[2023-03-16 18:09:07,754] [INFO] DFAST_QC pipeline started.
[2023-03-16 18:09:07,754] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 18:09:07,754] [INFO] DQC Reference Directory: /var/lib/cwl/stg1e96e5fa-09ad-4334-ace9-516adff480a1/dqc_reference
[2023-03-16 18:09:08,836] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 18:09:08,837] [INFO] Task started: Prodigal
[2023-03-16 18:09:08,837] [INFO] Running command: cat /var/lib/cwl/stg3b86f8c4-05df-4407-b92a-8fc01c5863f2/OceanDNA-b34025.fa | prodigal -d OceanDNA-b34025/cds.fna -a OceanDNA-b34025/protein.faa -g 11 -q > /dev/null
[2023-03-16 18:09:12,622] [INFO] Task succeeded: Prodigal
[2023-03-16 18:09:12,622] [INFO] Task started: HMMsearch
[2023-03-16 18:09:12,622] [INFO] Running command: hmmsearch --tblout OceanDNA-b34025/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1e96e5fa-09ad-4334-ace9-516adff480a1/dqc_reference/reference_markers.hmm OceanDNA-b34025/protein.faa > /dev/null
[2023-03-16 18:09:12,771] [INFO] Task succeeded: HMMsearch
[2023-03-16 18:09:12,772] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg3b86f8c4-05df-4407-b92a-8fc01c5863f2/OceanDNA-b34025.fa]
[2023-03-16 18:09:12,780] [INFO] Query marker FASTA was written to OceanDNA-b34025/markers.fasta
[2023-03-16 18:09:12,781] [INFO] Task started: Blastn
[2023-03-16 18:09:12,781] [INFO] Running command: blastn -query OceanDNA-b34025/markers.fasta -db /var/lib/cwl/stg1e96e5fa-09ad-4334-ace9-516adff480a1/dqc_reference/reference_markers.fasta -out OceanDNA-b34025/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 18:09:13,291] [INFO] Task succeeded: Blastn
[2023-03-16 18:09:13,292] [INFO] Selected 20 target genomes.
[2023-03-16 18:09:13,292] [INFO] Target genome list was writen to OceanDNA-b34025/target_genomes.txt
[2023-03-16 18:09:13,330] [INFO] Task started: fastANI
[2023-03-16 18:09:13,330] [INFO] Running command: fastANI --query /var/lib/cwl/stg3b86f8c4-05df-4407-b92a-8fc01c5863f2/OceanDNA-b34025.fa --refList OceanDNA-b34025/target_genomes.txt --output OceanDNA-b34025/fastani_result.tsv --threads 1
[2023-03-16 18:09:22,237] [INFO] Task succeeded: fastANI
[2023-03-16 18:09:22,237] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1e96e5fa-09ad-4334-ace9-516adff480a1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 18:09:22,237] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1e96e5fa-09ad-4334-ace9-516adff480a1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 18:09:22,238] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 18:09:22,238] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 18:09:22,238] [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
--------------------------------------------------------------------------------
[2023-03-16 18:09:22,238] [INFO] DFAST Taxonomy check result was written to OceanDNA-b34025/tc_result.tsv
[2023-03-16 18:09:22,238] [INFO] ===== Taxonomy check completed =====
[2023-03-16 18:09:22,238] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 18:09:22,238] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1e96e5fa-09ad-4334-ace9-516adff480a1/dqc_reference/checkm_data
[2023-03-16 18:09:22,241] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 18:09:22,245] [INFO] Task started: CheckM
[2023-03-16 18:09:22,245] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b34025/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b34025/checkm_input OceanDNA-b34025/checkm_result
[2023-03-16 18:09:37,755] [INFO] Task succeeded: CheckM
[2023-03-16 18:09:37,755] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 86.11%
Contamintation: 0.38%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-16 18:09:37,757] [INFO] ===== Completeness check finished =====
[2023-03-16 18:09:37,757] [INFO] ===== Start GTDB Search =====
[2023-03-16 18:09:37,757] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b34025/markers.fasta)
[2023-03-16 18:09:37,757] [INFO] Task started: Blastn
[2023-03-16 18:09:37,757] [INFO] Running command: blastn -query OceanDNA-b34025/markers.fasta -db /var/lib/cwl/stg1e96e5fa-09ad-4334-ace9-516adff480a1/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b34025/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 18:09:38,430] [INFO] Task succeeded: Blastn
[2023-03-16 18:09:38,431] [INFO] Selected 11 target genomes.
[2023-03-16 18:09:38,431] [INFO] Target genome list was writen to OceanDNA-b34025/target_genomes_gtdb.txt
[2023-03-16 18:09:38,440] [INFO] Task started: fastANI
[2023-03-16 18:09:38,440] [INFO] Running command: fastANI --query /var/lib/cwl/stg3b86f8c4-05df-4407-b92a-8fc01c5863f2/OceanDNA-b34025.fa --refList OceanDNA-b34025/target_genomes_gtdb.txt --output OceanDNA-b34025/fastani_result_gtdb.tsv --threads 1
[2023-03-16 18:09:41,046] [INFO] Task succeeded: fastANI
[2023-03-16 18:09:41,049] [INFO] Found 3 fastANI hits (2 hits with ANI > circumscription radius)
[2023-03-16 18:09:41,049] [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_001044335.1	s__BACL14 sp001044335	96.7335	215	217	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__BACL14	95.0	100.00	100.00	1.00	1.00	3	inconclusive
GCA_000156155.1	s__BACL14 sp000156155	95.1093	215	217	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__BACL14	95.0	N/A	N/A	N/A	N/A	1	inconclusive
GCA_010023085.1	s__BACL14 sp010023085	86.8876	191	217	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__BACL14	95.0	99.14	98.98	0.85	0.84	6	-
--------------------------------------------------------------------------------
[2023-03-16 18:09:41,050] [INFO] GTDB search result was written to OceanDNA-b34025/result_gtdb.tsv
[2023-03-16 18:09:41,050] [INFO] ===== GTDB Search completed =====
[2023-03-16 18:09:41,050] [INFO] DFAST_QC result json was written to OceanDNA-b34025/dqc_result.json
[2023-03-16 18:09:41,050] [INFO] DFAST_QC completed!
[2023-03-16 18:09:41,050] [INFO] Total running time: 0h0m33s