[2023-03-15 17:28:01,491] [INFO] DFAST_QC pipeline started.
[2023-03-15 17:28:01,491] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 17:28:01,491] [INFO] DQC Reference Directory: /var/lib/cwl/stg2761f686-d7d7-4016-acae-6edf495a8dad/dqc_reference
[2023-03-15 17:28:02,578] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 17:28:02,579] [INFO] Task started: Prodigal
[2023-03-15 17:28:02,579] [INFO] Running command: cat /var/lib/cwl/stgdf14e6cf-80db-41d0-be4b-923077eeb27a/OceanDNA-b25731.fa | prodigal -d OceanDNA-b25731/cds.fna -a OceanDNA-b25731/protein.faa -g 11 -q > /dev/null
[2023-03-15 17:28:07,016] [INFO] Task succeeded: Prodigal
[2023-03-15 17:28:07,016] [INFO] Task started: HMMsearch
[2023-03-15 17:28:07,016] [INFO] Running command: hmmsearch --tblout OceanDNA-b25731/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2761f686-d7d7-4016-acae-6edf495a8dad/dqc_reference/reference_markers.hmm OceanDNA-b25731/protein.faa > /dev/null
[2023-03-15 17:28:07,138] [INFO] Task succeeded: HMMsearch
[2023-03-15 17:28:07,138] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgdf14e6cf-80db-41d0-be4b-923077eeb27a/OceanDNA-b25731.fa]
[2023-03-15 17:28:07,146] [INFO] Query marker FASTA was written to OceanDNA-b25731/markers.fasta
[2023-03-15 17:28:07,147] [INFO] Task started: Blastn
[2023-03-15 17:28:07,147] [INFO] Running command: blastn -query OceanDNA-b25731/markers.fasta -db /var/lib/cwl/stg2761f686-d7d7-4016-acae-6edf495a8dad/dqc_reference/reference_markers.fasta -out OceanDNA-b25731/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 17:28:07,625] [INFO] Task succeeded: Blastn
[2023-03-15 17:28:07,627] [INFO] Selected 7 target genomes.
[2023-03-15 17:28:07,627] [INFO] Target genome list was writen to OceanDNA-b25731/target_genomes.txt
[2023-03-15 17:28:07,634] [INFO] Task started: fastANI
[2023-03-15 17:28:07,635] [INFO] Running command: fastANI --query /var/lib/cwl/stgdf14e6cf-80db-41d0-be4b-923077eeb27a/OceanDNA-b25731.fa --refList OceanDNA-b25731/target_genomes.txt --output OceanDNA-b25731/fastani_result.tsv --threads 1
[2023-03-15 17:28:10,487] [INFO] Task succeeded: fastANI
[2023-03-15 17:28:10,487] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2761f686-d7d7-4016-acae-6edf495a8dad/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 17:28:10,487] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2761f686-d7d7-4016-acae-6edf495a8dad/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 17:28:10,490] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 17:28:10,490] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 17:28:10,491] [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	77.0496	97	232	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 17:28:10,491] [INFO] DFAST Taxonomy check result was written to OceanDNA-b25731/tc_result.tsv
[2023-03-15 17:28:10,491] [INFO] ===== Taxonomy check completed =====
[2023-03-15 17:28:10,491] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 17:28:10,492] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2761f686-d7d7-4016-acae-6edf495a8dad/dqc_reference/checkm_data
[2023-03-15 17:28:10,492] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 17:28:10,496] [INFO] Task started: CheckM
[2023-03-15 17:28:10,496] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b25731/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b25731/checkm_input OceanDNA-b25731/checkm_result
[2023-03-15 17:28:27,334] [INFO] Task succeeded: CheckM
[2023-03-15 17:28:27,335] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 62.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 17:28:27,339] [INFO] ===== Completeness check finished =====
[2023-03-15 17:28:27,339] [INFO] ===== Start GTDB Search =====
[2023-03-15 17:28:27,339] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b25731/markers.fasta)
[2023-03-15 17:28:27,340] [INFO] Task started: Blastn
[2023-03-15 17:28:27,340] [INFO] Running command: blastn -query OceanDNA-b25731/markers.fasta -db /var/lib/cwl/stg2761f686-d7d7-4016-acae-6edf495a8dad/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b25731/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 17:28:27,855] [INFO] Task succeeded: Blastn
[2023-03-15 17:28:27,856] [INFO] Selected 14 target genomes.
[2023-03-15 17:28:27,856] [INFO] Target genome list was writen to OceanDNA-b25731/target_genomes_gtdb.txt
[2023-03-15 17:28:27,874] [INFO] Task started: fastANI
[2023-03-15 17:28:27,874] [INFO] Running command: fastANI --query /var/lib/cwl/stgdf14e6cf-80db-41d0-be4b-923077eeb27a/OceanDNA-b25731.fa --refList OceanDNA-b25731/target_genomes_gtdb.txt --output OceanDNA-b25731/fastani_result_gtdb.tsv --threads 1
[2023-03-15 17:28:30,399] [INFO] Task succeeded: fastANI
[2023-03-15 17:28:30,407] [INFO] Found 14 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 17:28:30,408] [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_902566775.1	s__Pelagibacter sp902566775	85.8956	157	232	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902560855.1	s__Pelagibacter sp902560855	82.2944	144	232	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902634695.1	s__Pelagibacter sp902634695	80.6266	102	232	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902570055.1	s__Pelagibacter sp902570055	80.2966	98	232	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902608305.1	s__Pelagibacter sp902608305	80.1798	105	232	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902634485.1	s__Pelagibacter sp902634485	80.0827	139	232	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902551735.1	s__Pelagibacter sp902551735	79.9825	105	232	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902592985.1	s__Pelagibacter sp902592985	79.4003	128	232	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902551215.1	s__Pelagibacter sp902551215	79.2888	88	232	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003215185.1	s__Pelagibacter sp003215185	79.1769	92	232	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	100.00	100.00	0.99	0.99	2	-
GCA_902607215.1	s__Pelagibacter sp902607215	78.4351	80	232	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902552985.1	s__Pelagibacter sp902552985	78.1813	108	232	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003212415.1	s__Pelagibacter sp003212415	77.7258	89	232	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCA_902564245.1	s__Pelagibacter sp902564245	77.6128	102	232	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 17:28:30,408] [INFO] GTDB search result was written to OceanDNA-b25731/result_gtdb.tsv
[2023-03-15 17:28:30,408] [INFO] ===== GTDB Search completed =====
[2023-03-15 17:28:30,410] [INFO] DFAST_QC result json was written to OceanDNA-b25731/dqc_result.json
[2023-03-15 17:28:30,410] [INFO] DFAST_QC completed!
[2023-03-15 17:28:30,410] [INFO] Total running time: 0h0m29s