[2023-03-19 01:35:27,745] [INFO] DFAST_QC pipeline started.
[2023-03-19 01:35:27,745] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 01:35:27,745] [INFO] DQC Reference Directory: /var/lib/cwl/stg6688da97-5495-4c42-85e9-cf6581f29bb4/dqc_reference
[2023-03-19 01:35:29,726] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 01:35:29,726] [INFO] Task started: Prodigal
[2023-03-19 01:35:29,727] [INFO] Running command: cat /var/lib/cwl/stg809fc0ff-3c9d-4441-b32f-92eefce06492/OceanDNA-b25376.fa | prodigal -d OceanDNA-b25376/cds.fna -a OceanDNA-b25376/protein.faa -g 11 -q > /dev/null
[2023-03-19 01:35:33,764] [INFO] Task succeeded: Prodigal
[2023-03-19 01:35:33,764] [INFO] Task started: HMMsearch
[2023-03-19 01:35:33,764] [INFO] Running command: hmmsearch --tblout OceanDNA-b25376/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6688da97-5495-4c42-85e9-cf6581f29bb4/dqc_reference/reference_markers.hmm OceanDNA-b25376/protein.faa > /dev/null
[2023-03-19 01:35:33,981] [INFO] Task succeeded: HMMsearch
[2023-03-19 01:35:33,982] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg809fc0ff-3c9d-4441-b32f-92eefce06492/OceanDNA-b25376.fa]
[2023-03-19 01:35:33,991] [INFO] Query marker FASTA was written to OceanDNA-b25376/markers.fasta
[2023-03-19 01:35:33,991] [INFO] Task started: Blastn
[2023-03-19 01:35:33,991] [INFO] Running command: blastn -query OceanDNA-b25376/markers.fasta -db /var/lib/cwl/stg6688da97-5495-4c42-85e9-cf6581f29bb4/dqc_reference/reference_markers.fasta -out OceanDNA-b25376/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 01:35:35,302] [INFO] Task succeeded: Blastn
[2023-03-19 01:35:35,303] [INFO] Selected 16 target genomes.
[2023-03-19 01:35:35,304] [INFO] Target genome list was writen to OceanDNA-b25376/target_genomes.txt
[2023-03-19 01:35:35,316] [INFO] Task started: fastANI
[2023-03-19 01:35:35,317] [INFO] Running command: fastANI --query /var/lib/cwl/stg809fc0ff-3c9d-4441-b32f-92eefce06492/OceanDNA-b25376.fa --refList OceanDNA-b25376/target_genomes.txt --output OceanDNA-b25376/fastani_result.tsv --threads 1
[2023-03-19 01:35:42,944] [INFO] Task succeeded: fastANI
[2023-03-19 01:35:42,944] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6688da97-5495-4c42-85e9-cf6581f29bb4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 01:35:42,945] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6688da97-5495-4c42-85e9-cf6581f29bb4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 01:35:42,945] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 01:35:42,945] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 01:35:42,945] [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 01:35:42,945] [INFO] DFAST Taxonomy check result was written to OceanDNA-b25376/tc_result.tsv
[2023-03-19 01:35:42,945] [INFO] ===== Taxonomy check completed =====
[2023-03-19 01:35:42,945] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 01:35:42,945] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6688da97-5495-4c42-85e9-cf6581f29bb4/dqc_reference/checkm_data
[2023-03-19 01:35:42,948] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 01:35:42,950] [INFO] Task started: CheckM
[2023-03-19 01:35:42,950] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b25376/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b25376/checkm_input OceanDNA-b25376/checkm_result
[2023-03-19 01:35:59,577] [INFO] Task succeeded: CheckM
[2023-03-19 01:35:59,577] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 72.73%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 01:35:59,579] [INFO] ===== Completeness check finished =====
[2023-03-19 01:35:59,579] [INFO] ===== Start GTDB Search =====
[2023-03-19 01:35:59,579] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b25376/markers.fasta)
[2023-03-19 01:35:59,580] [INFO] Task started: Blastn
[2023-03-19 01:35:59,580] [INFO] Running command: blastn -query OceanDNA-b25376/markers.fasta -db /var/lib/cwl/stg6688da97-5495-4c42-85e9-cf6581f29bb4/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b25376/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 01:36:00,261] [INFO] Task succeeded: Blastn
[2023-03-19 01:36:00,262] [INFO] Selected 23 target genomes.
[2023-03-19 01:36:00,262] [INFO] Target genome list was writen to OceanDNA-b25376/target_genomes_gtdb.txt
[2023-03-19 01:36:00,286] [INFO] Task started: fastANI
[2023-03-19 01:36:00,286] [INFO] Running command: fastANI --query /var/lib/cwl/stg809fc0ff-3c9d-4441-b32f-92eefce06492/OceanDNA-b25376.fa --refList OceanDNA-b25376/target_genomes_gtdb.txt --output OceanDNA-b25376/fastani_result_gtdb.tsv --threads 1
[2023-03-19 01:36:03,803] [INFO] Task succeeded: fastANI
[2023-03-19 01:36:03,815] [INFO] Found 16 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 01:36:03,816] [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_902604695.1	s__TMED170 sp902604695	77.4387	77	216	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__TMED170	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902582875.1	s__Pelagibacter_A sp902582875	77.2517	64	216	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014654415.1	s__Pelagibacter_A sp014654415	77.2129	67	216	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902580565.1	s__Pelagibacter_A sp902580565	77.1979	55	216	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter_A	95.0	99.69	99.69	0.75	0.75	2	-
GCA_003213115.1	s__MED-G40 sp003213115	77.0237	70	216	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__MED-G40	95.0	96.48	95.17	0.92	0.87	6	-
GCA_014653815.1	s__Pelagibacter_A sp014653815	76.9558	70	216	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902613545.1	s__Pelagibacter_A sp902613545	76.8419	59	216	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter_A	95.0	95.67	95.67	0.79	0.79	2	-
GCA_003278125.1	s__Pelagibacter_A sp003278125	76.827	75	216	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter_A	95.0	97.41	96.01	0.86	0.77	4	-
GCA_902596745.1	s__MED727 sp902596745	76.7904	66	216	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__MED727	95.0	97.74	97.74	0.88	0.88	2	-
GCA_902598595.1	s__Pelagibacter_A sp902598595	76.7639	60	216	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902569735.1	s__Pelagibacter_A sp902569735	76.6641	54	216	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter_A	95.0	95.22	95.22	0.72	0.72	2	-
GCA_003283025.1	s__Pelagibacter_A sp003283025	76.6334	53	216	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter_A	95.0	100.00	100.00	0.99	0.99	2	-
GCA_902524945.1	s__Pelagibacter_A sp902524945	76.4318	75	216	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902536305.1	s__Pelagibacter_A sp902536305	76.4145	50	216	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902630925.1	s__Pelagibacter_A sp902630925	76.3044	56	216	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902590625.1	s__Pelagibacter_A sp902590625	76.0358	55	216	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 01:36:03,816] [INFO] GTDB search result was written to OceanDNA-b25376/result_gtdb.tsv
[2023-03-19 01:36:03,816] [INFO] ===== GTDB Search completed =====
[2023-03-19 01:36:03,817] [INFO] DFAST_QC result json was written to OceanDNA-b25376/dqc_result.json
[2023-03-19 01:36:03,817] [INFO] DFAST_QC completed!
[2023-03-19 01:36:03,817] [INFO] Total running time: 0h0m36s