[2023-03-16 00:19:47,516] [INFO] DFAST_QC pipeline started.
[2023-03-16 00:19:47,516] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 00:19:47,516] [INFO] DQC Reference Directory: /var/lib/cwl/stgf48ddd3d-cd58-4349-ad5d-d4acc4959cd1/dqc_reference
[2023-03-16 00:19:48,611] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 00:19:48,611] [INFO] Task started: Prodigal
[2023-03-16 00:19:48,612] [INFO] Running command: cat /var/lib/cwl/stg49917620-0658-4ba4-a65d-3fcbc608ccd6/OceanDNA-b42311.fa | prodigal -d OceanDNA-b42311/cds.fna -a OceanDNA-b42311/protein.faa -g 11 -q > /dev/null
[2023-03-16 00:19:52,117] [INFO] Task succeeded: Prodigal
[2023-03-16 00:19:52,118] [INFO] Task started: HMMsearch
[2023-03-16 00:19:52,118] [INFO] Running command: hmmsearch --tblout OceanDNA-b42311/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf48ddd3d-cd58-4349-ad5d-d4acc4959cd1/dqc_reference/reference_markers.hmm OceanDNA-b42311/protein.faa > /dev/null
[2023-03-16 00:19:52,275] [INFO] Task succeeded: HMMsearch
[2023-03-16 00:19:52,275] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg49917620-0658-4ba4-a65d-3fcbc608ccd6/OceanDNA-b42311.fa]
[2023-03-16 00:19:52,284] [INFO] Query marker FASTA was written to OceanDNA-b42311/markers.fasta
[2023-03-16 00:19:52,286] [INFO] Task started: Blastn
[2023-03-16 00:19:52,286] [INFO] Running command: blastn -query OceanDNA-b42311/markers.fasta -db /var/lib/cwl/stgf48ddd3d-cd58-4349-ad5d-d4acc4959cd1/dqc_reference/reference_markers.fasta -out OceanDNA-b42311/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 00:19:52,762] [INFO] Task succeeded: Blastn
[2023-03-16 00:19:52,766] [INFO] Selected 8 target genomes.
[2023-03-16 00:19:52,767] [INFO] Target genome list was writen to OceanDNA-b42311/target_genomes.txt
[2023-03-16 00:19:52,771] [INFO] Task started: fastANI
[2023-03-16 00:19:52,771] [INFO] Running command: fastANI --query /var/lib/cwl/stg49917620-0658-4ba4-a65d-3fcbc608ccd6/OceanDNA-b42311.fa --refList OceanDNA-b42311/target_genomes.txt --output OceanDNA-b42311/fastani_result.tsv --threads 1
[2023-03-16 00:19:56,622] [INFO] Task succeeded: fastANI
[2023-03-16 00:19:56,623] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf48ddd3d-cd58-4349-ad5d-d4acc4959cd1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 00:19:56,623] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf48ddd3d-cd58-4349-ad5d-d4acc4959cd1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 00:19:56,623] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 00:19:56,623] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 00:19:56,623] [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 00:19:56,653] [INFO] DFAST Taxonomy check result was written to OceanDNA-b42311/tc_result.tsv
[2023-03-16 00:19:56,654] [INFO] ===== Taxonomy check completed =====
[2023-03-16 00:19:56,655] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 00:19:56,655] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf48ddd3d-cd58-4349-ad5d-d4acc4959cd1/dqc_reference/checkm_data
[2023-03-16 00:19:56,665] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 00:19:56,669] [INFO] Task started: CheckM
[2023-03-16 00:19:56,669] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b42311/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b42311/checkm_input OceanDNA-b42311/checkm_result
[2023-03-16 00:20:12,372] [INFO] Task succeeded: CheckM
[2023-03-16 00:20:12,373] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 37.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 00:20:12,376] [INFO] ===== Completeness check finished =====
[2023-03-16 00:20:12,376] [INFO] ===== Start GTDB Search =====
[2023-03-16 00:20:12,376] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b42311/markers.fasta)
[2023-03-16 00:20:12,377] [INFO] Task started: Blastn
[2023-03-16 00:20:12,378] [INFO] Running command: blastn -query OceanDNA-b42311/markers.fasta -db /var/lib/cwl/stgf48ddd3d-cd58-4349-ad5d-d4acc4959cd1/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b42311/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 00:20:13,009] [INFO] Task succeeded: Blastn
[2023-03-16 00:20:13,010] [INFO] Selected 16 target genomes.
[2023-03-16 00:20:13,010] [INFO] Target genome list was writen to OceanDNA-b42311/target_genomes_gtdb.txt
[2023-03-16 00:20:13,019] [INFO] Task started: fastANI
[2023-03-16 00:20:13,019] [INFO] Running command: fastANI --query /var/lib/cwl/stg49917620-0658-4ba4-a65d-3fcbc608ccd6/OceanDNA-b42311.fa --refList OceanDNA-b42311/target_genomes_gtdb.txt --output OceanDNA-b42311/fastani_result_gtdb.tsv --threads 1
[2023-03-16 00:20:16,347] [INFO] Task succeeded: fastANI
[2023-03-16 00:20:16,356] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 00:20:16,356] [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_003213495.1	s__SAR86A sp003213495	96.478	222	228	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	98.20	96.41	0.97	0.94	3	conclusive
GCA_902579825.1	s__SAR86A sp902579825	91.224	176	228	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902559345.1	s__SAR86A sp902559345	78.741	90	228	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902520495.1	s__SAR86A sp902520495	78.7319	94	228	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902591925.1	s__SAR86A sp902591925	78.488	104	228	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	97.32	97.27	0.90	0.89	3	-
GCA_902631785.1	s__SAR86A sp902631785	78.2914	75	228	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	96.84	96.84	0.79	0.79	2	-
GCA_002690725.1	s__SAR86A sp002690725	78.1186	68	228	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	95.15	95.15	0.80	0.80	2	-
GCA_902556105.1	s__SAR86A sp902556105	77.9711	76	228	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902517425.1	s__SAR86A sp902517425	77.9402	85	228	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902560315.1	s__SAR86A sp902560315	77.857	91	228	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	95.47	95.47	0.82	0.82	2	-
GCA_902557965.1	s__SAR86A sp902557965	77.8344	79	228	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	97.42	97.04	0.73	0.71	3	-
GCA_902517505.1	s__SAR86A sp902517505	77.7414	82	228	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	97.73	97.59	0.82	0.80	3	-
GCA_902586925.1	s__SAR86A sp902586925	77.6284	105	228	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	96.82	96.82	0.89	0.89	2	-
GCA_002169625.2	s__SAR86A sp002169625	77.3195	71	228	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	98.57	98.54	0.85	0.74	4	-
GCA_002710265.1	s__SAR86A sp002710265	76.8111	76	228	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 00:20:16,357] [INFO] GTDB search result was written to OceanDNA-b42311/result_gtdb.tsv
[2023-03-16 00:20:16,358] [INFO] ===== GTDB Search completed =====
[2023-03-16 00:20:16,359] [INFO] DFAST_QC result json was written to OceanDNA-b42311/dqc_result.json
[2023-03-16 00:20:16,359] [INFO] DFAST_QC completed!
[2023-03-16 00:20:16,359] [INFO] Total running time: 0h0m29s