[2023-03-19 01:50:01,533] [INFO] DFAST_QC pipeline started.
[2023-03-19 01:50:01,533] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 01:50:01,533] [INFO] DQC Reference Directory: /var/lib/cwl/stgd6b182dd-dbe6-45e7-bda5-35db232e5865/dqc_reference
[2023-03-19 01:50:02,654] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 01:50:02,654] [INFO] Task started: Prodigal
[2023-03-19 01:50:02,654] [INFO] Running command: cat /var/lib/cwl/stg1bc53890-3e17-4c1e-ad73-6fd90aaadbbf/OceanDNA-b33692.fa | prodigal -d OceanDNA-b33692/cds.fna -a OceanDNA-b33692/protein.faa -g 11 -q > /dev/null
[2023-03-19 01:50:05,830] [INFO] Task succeeded: Prodigal
[2023-03-19 01:50:05,830] [INFO] Task started: HMMsearch
[2023-03-19 01:50:05,830] [INFO] Running command: hmmsearch --tblout OceanDNA-b33692/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd6b182dd-dbe6-45e7-bda5-35db232e5865/dqc_reference/reference_markers.hmm OceanDNA-b33692/protein.faa > /dev/null
[2023-03-19 01:50:05,981] [INFO] Task succeeded: HMMsearch
[2023-03-19 01:50:05,982] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg1bc53890-3e17-4c1e-ad73-6fd90aaadbbf/OceanDNA-b33692.fa]
[2023-03-19 01:50:05,990] [INFO] Query marker FASTA was written to OceanDNA-b33692/markers.fasta
[2023-03-19 01:50:05,992] [INFO] Task started: Blastn
[2023-03-19 01:50:05,992] [INFO] Running command: blastn -query OceanDNA-b33692/markers.fasta -db /var/lib/cwl/stgd6b182dd-dbe6-45e7-bda5-35db232e5865/dqc_reference/reference_markers.fasta -out OceanDNA-b33692/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 01:50:06,638] [INFO] Task succeeded: Blastn
[2023-03-19 01:50:06,639] [INFO] Selected 21 target genomes.
[2023-03-19 01:50:06,639] [INFO] Target genome list was writen to OceanDNA-b33692/target_genomes.txt
[2023-03-19 01:50:06,671] [INFO] Task started: fastANI
[2023-03-19 01:50:06,671] [INFO] Running command: fastANI --query /var/lib/cwl/stg1bc53890-3e17-4c1e-ad73-6fd90aaadbbf/OceanDNA-b33692.fa --refList OceanDNA-b33692/target_genomes.txt --output OceanDNA-b33692/fastani_result.tsv --threads 1
[2023-03-19 01:50:14,948] [INFO] Task succeeded: fastANI
[2023-03-19 01:50:14,949] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd6b182dd-dbe6-45e7-bda5-35db232e5865/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 01:50:14,949] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd6b182dd-dbe6-45e7-bda5-35db232e5865/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 01:50:14,949] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 01:50:14,949] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 01:50:14,949] [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 01:50:14,949] [INFO] DFAST Taxonomy check result was written to OceanDNA-b33692/tc_result.tsv
[2023-03-19 01:50:14,950] [INFO] ===== Taxonomy check completed =====
[2023-03-19 01:50:14,950] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 01:50:14,950] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd6b182dd-dbe6-45e7-bda5-35db232e5865/dqc_reference/checkm_data
[2023-03-19 01:50:14,953] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 01:50:14,955] [INFO] Task started: CheckM
[2023-03-19 01:50:14,955] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b33692/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b33692/checkm_input OceanDNA-b33692/checkm_result
[2023-03-19 01:50:32,413] [INFO] Task succeeded: CheckM
[2023-03-19 01:50:32,414] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.37%
Contamintation: 5.15%
Strain heterogeneity: 66.67%
--------------------------------------------------------------------------------
[2023-03-19 01:50:32,415] [INFO] ===== Completeness check finished =====
[2023-03-19 01:50:32,416] [INFO] ===== Start GTDB Search =====
[2023-03-19 01:50:32,416] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b33692/markers.fasta)
[2023-03-19 01:50:32,416] [INFO] Task started: Blastn
[2023-03-19 01:50:32,416] [INFO] Running command: blastn -query OceanDNA-b33692/markers.fasta -db /var/lib/cwl/stgd6b182dd-dbe6-45e7-bda5-35db232e5865/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b33692/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 01:50:33,226] [INFO] Task succeeded: Blastn
[2023-03-19 01:50:33,227] [INFO] Selected 22 target genomes.
[2023-03-19 01:50:33,227] [INFO] Target genome list was writen to OceanDNA-b33692/target_genomes_gtdb.txt
[2023-03-19 01:50:33,246] [INFO] Task started: fastANI
[2023-03-19 01:50:33,246] [INFO] Running command: fastANI --query /var/lib/cwl/stg1bc53890-3e17-4c1e-ad73-6fd90aaadbbf/OceanDNA-b33692.fa --refList OceanDNA-b33692/target_genomes_gtdb.txt --output OceanDNA-b33692/fastani_result_gtdb.tsv --threads 1
[2023-03-19 01:50:39,186] [INFO] Task succeeded: fastANI
[2023-03-19 01:50:39,189] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-19 01:50:39,189] [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_902558495.1	s__BACL14 sp902558495	95.3879	114	172	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__BACL14	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_000168995.1	s__BACL14 sp000168995	77.1797	50	172	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__BACL14	95.0	98.71	98.43	0.97	0.92	10	-
--------------------------------------------------------------------------------
[2023-03-19 01:50:39,189] [INFO] GTDB search result was written to OceanDNA-b33692/result_gtdb.tsv
[2023-03-19 01:50:39,189] [INFO] ===== GTDB Search completed =====
[2023-03-19 01:50:39,190] [INFO] DFAST_QC result json was written to OceanDNA-b33692/dqc_result.json
[2023-03-19 01:50:39,190] [INFO] DFAST_QC completed!
[2023-03-19 01:50:39,190] [INFO] Total running time: 0h0m38s