[2023-03-19 02:46:09,184] [INFO] DFAST_QC pipeline started.
[2023-03-19 02:46:09,185] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 02:46:09,185] [INFO] DQC Reference Directory: /var/lib/cwl/stg8f66ee46-ac01-4b48-a30d-4a29d33dbc93/dqc_reference
[2023-03-19 02:46:10,281] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 02:46:10,281] [INFO] Task started: Prodigal
[2023-03-19 02:46:10,281] [INFO] Running command: cat /var/lib/cwl/stg52a20ef0-fef6-429f-9a6a-a0cc5d1456c8/OceanDNA-b25463.fa | prodigal -d OceanDNA-b25463/cds.fna -a OceanDNA-b25463/protein.faa -g 11 -q > /dev/null
[2023-03-19 02:46:13,740] [INFO] Task succeeded: Prodigal
[2023-03-19 02:46:13,740] [INFO] Task started: HMMsearch
[2023-03-19 02:46:13,740] [INFO] Running command: hmmsearch --tblout OceanDNA-b25463/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8f66ee46-ac01-4b48-a30d-4a29d33dbc93/dqc_reference/reference_markers.hmm OceanDNA-b25463/protein.faa > /dev/null
[2023-03-19 02:46:13,879] [INFO] Task succeeded: HMMsearch
[2023-03-19 02:46:13,879] [INFO] Found 6/6 markers.
[2023-03-19 02:46:13,885] [INFO] Query marker FASTA was written to OceanDNA-b25463/markers.fasta
[2023-03-19 02:46:13,887] [INFO] Task started: Blastn
[2023-03-19 02:46:13,887] [INFO] Running command: blastn -query OceanDNA-b25463/markers.fasta -db /var/lib/cwl/stg8f66ee46-ac01-4b48-a30d-4a29d33dbc93/dqc_reference/reference_markers.fasta -out OceanDNA-b25463/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 02:46:14,626] [INFO] Task succeeded: Blastn
[2023-03-19 02:46:14,627] [INFO] Selected 12 target genomes.
[2023-03-19 02:46:14,627] [INFO] Target genome list was writen to OceanDNA-b25463/target_genomes.txt
[2023-03-19 02:46:14,639] [INFO] Task started: fastANI
[2023-03-19 02:46:14,639] [INFO] Running command: fastANI --query /var/lib/cwl/stg52a20ef0-fef6-429f-9a6a-a0cc5d1456c8/OceanDNA-b25463.fa --refList OceanDNA-b25463/target_genomes.txt --output OceanDNA-b25463/fastani_result.tsv --threads 1
[2023-03-19 02:46:18,632] [INFO] Task succeeded: fastANI
[2023-03-19 02:46:18,633] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8f66ee46-ac01-4b48-a30d-4a29d33dbc93/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 02:46:18,633] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8f66ee46-ac01-4b48-a30d-4a29d33dbc93/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 02:46:18,633] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 02:46:18,633] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 02:46:18,633] [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 02:46:18,634] [INFO] DFAST Taxonomy check result was written to OceanDNA-b25463/tc_result.tsv
[2023-03-19 02:46:18,634] [INFO] ===== Taxonomy check completed =====
[2023-03-19 02:46:18,634] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 02:46:18,634] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8f66ee46-ac01-4b48-a30d-4a29d33dbc93/dqc_reference/checkm_data
[2023-03-19 02:46:18,685] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 02:46:18,687] [INFO] Task started: CheckM
[2023-03-19 02:46:18,687] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b25463/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b25463/checkm_input OceanDNA-b25463/checkm_result
[2023-03-19 02:46:34,722] [INFO] Task succeeded: CheckM
[2023-03-19 02:46:34,722] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.46%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-19 02:46:34,725] [INFO] ===== Completeness check finished =====
[2023-03-19 02:46:34,725] [INFO] ===== Start GTDB Search =====
[2023-03-19 02:46:34,725] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b25463/markers.fasta)
[2023-03-19 02:46:34,726] [INFO] Task started: Blastn
[2023-03-19 02:46:34,726] [INFO] Running command: blastn -query OceanDNA-b25463/markers.fasta -db /var/lib/cwl/stg8f66ee46-ac01-4b48-a30d-4a29d33dbc93/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b25463/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 02:46:35,772] [INFO] Task succeeded: Blastn
[2023-03-19 02:46:35,774] [INFO] Selected 22 target genomes.
[2023-03-19 02:46:35,774] [INFO] Target genome list was writen to OceanDNA-b25463/target_genomes_gtdb.txt
[2023-03-19 02:46:35,810] [INFO] Task started: fastANI
[2023-03-19 02:46:35,811] [INFO] Running command: fastANI --query /var/lib/cwl/stg52a20ef0-fef6-429f-9a6a-a0cc5d1456c8/OceanDNA-b25463.fa --refList OceanDNA-b25463/target_genomes_gtdb.txt --output OceanDNA-b25463/fastani_result_gtdb.tsv --threads 1
[2023-03-19 02:46:39,363] [INFO] Task succeeded: fastANI
[2023-03-19 02:46:39,372] [INFO] Found 15 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 02:46:39,373] [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_905612235.1	s__AG-414-E02 sp905612235	79.48	74	185	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__AG-414-E02	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905612415.1	s__AG-414-E02 sp905612415	79.2457	62	185	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__AG-414-E02	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902588625.1	s__AG-414-E02 sp902588625	78.4583	76	185	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__AG-414-E02	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004213215.1	s__AG-414-E02 sp004213215	78.4497	91	185	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__AG-414-E02	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902607585.1	s__AG-414-E02 sp902607585	78.4265	59	185	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__AG-414-E02	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902567785.1	s__AG-414-E02 sp902567785	78.3314	72	185	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__AG-414-E02	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902607625.1	s__AG-414-E02 sp902607625	78.2793	69	185	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__AG-414-E02	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902567945.1	s__AG-414-E02 sp902567945	77.851	74	185	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__AG-414-E02	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902606835.1	s__AG-414-E02 sp902606835	77.8041	83	185	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__AG-414-E02	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902588335.1	s__AG-414-E02 sp902588335	77.6404	65	185	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__AG-414-E02	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902589795.1	s__AG-414-E02 sp902589795	77.5538	69	185	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__AG-414-E02	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902590395.1	s__AG-414-E02 sp902590395	77.5072	73	185	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__AG-414-E02	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902561465.1	s__AG-414-E02 sp902561465	77.385	56	185	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__AG-414-E02	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002689925.1	s__GCA-2689925 sp002689925	77.1235	64	185	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__GCA-2689925	95.0	99.81	99.81	0.69	0.69	2	-
GCA_902606665.1	s__AG-414-E02 sp902606665	77.1025	55	185	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__AG-414-E02	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 02:46:39,373] [INFO] GTDB search result was written to OceanDNA-b25463/result_gtdb.tsv
[2023-03-19 02:46:39,373] [INFO] ===== GTDB Search completed =====
[2023-03-19 02:46:39,375] [INFO] DFAST_QC result json was written to OceanDNA-b25463/dqc_result.json
[2023-03-19 02:46:39,376] [INFO] DFAST_QC completed!
[2023-03-19 02:46:39,376] [INFO] Total running time: 0h0m30s