[2023-03-18 05:27:36,805] [INFO] DFAST_QC pipeline started.
[2023-03-18 05:27:36,805] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 05:27:36,805] [INFO] DQC Reference Directory: /var/lib/cwl/stg5f62d85e-307a-467e-93f9-6446dfe102ac/dqc_reference
[2023-03-18 05:27:37,888] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 05:27:37,889] [INFO] Task started: Prodigal
[2023-03-18 05:27:37,889] [INFO] Running command: cat /var/lib/cwl/stgb577207a-730b-488c-a657-e2bb48e5ea78/OceanDNA-b40885.fa | prodigal -d OceanDNA-b40885/cds.fna -a OceanDNA-b40885/protein.faa -g 11 -q > /dev/null
[2023-03-18 05:27:45,885] [INFO] Task succeeded: Prodigal
[2023-03-18 05:27:45,885] [INFO] Task started: HMMsearch
[2023-03-18 05:27:45,885] [INFO] Running command: hmmsearch --tblout OceanDNA-b40885/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5f62d85e-307a-467e-93f9-6446dfe102ac/dqc_reference/reference_markers.hmm OceanDNA-b40885/protein.faa > /dev/null
[2023-03-18 05:27:46,047] [INFO] Task succeeded: HMMsearch
[2023-03-18 05:27:46,048] [INFO] Found 6/6 markers.
[2023-03-18 05:27:46,062] [INFO] Query marker FASTA was written to OceanDNA-b40885/markers.fasta
[2023-03-18 05:27:46,063] [INFO] Task started: Blastn
[2023-03-18 05:27:46,063] [INFO] Running command: blastn -query OceanDNA-b40885/markers.fasta -db /var/lib/cwl/stg5f62d85e-307a-467e-93f9-6446dfe102ac/dqc_reference/reference_markers.fasta -out OceanDNA-b40885/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 05:27:46,644] [INFO] Task succeeded: Blastn
[2023-03-18 05:27:46,645] [INFO] Selected 33 target genomes.
[2023-03-18 05:27:46,645] [INFO] Target genome list was writen to OceanDNA-b40885/target_genomes.txt
[2023-03-18 05:27:46,663] [INFO] Task started: fastANI
[2023-03-18 05:27:46,663] [INFO] Running command: fastANI --query /var/lib/cwl/stgb577207a-730b-488c-a657-e2bb48e5ea78/OceanDNA-b40885.fa --refList OceanDNA-b40885/target_genomes.txt --output OceanDNA-b40885/fastani_result.tsv --threads 1
[2023-03-18 05:28:06,184] [INFO] Task succeeded: fastANI
[2023-03-18 05:28:06,184] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5f62d85e-307a-467e-93f9-6446dfe102ac/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 05:28:06,184] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5f62d85e-307a-467e-93f9-6446dfe102ac/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 05:28:06,185] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 05:28:06,185] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 05:28:06,185] [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
--------------------------------------------------------------------------------
[2023-03-18 05:28:06,185] [INFO] DFAST Taxonomy check result was written to OceanDNA-b40885/tc_result.tsv
[2023-03-18 05:28:06,185] [INFO] ===== Taxonomy check completed =====
[2023-03-18 05:28:06,185] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 05:28:06,185] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5f62d85e-307a-467e-93f9-6446dfe102ac/dqc_reference/checkm_data
[2023-03-18 05:28:06,188] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 05:28:06,192] [INFO] Task started: CheckM
[2023-03-18 05:28:06,192] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b40885/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b40885/checkm_input OceanDNA-b40885/checkm_result
[2023-03-18 05:28:32,371] [INFO] Task succeeded: CheckM
[2023-03-18 05:28:32,371] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 69.03%
Contamintation: 1.50%
Strain heterogeneity: 33.33%
--------------------------------------------------------------------------------
[2023-03-18 05:28:32,422] [INFO] ===== Completeness check finished =====
[2023-03-18 05:28:32,423] [INFO] ===== Start GTDB Search =====
[2023-03-18 05:28:32,423] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b40885/markers.fasta)
[2023-03-18 05:28:32,424] [INFO] Task started: Blastn
[2023-03-18 05:28:32,424] [INFO] Running command: blastn -query OceanDNA-b40885/markers.fasta -db /var/lib/cwl/stg5f62d85e-307a-467e-93f9-6446dfe102ac/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b40885/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 05:28:33,408] [INFO] Task succeeded: Blastn
[2023-03-18 05:28:33,413] [INFO] Selected 19 target genomes.
[2023-03-18 05:28:33,413] [INFO] Target genome list was writen to OceanDNA-b40885/target_genomes_gtdb.txt
[2023-03-18 05:28:33,437] [INFO] Task started: fastANI
[2023-03-18 05:28:33,438] [INFO] Running command: fastANI --query /var/lib/cwl/stgb577207a-730b-488c-a657-e2bb48e5ea78/OceanDNA-b40885.fa --refList OceanDNA-b40885/target_genomes_gtdb.txt --output OceanDNA-b40885/fastani_result_gtdb.tsv --threads 1
[2023-03-18 05:28:43,678] [INFO] Task succeeded: fastANI
[2023-03-18 05:28:43,683] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 05:28:43,684] [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_002719575.1	s__UBA9145 sp002719575	97.6466	415	448	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__UBA9145	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_003514305.1	s__UBA9145 sp003514305	80.8587	335	448	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__UBA9145	95.0	99.49	99.49	0.60	0.60	2	-
GCA_008081045.1	s__UBA9145 sp008081045	78.42	233	448	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__UBA9145	95.0	98.92	98.40	0.89	0.82	4	-
GCA_002691885.1	s__UBA9145 sp002691885	78.307	209	448	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__UBA9145	95.0	100.00	100.00	0.99	0.99	2	-
GCA_002729315.1	s__UBA9145 sp002729315	78.2953	213	448	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__UBA9145	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902597095.1	s__UBA9145 sp902597095	78.2806	160	448	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__UBA9145	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902537815.1	s__UBA9145 sp902537815	77.9111	164	448	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__UBA9145	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 05:28:43,684] [INFO] GTDB search result was written to OceanDNA-b40885/result_gtdb.tsv
[2023-03-18 05:28:43,686] [INFO] ===== GTDB Search completed =====
[2023-03-18 05:28:43,690] [INFO] DFAST_QC result json was written to OceanDNA-b40885/dqc_result.json
[2023-03-18 05:28:43,690] [INFO] DFAST_QC completed!
[2023-03-18 05:28:43,690] [INFO] Total running time: 0h1m7s