-f6fa2e33128b/OceanDNA-b11595.fa --refList OceanDNA-b11595/target_genomes.txt --output OceanDNA-b11595/fastani_result.tsv --threads 1
[2023-03-14 11:14:39,434] [INFO] Task succeeded: fastANI
[2023-03-14 11:14:39,434] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge33869f2-8e54-4369-8b32-52c79b1abf86/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 11:14:39,434] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge33869f2-8e54-4369-8b32-52c79b1abf86/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 11:14:39,435] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 11:14:39,435] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-14 11:14:39,435] [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
--------------------------------------------------------------------------------
[2023-03-14 11:14:39,435] [INFO] DFAST Taxonomy check result was written to OceanDNA-b11595/tc_result.tsv
[2023-03-14 11:14:39,435] [INFO] ===== Taxonomy check completed =====
[2023-03-14 11:14:39,435] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 11:14:39,436] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge33869f2-8e54-4369-8b32-52c79b1abf86/dqc_reference/checkm_data
[2023-03-14 11:14:39,439] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 11:14:39,445] [INFO] Task started: CheckM
[2023-03-14 11:14:39,445] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b11595/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b11595/checkm_input OceanDNA-b11595/checkm_result
[2023-03-14 11:15:04,993] [INFO] Task succeeded: CheckM
[2023-03-14 11:15:04,993] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 11:15:04,995] [INFO] ===== Completeness check finished =====
[2023-03-14 11:15:04,996] [INFO] ===== Start GTDB Search =====
[2023-03-14 11:15:04,996] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b11595/markers.fasta)
[2023-03-14 11:15:04,996] [INFO] Task started: Blastn
[2023-03-14 11:15:04,996] [INFO] Running command: blastn -query OceanDNA-b11595/markers.fasta -db /var/lib/cwl/stge33869f2-8e54-4369-8b32-52c79b1abf86/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b11595/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 11:15:05,909] [INFO] Task succeeded: Blastn
[2023-03-14 11:15:05,910] [INFO] Selected 27 target genomes.
[2023-03-14 11:15:05,911] [INFO] Target genome list was writen to OceanDNA-b11595/target_genomes_gtdb.txt
[2023-03-14 11:15:05,940] [INFO] Task started: fastANI
[2023-03-14 11:15:05,941] [INFO] Running command: fastANI --query /var/lib/cwl/stgc61028d9-d00f-440e-92b2-f6fa2e33128b/OceanDNA-b11595.fa --refList OceanDNA-b11595/target_genomes_gtdb.txt --output OceanDNA-b11595/fastani_result_gtdb.tsv --threads 1
[2023-03-14 11:15:14,929] [INFO] Task succeeded: fastANI
[2023-03-14 11:15:14,934] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-14 11:15:14,934] [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_902520385.1	s__GCA-2718035 sp902520385	79.6845	146	462	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__TMED113;g__GCA-2718035	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002715445.1	s__TMED113 sp002715445	78.836	90	462	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__TMED113;g__TMED113	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902533035.1	s__GCA-2718035 sp902533035	78.7413	174	462	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__TMED113;g__GCA-2718035	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002718035.1	s__GCA-2718035 sp002718035	78.5837	203	462	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__TMED113;g__GCA-2718035	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002170235.1	s__TMED113 sp002170235	76.5187	85	462	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__TMED113;g__TMED113	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002701365.1	s__GCA-002701365 sp002701365	76.0088	60	462	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__TMED113;g__GCA-002701365	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-14 11:15:14,934] [INFO] GTDB search result was written to OceanDNA-b11595/result_gtdb.tsv
[2023-03-14 11:15:14,934] [INFO] ===== GTDB Search completed =====
[2023-03-14 11:15:14,935] [INFO] DFAST_QC result json was written to OceanDNA-b11595/dqc_result.json
[2023-03-14 11:15:14,935] [INFO] DFAST_QC completed!
[2023-03-14 11:15:14,935] [INFO] Total running time: 0h1m2s