[2023-03-19 03:10:00,719] [INFO] DFAST_QC pipeline started.
[2023-03-19 03:10:00,719] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 03:10:00,719] [INFO] DQC Reference Directory: /var/lib/cwl/stgc077881b-d3de-4155-8b0d-ce8ed7ad78a9/dqc_reference
[2023-03-19 03:10:01,825] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 03:10:01,825] [INFO] Task started: Prodigal
[2023-03-19 03:10:01,825] [INFO] Running command: cat /var/lib/cwl/stg516e041c-7225-4cf4-8c69-d16fd0a86b95/OceanDNA-b47035.fa | prodigal -d OceanDNA-b47035/cds.fna -a OceanDNA-b47035/protein.faa -g 11 -q > /dev/null
[2023-03-19 03:10:18,443] [INFO] Task succeeded: Prodigal
[2023-03-19 03:10:18,443] [INFO] Task started: HMMsearch
[2023-03-19 03:10:18,443] [INFO] Running command: hmmsearch --tblout OceanDNA-b47035/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc077881b-d3de-4155-8b0d-ce8ed7ad78a9/dqc_reference/reference_markers.hmm OceanDNA-b47035/protein.faa > /dev/null
[2023-03-19 03:10:18,655] [INFO] Task succeeded: HMMsearch
[2023-03-19 03:10:18,656] [INFO] Found 6/6 markers.
[2023-03-19 03:10:18,676] [INFO] Query marker FASTA was written to OceanDNA-b47035/markers.fasta
[2023-03-19 03:10:18,676] [INFO] Task started: Blastn
[2023-03-19 03:10:18,676] [INFO] Running command: blastn -query OceanDNA-b47035/markers.fasta -db /var/lib/cwl/stgc077881b-d3de-4155-8b0d-ce8ed7ad78a9/dqc_reference/reference_markers.fasta -out OceanDNA-b47035/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 03:10:19,227] [INFO] Task succeeded: Blastn
[2023-03-19 03:10:19,227] [INFO] Selected 11 target genomes.
[2023-03-19 03:10:19,228] [INFO] Target genome list was writen to OceanDNA-b47035/target_genomes.txt
[2023-03-19 03:10:19,233] [INFO] Task started: fastANI
[2023-03-19 03:10:19,234] [INFO] Running command: fastANI --query /var/lib/cwl/stg516e041c-7225-4cf4-8c69-d16fd0a86b95/OceanDNA-b47035.fa --refList OceanDNA-b47035/target_genomes.txt --output OceanDNA-b47035/fastani_result.tsv --threads 1
[2023-03-19 03:10:24,005] [INFO] Task succeeded: fastANI
[2023-03-19 03:10:24,005] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc077881b-d3de-4155-8b0d-ce8ed7ad78a9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 03:10:24,005] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc077881b-d3de-4155-8b0d-ce8ed7ad78a9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 03:10:24,006] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 03:10:24,006] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 03:10:24,006] [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
--------------------------------------------------------------------------------
[2023-03-19 03:10:24,006] [INFO] DFAST Taxonomy check result was written to OceanDNA-b47035/tc_result.tsv
[2023-03-19 03:10:24,006] [INFO] ===== Taxonomy check completed =====
[2023-03-19 03:10:24,006] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 03:10:24,006] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc077881b-d3de-4155-8b0d-ce8ed7ad78a9/dqc_reference/checkm_data
[2023-03-19 03:10:24,008] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 03:10:24,013] [INFO] Task started: CheckM
[2023-03-19 03:10:24,013] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b47035/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b47035/checkm_input OceanDNA-b47035/checkm_result
[2023-03-19 03:11:09,235] [INFO] Task succeeded: CheckM
[2023-03-19 03:11:09,235] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.85%
Contamintation: 0.38%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-19 03:11:09,237] [INFO] ===== Completeness check finished =====
[2023-03-19 03:11:09,238] [INFO] ===== Start GTDB Search =====
[2023-03-19 03:11:09,238] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b47035/markers.fasta)
[2023-03-19 03:11:09,238] [INFO] Task started: Blastn
[2023-03-19 03:11:09,238] [INFO] Running command: blastn -query OceanDNA-b47035/markers.fasta -db /var/lib/cwl/stgc077881b-d3de-4155-8b0d-ce8ed7ad78a9/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b47035/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 03:11:10,140] [INFO] Task succeeded: Blastn
[2023-03-19 03:11:10,141] [INFO] Selected 17 target genomes.
[2023-03-19 03:11:10,141] [INFO] Target genome list was writen to OceanDNA-b47035/target_genomes_gtdb.txt
[2023-03-19 03:11:10,170] [INFO] Task started: fastANI
[2023-03-19 03:11:10,170] [INFO] Running command: fastANI --query /var/lib/cwl/stg516e041c-7225-4cf4-8c69-d16fd0a86b95/OceanDNA-b47035.fa --refList OceanDNA-b47035/target_genomes_gtdb.txt --output OceanDNA-b47035/fastani_result_gtdb.tsv --threads 1
[2023-03-19 03:11:18,415] [INFO] Task succeeded: fastANI
[2023-03-19 03:11:18,420] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-19 03:11:18,420] [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_002684575.1	s__EC70 sp002684575	95.8727	581	781	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__DEV007;g__EC70	95.0	96.27	95.80	0.72	0.71	3	conclusive
GCA_013911195.1	s__EC70 sp013911195	92.7085	480	781	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__DEV007;g__EC70	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002696885.1	s__EC70 sp002696885	80.1144	196	781	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__DEV007;g__EC70	95.0	97.67	96.84	0.77	0.68	3	-
GCA_902510815.1	s__EC70 sp902510815	78.8436	147	781	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__DEV007;g__EC70	95.0	98.37	98.17	0.57	0.51	4	-
GCA_002705125.1	s__EC70 sp002705125	78.5486	210	781	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__DEV007;g__EC70	95.0	98.42	98.38	0.81	0.78	3	-
GCA_004211885.1	s__EC70 sp004211885	76.9703	76	781	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__DEV007;g__EC70	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 03:11:18,420] [INFO] GTDB search result was written to OceanDNA-b47035/result_gtdb.tsv
[2023-03-19 03:11:18,420] [INFO] ===== GTDB Search completed =====
[2023-03-19 03:11:18,421] [INFO] DFAST_QC result json was written to OceanDNA-b47035/dqc_result.json
[2023-03-19 03:11:18,421] [INFO] DFAST_QC completed!
[2023-03-19 03:11:18,421] [INFO] Total running time: 0h1m18s