[2023-03-14 12:33:24,207] [INFO] DFAST_QC pipeline started.
[2023-03-14 12:33:24,207] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 12:33:24,207] [INFO] DQC Reference Directory: /var/lib/cwl/stg5179de8b-f95c-4fe6-ae42-cd5051e1e00e/dqc_reference
[2023-03-14 12:33:25,343] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 12:33:25,344] [INFO] Task started: Prodigal
[2023-03-14 12:33:25,344] [INFO] Running command: cat /var/lib/cwl/stg90dd9bec-1af9-444d-93e0-649ddc019aca/OceanDNA-b45663.fa | prodigal -d OceanDNA-b45663/cds.fna -a OceanDNA-b45663/protein.faa -g 11 -q > /dev/null
[2023-03-14 12:33:41,554] [INFO] Task succeeded: Prodigal
[2023-03-14 12:33:41,555] [INFO] Task started: HMMsearch
[2023-03-14 12:33:41,555] [INFO] Running command: hmmsearch --tblout OceanDNA-b45663/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5179de8b-f95c-4fe6-ae42-cd5051e1e00e/dqc_reference/reference_markers.hmm OceanDNA-b45663/protein.faa > /dev/null
[2023-03-14 12:33:41,728] [INFO] Task succeeded: HMMsearch
[2023-03-14 12:33:41,728] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg90dd9bec-1af9-444d-93e0-649ddc019aca/OceanDNA-b45663.fa]
[2023-03-14 12:33:41,751] [INFO] Query marker FASTA was written to OceanDNA-b45663/markers.fasta
[2023-03-14 12:33:41,752] [INFO] Task started: Blastn
[2023-03-14 12:33:41,752] [INFO] Running command: blastn -query OceanDNA-b45663/markers.fasta -db /var/lib/cwl/stg5179de8b-f95c-4fe6-ae42-cd5051e1e00e/dqc_reference/reference_markers.fasta -out OceanDNA-b45663/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 12:33:42,245] [INFO] Task succeeded: Blastn
[2023-03-14 12:33:42,246] [INFO] Selected 14 target genomes.
[2023-03-14 12:33:42,246] [INFO] Target genome list was writen to OceanDNA-b45663/target_genomes.txt
[2023-03-14 12:33:42,255] [INFO] Task started: fastANI
[2023-03-14 12:33:42,255] [INFO] Running command: fastANI --query /var/lib/cwl/stg90dd9bec-1af9-444d-93e0-649ddc019aca/OceanDNA-b45663.fa --refList OceanDNA-b45663/target_genomes.txt --output OceanDNA-b45663/fastani_result.tsv --threads 1
[2023-03-14 12:33:48,683] [INFO] Task succeeded: fastANI
[2023-03-14 12:33:48,684] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5179de8b-f95c-4fe6-ae42-cd5051e1e00e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 12:33:48,684] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5179de8b-f95c-4fe6-ae42-cd5051e1e00e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 12:33:48,684] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 12:33:48,684] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-14 12:33:48,684] [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 12:33:48,685] [INFO] DFAST Taxonomy check result was written to OceanDNA-b45663/tc_result.tsv
[2023-03-14 12:33:48,685] [INFO] ===== Taxonomy check completed =====
[2023-03-14 12:33:48,685] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 12:33:48,685] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5179de8b-f95c-4fe6-ae42-cd5051e1e00e/dqc_reference/checkm_data
[2023-03-14 12:33:48,688] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 12:33:48,694] [INFO] Task started: CheckM
[2023-03-14 12:33:48,694] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b45663/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b45663/checkm_input OceanDNA-b45663/checkm_result
[2023-03-14 12:34:33,603] [INFO] Task succeeded: CheckM
[2023-03-14 12:34:33,603] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.29%
Contamintation: 0.46%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-14 12:34:33,608] [INFO] ===== Completeness check finished =====
[2023-03-14 12:34:33,608] [INFO] ===== Start GTDB Search =====
[2023-03-14 12:34:33,608] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b45663/markers.fasta)
[2023-03-14 12:34:33,609] [INFO] Task started: Blastn
[2023-03-14 12:34:33,609] [INFO] Running command: blastn -query OceanDNA-b45663/markers.fasta -db /var/lib/cwl/stg5179de8b-f95c-4fe6-ae42-cd5051e1e00e/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b45663/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 12:34:34,263] [INFO] Task succeeded: Blastn
[2023-03-14 12:34:34,264] [INFO] Selected 20 target genomes.
[2023-03-14 12:34:34,264] [INFO] Target genome list was writen to OceanDNA-b45663/target_genomes_gtdb.txt
[2023-03-14 12:34:34,281] [INFO] Task started: fastANI
[2023-03-14 12:34:34,281] [INFO] Running command: fastANI --query /var/lib/cwl/stg90dd9bec-1af9-444d-93e0-649ddc019aca/OceanDNA-b45663.fa --refList OceanDNA-b45663/target_genomes_gtdb.txt --output OceanDNA-b45663/fastani_result_gtdb.tsv --threads 1
[2023-03-14 12:34:42,867] [INFO] Task succeeded: fastANI
[2023-03-14 12:34:42,871] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-14 12:34:42,872] [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_002689665.1	s__MB11C04 sp002689665	87.2474	276	513	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__MB11C04;g__MB11C04	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902569115.1	s__MB11C04 sp902569115	83.8158	231	513	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__MB11C04;g__MB11C04	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002713685.1	s__MB11C04 sp002713685	83.304	132	513	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__MB11C04;g__MB11C04	95.0	99.64	99.64	0.63	0.63	2	-
GCA_902612125.1	s__MB11C04 sp902612125	79.3967	202	513	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__MB11C04;g__MB11C04	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902615835.1	s__MB11C04 sp902615835	79.3666	139	513	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__MB11C04;g__MB11C04	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002168015.1	s__MB11C04 sp002168015	79.0972	88	513	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__MB11C04;g__MB11C04	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-14 12:34:42,872] [INFO] GTDB search result was written to OceanDNA-b45663/result_gtdb.tsv
[2023-03-14 12:34:42,872] [INFO] ===== GTDB Search completed =====
[2023-03-14 12:34:42,873] [INFO] DFAST_QC result json was written to OceanDNA-b45663/dqc_result.json
[2023-03-14 12:34:42,873] [INFO] DFAST_QC completed!
[2023-03-14 12:34:42,873] [INFO] Total running time: 0h1m19s