[2023-03-16 03:23:47,623] [INFO] DFAST_QC pipeline started.
[2023-03-16 03:23:47,623] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 03:23:47,623] [INFO] DQC Reference Directory: /var/lib/cwl/stg331c8f92-27ed-4c5a-b1d9-4b4689c52a17/dqc_reference
[2023-03-16 03:23:49,403] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 03:23:49,415] [INFO] Task started: Prodigal
[2023-03-16 03:23:49,415] [INFO] Running command: cat /var/lib/cwl/stg188949ce-73e6-410a-9d3f-63b3cc52a9eb/OceanDNA-b25827.fa | prodigal -d OceanDNA-b25827/cds.fna -a OceanDNA-b25827/protein.faa -g 11 -q > /dev/null
[2023-03-16 03:23:53,142] [INFO] Task succeeded: Prodigal
[2023-03-16 03:23:53,142] [INFO] Task started: HMMsearch
[2023-03-16 03:23:53,143] [INFO] Running command: hmmsearch --tblout OceanDNA-b25827/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg331c8f92-27ed-4c5a-b1d9-4b4689c52a17/dqc_reference/reference_markers.hmm OceanDNA-b25827/protein.faa > /dev/null
[2023-03-16 03:23:53,314] [INFO] Task succeeded: HMMsearch
[2023-03-16 03:23:53,314] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg188949ce-73e6-410a-9d3f-63b3cc52a9eb/OceanDNA-b25827.fa]
[2023-03-16 03:23:53,321] [INFO] Query marker FASTA was written to OceanDNA-b25827/markers.fasta
[2023-03-16 03:23:53,324] [INFO] Task started: Blastn
[2023-03-16 03:23:53,324] [INFO] Running command: blastn -query OceanDNA-b25827/markers.fasta -db /var/lib/cwl/stg331c8f92-27ed-4c5a-b1d9-4b4689c52a17/dqc_reference/reference_markers.fasta -out OceanDNA-b25827/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 03:23:55,602] [INFO] Task succeeded: Blastn
[2023-03-16 03:23:55,602] [INFO] Selected 14 target genomes.
[2023-03-16 03:23:55,603] [INFO] Target genome list was writen to OceanDNA-b25827/target_genomes.txt
[2023-03-16 03:23:55,610] [INFO] Task started: fastANI
[2023-03-16 03:23:55,610] [INFO] Running command: fastANI --query /var/lib/cwl/stg188949ce-73e6-410a-9d3f-63b3cc52a9eb/OceanDNA-b25827.fa --refList OceanDNA-b25827/target_genomes.txt --output OceanDNA-b25827/fastani_result.tsv --threads 1
[2023-03-16 03:23:59,835] [INFO] Task succeeded: fastANI
[2023-03-16 03:23:59,836] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg331c8f92-27ed-4c5a-b1d9-4b4689c52a17/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 03:23:59,836] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg331c8f92-27ed-4c5a-b1d9-4b4689c52a17/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 03:23:59,839] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 03:23:59,839] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 03:23:59,839] [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
Candidatus Pelagibacter ubique	strain=HTCC1062	GCA_000012345.1	198252	198252	suspected-type	True	76.8532	89	183	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 03:23:59,839] [INFO] DFAST Taxonomy check result was written to OceanDNA-b25827/tc_result.tsv
[2023-03-16 03:23:59,839] [INFO] ===== Taxonomy check completed =====
[2023-03-16 03:23:59,839] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 03:23:59,839] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg331c8f92-27ed-4c5a-b1d9-4b4689c52a17/dqc_reference/checkm_data
[2023-03-16 03:23:59,840] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 03:23:59,851] [INFO] Task started: CheckM
[2023-03-16 03:23:59,852] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b25827/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b25827/checkm_input OceanDNA-b25827/checkm_result
[2023-03-16 03:24:19,497] [INFO] Task succeeded: CheckM
[2023-03-16 03:24:19,497] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 56.48%
Contamintation: 1.28%
Strain heterogeneity: 66.67%
--------------------------------------------------------------------------------
[2023-03-16 03:24:19,499] [INFO] ===== Completeness check finished =====
[2023-03-16 03:24:19,499] [INFO] ===== Start GTDB Search =====
[2023-03-16 03:24:19,499] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b25827/markers.fasta)
[2023-03-16 03:24:19,501] [INFO] Task started: Blastn
[2023-03-16 03:24:19,501] [INFO] Running command: blastn -query OceanDNA-b25827/markers.fasta -db /var/lib/cwl/stg331c8f92-27ed-4c5a-b1d9-4b4689c52a17/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b25827/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 03:24:20,836] [INFO] Task succeeded: Blastn
[2023-03-16 03:24:20,836] [INFO] Selected 9 target genomes.
[2023-03-16 03:24:20,837] [INFO] Target genome list was writen to OceanDNA-b25827/target_genomes_gtdb.txt
[2023-03-16 03:24:21,087] [INFO] Task started: fastANI
[2023-03-16 03:24:21,088] [INFO] Running command: fastANI --query /var/lib/cwl/stg188949ce-73e6-410a-9d3f-63b3cc52a9eb/OceanDNA-b25827.fa --refList OceanDNA-b25827/target_genomes_gtdb.txt --output OceanDNA-b25827/fastani_result_gtdb.tsv --threads 1
[2023-03-16 03:24:22,656] [INFO] Task succeeded: fastANI
[2023-03-16 03:24:22,662] [INFO] Found 9 fastANI hits (2 hits with ANI > circumscription radius)
[2023-03-16 03:24:22,662] [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_002692475.1	s__Pelagibacter sp002692475	97.8947	133	183	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	inconclusive
GCA_014654065.1	s__Pelagibacter sp014654065	95.2937	170	183	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	inconclusive
GCA_902515185.1	s__Pelagibacter sp902515185	87.6336	139	183	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902574695.1	s__Pelagibacter sp902574695	81.1257	122	183	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902545825.1	s__Pelagibacter sp902545825	80.793	99	183	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902598425.1	s__Pelagibacter sp902598425	80.7642	106	183	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001179965.1	s__Pelagibacter sp902587665	80.6341	92	183	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	96.05	95.63	0.60	0.56	5	-
GCA_902628635.1	s__Pelagibacter sp902628635	80.623	108	183	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902626575.1	s__Pelagibacter sp902626575	80.1049	104	183	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 03:24:22,662] [INFO] GTDB search result was written to OceanDNA-b25827/result_gtdb.tsv
[2023-03-16 03:24:22,663] [INFO] ===== GTDB Search completed =====
[2023-03-16 03:24:22,663] [INFO] DFAST_QC result json was written to OceanDNA-b25827/dqc_result.json
[2023-03-16 03:24:22,664] [INFO] DFAST_QC completed!
[2023-03-16 03:24:22,664] [INFO] Total running time: 0h0m35s