[2023-03-17 23:49:09,993] [INFO] DFAST_QC pipeline started.
[2023-03-17 23:49:09,996] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 23:49:09,996] [INFO] DQC Reference Directory: /var/lib/cwl/stg77cdb0c1-93ab-495e-bee8-b01849f17833/dqc_reference
[2023-03-17 23:49:11,166] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 23:49:11,166] [INFO] Task started: Prodigal
[2023-03-17 23:49:11,166] [INFO] Running command: cat /var/lib/cwl/stg07fad09d-d6f6-4f54-84bf-5de144984a0a/OceanDNA-b45790.fa | prodigal -d OceanDNA-b45790/cds.fna -a OceanDNA-b45790/protein.faa -g 11 -q > /dev/null
[2023-03-17 23:49:20,627] [INFO] Task succeeded: Prodigal
[2023-03-17 23:49:20,628] [INFO] Task started: HMMsearch
[2023-03-17 23:49:20,628] [INFO] Running command: hmmsearch --tblout OceanDNA-b45790/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg77cdb0c1-93ab-495e-bee8-b01849f17833/dqc_reference/reference_markers.hmm OceanDNA-b45790/protein.faa > /dev/null
[2023-03-17 23:49:20,769] [INFO] Task succeeded: HMMsearch
[2023-03-17 23:49:20,769] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg07fad09d-d6f6-4f54-84bf-5de144984a0a/OceanDNA-b45790.fa]
[2023-03-17 23:49:20,782] [INFO] Query marker FASTA was written to OceanDNA-b45790/markers.fasta
[2023-03-17 23:49:20,783] [INFO] Task started: Blastn
[2023-03-17 23:49:20,783] [INFO] Running command: blastn -query OceanDNA-b45790/markers.fasta -db /var/lib/cwl/stg77cdb0c1-93ab-495e-bee8-b01849f17833/dqc_reference/reference_markers.fasta -out OceanDNA-b45790/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 23:49:21,268] [INFO] Task succeeded: Blastn
[2023-03-17 23:49:21,269] [INFO] Selected 7 target genomes.
[2023-03-17 23:49:21,269] [INFO] Target genome list was writen to OceanDNA-b45790/target_genomes.txt
[2023-03-17 23:49:21,274] [INFO] Task started: fastANI
[2023-03-17 23:49:21,274] [INFO] Running command: fastANI --query /var/lib/cwl/stg07fad09d-d6f6-4f54-84bf-5de144984a0a/OceanDNA-b45790.fa --refList OceanDNA-b45790/target_genomes.txt --output OceanDNA-b45790/fastani_result.tsv --threads 1
[2023-03-17 23:49:25,077] [INFO] Task succeeded: fastANI
[2023-03-17 23:49:25,077] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg77cdb0c1-93ab-495e-bee8-b01849f17833/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 23:49:25,078] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg77cdb0c1-93ab-495e-bee8-b01849f17833/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 23:49:25,078] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 23:49:25,078] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 23:49:25,078] [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
--------------------------------------------------------------------------------
[2023-03-17 23:49:25,078] [INFO] DFAST Taxonomy check result was written to OceanDNA-b45790/tc_result.tsv
[2023-03-17 23:49:25,078] [INFO] ===== Taxonomy check completed =====
[2023-03-17 23:49:25,078] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 23:49:25,078] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg77cdb0c1-93ab-495e-bee8-b01849f17833/dqc_reference/checkm_data
[2023-03-17 23:49:25,081] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 23:49:25,084] [INFO] Task started: CheckM
[2023-03-17 23:49:25,084] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b45790/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b45790/checkm_input OceanDNA-b45790/checkm_result
[2023-03-17 23:49:54,097] [INFO] Task succeeded: CheckM
[2023-03-17 23:49:54,097] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.17%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 23:49:54,121] [INFO] ===== Completeness check finished =====
[2023-03-17 23:49:54,121] [INFO] ===== Start GTDB Search =====
[2023-03-17 23:49:54,121] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b45790/markers.fasta)
[2023-03-17 23:49:54,122] [INFO] Task started: Blastn
[2023-03-17 23:49:54,122] [INFO] Running command: blastn -query OceanDNA-b45790/markers.fasta -db /var/lib/cwl/stg77cdb0c1-93ab-495e-bee8-b01849f17833/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b45790/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 23:49:54,769] [INFO] Task succeeded: Blastn
[2023-03-17 23:49:54,782] [INFO] Selected 16 target genomes.
[2023-03-17 23:49:54,782] [INFO] Target genome list was writen to OceanDNA-b45790/target_genomes_gtdb.txt
[2023-03-17 23:49:54,789] [INFO] Task started: fastANI
[2023-03-17 23:49:54,789] [INFO] Running command: fastANI --query /var/lib/cwl/stg07fad09d-d6f6-4f54-84bf-5de144984a0a/OceanDNA-b45790.fa --refList OceanDNA-b45790/target_genomes_gtdb.txt --output OceanDNA-b45790/fastani_result_gtdb.tsv --threads 1
[2023-03-17 23:50:01,488] [INFO] Task succeeded: fastANI
[2023-03-17 23:50:01,492] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 23:50:01,492] [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_002713685.1	s__MB11C04 sp002713685	99.7372	233	410	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__MB11C04;g__MB11C04	95.0	99.64	99.64	0.63	0.63	2	conclusive
GCA_902569115.1	s__MB11C04 sp902569115	93.4278	286	410	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__MB11C04;g__MB11C04	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002689665.1	s__MB11C04 sp002689665	85.9773	181	410	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	78.6116	115	410	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	78.3589	80	410	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__MB11C04;g__MB11C04	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 23:50:01,492] [INFO] GTDB search result was written to OceanDNA-b45790/result_gtdb.tsv
[2023-03-17 23:50:01,492] [INFO] ===== GTDB Search completed =====
[2023-03-17 23:50:01,493] [INFO] DFAST_QC result json was written to OceanDNA-b45790/dqc_result.json
[2023-03-17 23:50:01,493] [INFO] DFAST_QC completed!
[2023-03-17 23:50:01,493] [INFO] Total running time: 0h0m52s