[2023-03-14 11:13:58,985] [INFO] DFAST_QC pipeline started.
[2023-03-14 11:13:58,985] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 11:13:58,985] [INFO] DQC Reference Directory: /var/lib/cwl/stg0febab17-93bc-4172-a829-734caf074bf8/dqc_reference
[2023-03-14 11:14:00,596] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 11:14:00,597] [INFO] Task started: Prodigal
[2023-03-14 11:14:00,597] [INFO] Running command: cat /var/lib/cwl/stg0c84315f-d0ce-43f2-909e-05756d729f3e/OceanDNA-b45658.fa | prodigal -d OceanDNA-b45658/cds.fna -a OceanDNA-b45658/protein.faa -g 11 -q > /dev/null
[2023-03-14 11:14:17,186] [INFO] Task succeeded: Prodigal
[2023-03-14 11:14:17,186] [INFO] Task started: HMMsearch
[2023-03-14 11:14:17,186] [INFO] Running command: hmmsearch --tblout OceanDNA-b45658/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0febab17-93bc-4172-a829-734caf074bf8/dqc_reference/reference_markers.hmm OceanDNA-b45658/protein.faa > /dev/null
[2023-03-14 11:14:17,358] [INFO] Task succeeded: HMMsearch
[2023-03-14 11:14:17,359] [INFO] Found 6/6 markers.
[2023-03-14 11:14:17,375] [INFO] Query marker FASTA was written to OceanDNA-b45658/markers.fasta
[2023-03-14 11:14:17,376] [INFO] Task started: Blastn
[2023-03-14 11:14:17,377] [INFO] Running command: blastn -query OceanDNA-b45658/markers.fasta -db /var/lib/cwl/stg0febab17-93bc-4172-a829-734caf074bf8/dqc_reference/reference_markers.fasta -out OceanDNA-b45658/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 11:14:17,895] [INFO] Task succeeded: Blastn
[2023-03-14 11:14:17,896] [INFO] Selected 13 target genomes.
[2023-03-14 11:14:17,896] [INFO] Target genome list was writen to OceanDNA-b45658/target_genomes.txt
[2023-03-14 11:14:17,906] [INFO] Task started: fastANI
[2023-03-14 11:14:17,906] [INFO] Running command: fastANI --query /var/lib/cwl/stg0c84315f-d0ce-43f2-909e-05756d729f3e/OceanDNA-b45658.fa --refList OceanDNA-b45658/target_genomes.txt --output OceanDNA-b45658/fastani_result.tsv --threads 1
[2023-03-14 11:14:24,895] [INFO] Task succeeded: fastANI
[2023-03-14 11:14:24,895] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0febab17-93bc-4172-a829-734caf074bf8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 11:14:24,895] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0febab17-93bc-4172-a829-734caf074bf8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 11:14:24,895] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 11:14:24,895] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-14 11:14:24,895] [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 11:14:24,896] [INFO] DFAST Taxonomy check result was written to OceanDNA-b45658/tc_result.tsv
[2023-03-14 11:14:24,896] [INFO] ===== Taxonomy check completed =====
[2023-03-14 11:14:24,896] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 11:14:24,896] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0febab17-93bc-4172-a829-734caf074bf8/dqc_reference/checkm_data
[2023-03-14 11:14:24,899] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 11:14:24,903] [INFO] Task started: CheckM
[2023-03-14 11:14:24,903] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b45658/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b45658/checkm_input OceanDNA-b45658/checkm_result
[2023-03-14 11:15:10,122] [INFO] Task succeeded: CheckM
[2023-03-14 11:15:10,123] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 4.63%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-14 11:15:10,125] [INFO] ===== Completeness check finished =====
[2023-03-14 11:15:10,125] [INFO] ===== Start GTDB Search =====
[2023-03-14 11:15:10,125] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b45658/markers.fasta)
[2023-03-14 11:15:10,126] [INFO] Task started: Blastn
[2023-03-14 11:15:10,126] [INFO] Running command: blastn -query OceanDNA-b45658/markers.fasta -db /var/lib/cwl/stg0febab17-93bc-4172-a829-734caf074bf8/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b45658/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 11:15:10,812] [INFO] Task succeeded: Blastn
[2023-03-14 11:15:10,813] [INFO] Selected 22 target genomes.
[2023-03-14 11:15:10,813] [INFO] Target genome list was writen to OceanDNA-b45658/target_genomes_gtdb.txt
[2023-03-14 11:15:10,839] [INFO] Task started: fastANI
[2023-03-14 11:15:10,839] [INFO] Running command: fastANI --query /var/lib/cwl/stg0c84315f-d0ce-43f2-909e-05756d729f3e/OceanDNA-b45658.fa --refList OceanDNA-b45658/target_genomes_gtdb.txt --output OceanDNA-b45658/fastani_result_gtdb.tsv --threads 1
[2023-03-14 11:15:21,351] [INFO] Task succeeded: fastANI
[2023-03-14 11:15:21,356] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-14 11:15:21,356] [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_902569115.1	s__MB11C04 sp902569115	93.1328	460	695	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	92.4673	280	695	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__MB11C04;g__MB11C04	95.0	99.64	99.64	0.63	0.63	2	-
GCA_002689665.1	s__MB11C04 sp002689665	84.8716	253	695	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__MB11C04;g__MB11C04	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902612125.1	s__MB11C04 sp902612125	79.8464	193	695	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	79.6451	128	695	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__MB11C04;g__MB11C04	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002167265.1	s__MB11C04 sp002167265	78.4287	94	695	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 11:15:21,356] [INFO] GTDB search result was written to OceanDNA-b45658/result_gtdb.tsv
[2023-03-14 11:15:21,356] [INFO] ===== GTDB Search completed =====
[2023-03-14 11:15:21,357] [INFO] DFAST_QC result json was written to OceanDNA-b45658/dqc_result.json
[2023-03-14 11:15:21,357] [INFO] DFAST_QC completed!
[2023-03-14 11:15:21,357] [INFO] Total running time: 0h1m22s