[2023-03-16 05:07:01,487] [INFO] DFAST_QC pipeline started.
[2023-03-16 05:07:01,487] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 05:07:01,487] [INFO] DQC Reference Directory: /var/lib/cwl/stg41cae8ad-c260-4e8c-91ab-d79f5f8c0edd/dqc_reference
[2023-03-16 05:07:04,496] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 05:07:04,496] [INFO] Task started: Prodigal
[2023-03-16 05:07:04,497] [INFO] Running command: cat /var/lib/cwl/stg10f6aee8-7e38-4d88-8f07-335663e3f630/OceanDNA-b40086.fa | prodigal -d OceanDNA-b40086/cds.fna -a OceanDNA-b40086/protein.faa -g 11 -q > /dev/null
[2023-03-16 05:07:17,951] [INFO] Task succeeded: Prodigal
[2023-03-16 05:07:17,951] [INFO] Task started: HMMsearch
[2023-03-16 05:07:17,951] [INFO] Running command: hmmsearch --tblout OceanDNA-b40086/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg41cae8ad-c260-4e8c-91ab-d79f5f8c0edd/dqc_reference/reference_markers.hmm OceanDNA-b40086/protein.faa > /dev/null
[2023-03-16 05:07:18,137] [INFO] Task succeeded: HMMsearch
[2023-03-16 05:07:18,137] [INFO] Found 6/6 markers.
[2023-03-16 05:07:18,152] [INFO] Query marker FASTA was written to OceanDNA-b40086/markers.fasta
[2023-03-16 05:07:18,153] [INFO] Task started: Blastn
[2023-03-16 05:07:18,153] [INFO] Running command: blastn -query OceanDNA-b40086/markers.fasta -db /var/lib/cwl/stg41cae8ad-c260-4e8c-91ab-d79f5f8c0edd/dqc_reference/reference_markers.fasta -out OceanDNA-b40086/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 05:07:18,774] [INFO] Task succeeded: Blastn
[2023-03-16 05:07:18,775] [INFO] Selected 29 target genomes.
[2023-03-16 05:07:18,775] [INFO] Target genome list was writen to OceanDNA-b40086/target_genomes.txt
[2023-03-16 05:07:18,797] [INFO] Task started: fastANI
[2023-03-16 05:07:18,798] [INFO] Running command: fastANI --query /var/lib/cwl/stg10f6aee8-7e38-4d88-8f07-335663e3f630/OceanDNA-b40086.fa --refList OceanDNA-b40086/target_genomes.txt --output OceanDNA-b40086/fastani_result.tsv --threads 1
[2023-03-16 05:07:36,492] [INFO] Task succeeded: fastANI
[2023-03-16 05:07:36,492] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg41cae8ad-c260-4e8c-91ab-d79f5f8c0edd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 05:07:36,492] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg41cae8ad-c260-4e8c-91ab-d79f5f8c0edd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 05:07:36,496] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 05:07:36,496] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 05:07:36,496] [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
Porticoccus hydrocarbonoclasticus	strain=MCTG13d	GCA_000744735.1	1073414	1073414	type	True	93.1293	663	726	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 05:07:36,496] [INFO] DFAST Taxonomy check result was written to OceanDNA-b40086/tc_result.tsv
[2023-03-16 05:07:36,496] [INFO] ===== Taxonomy check completed =====
[2023-03-16 05:07:36,496] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 05:07:36,496] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg41cae8ad-c260-4e8c-91ab-d79f5f8c0edd/dqc_reference/checkm_data
[2023-03-16 05:07:36,497] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 05:07:36,501] [INFO] Task started: CheckM
[2023-03-16 05:07:36,501] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b40086/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b40086/checkm_input OceanDNA-b40086/checkm_result
[2023-03-16 05:08:13,654] [INFO] Task succeeded: CheckM
[2023-03-16 05:08:13,655] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 05:08:13,656] [INFO] ===== Completeness check finished =====
[2023-03-16 05:08:13,656] [INFO] ===== Start GTDB Search =====
[2023-03-16 05:08:13,657] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b40086/markers.fasta)
[2023-03-16 05:08:13,658] [INFO] Task started: Blastn
[2023-03-16 05:08:13,658] [INFO] Running command: blastn -query OceanDNA-b40086/markers.fasta -db /var/lib/cwl/stg41cae8ad-c260-4e8c-91ab-d79f5f8c0edd/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b40086/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 05:08:14,683] [INFO] Task succeeded: Blastn
[2023-03-16 05:08:14,684] [INFO] Selected 8 target genomes.
[2023-03-16 05:08:14,684] [INFO] Target genome list was writen to OceanDNA-b40086/target_genomes_gtdb.txt
[2023-03-16 05:08:14,690] [INFO] Task started: fastANI
[2023-03-16 05:08:14,690] [INFO] Running command: fastANI --query /var/lib/cwl/stg10f6aee8-7e38-4d88-8f07-335663e3f630/OceanDNA-b40086.fa --refList OceanDNA-b40086/target_genomes_gtdb.txt --output OceanDNA-b40086/fastani_result_gtdb.tsv --threads 1
[2023-03-16 05:08:18,409] [INFO] Task succeeded: fastANI
[2023-03-16 05:08:18,414] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 05:08:18,414] [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_002733125.1	s__Porticoccus sp002733125	94.1814	551	726	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__Porticoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000744735.1	s__Porticoccus hydrocarbonoclasticus	93.1293	663	726	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__Porticoccus	95.0	99.20	98.73	0.89	0.78	4	-
GCA_002341315.1	s__Porticoccus sp002341315	92.9847	638	726	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__Porticoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002707685.1	s__Porticoccus sp002707685	92.6847	656	726	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__Porticoccus	95.0	99.58	99.58	0.96	0.96	2	-
GCA_002390285.1	s__Porticoccus sp002390285	76.8014	64	726	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__Porticoccus	95.0	99.85	99.48	0.95	0.89	6	-
GCA_002746985.1	s__Porticoccus sp002746985	76.7444	66	726	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__Porticoccus	95.0	97.07	97.07	0.91	0.91	2	-
GCA_006227015.1	s__Porticoccus sp006227015	76.5096	74	726	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__Porticoccus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 05:08:18,415] [INFO] GTDB search result was written to OceanDNA-b40086/result_gtdb.tsv
[2023-03-16 05:08:18,415] [INFO] ===== GTDB Search completed =====
[2023-03-16 05:08:18,415] [INFO] DFAST_QC result json was written to OceanDNA-b40086/dqc_result.json
[2023-03-16 05:08:18,416] [INFO] DFAST_QC completed!
[2023-03-16 05:08:18,416] [INFO] Total running time: 0h1m17s