[2023-03-18 23:27:53,713] [INFO] DFAST_QC pipeline started.
[2023-03-18 23:27:53,713] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 23:27:53,713] [INFO] DQC Reference Directory: /var/lib/cwl/stgda913b6b-2164-41f0-85ab-92e34be9329d/dqc_reference
[2023-03-18 23:27:55,544] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 23:27:55,545] [INFO] Task started: Prodigal
[2023-03-18 23:27:55,545] [INFO] Running command: cat /var/lib/cwl/stgef1abbf4-e8fa-4855-b6d5-313f19087c99/OceanDNA-b22205.fa | prodigal -d OceanDNA-b22205/cds.fna -a OceanDNA-b22205/protein.faa -g 11 -q > /dev/null
[2023-03-18 23:28:07,979] [INFO] Task succeeded: Prodigal
[2023-03-18 23:28:07,980] [INFO] Task started: HMMsearch
[2023-03-18 23:28:07,980] [INFO] Running command: hmmsearch --tblout OceanDNA-b22205/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgda913b6b-2164-41f0-85ab-92e34be9329d/dqc_reference/reference_markers.hmm OceanDNA-b22205/protein.faa > /dev/null
[2023-03-18 23:28:08,171] [INFO] Task succeeded: HMMsearch
[2023-03-18 23:28:08,171] [INFO] Found 6/6 markers.
[2023-03-18 23:28:08,192] [INFO] Query marker FASTA was written to OceanDNA-b22205/markers.fasta
[2023-03-18 23:28:08,193] [INFO] Task started: Blastn
[2023-03-18 23:28:08,193] [INFO] Running command: blastn -query OceanDNA-b22205/markers.fasta -db /var/lib/cwl/stgda913b6b-2164-41f0-85ab-92e34be9329d/dqc_reference/reference_markers.fasta -out OceanDNA-b22205/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:28:08,757] [INFO] Task succeeded: Blastn
[2023-03-18 23:28:08,758] [INFO] Selected 17 target genomes.
[2023-03-18 23:28:08,758] [INFO] Target genome list was writen to OceanDNA-b22205/target_genomes.txt
[2023-03-18 23:28:08,768] [INFO] Task started: fastANI
[2023-03-18 23:28:08,768] [INFO] Running command: fastANI --query /var/lib/cwl/stgef1abbf4-e8fa-4855-b6d5-313f19087c99/OceanDNA-b22205.fa --refList OceanDNA-b22205/target_genomes.txt --output OceanDNA-b22205/fastani_result.tsv --threads 1
[2023-03-18 23:28:22,175] [INFO] Task succeeded: fastANI
[2023-03-18 23:28:22,176] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgda913b6b-2164-41f0-85ab-92e34be9329d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 23:28:22,176] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgda913b6b-2164-41f0-85ab-92e34be9329d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 23:28:22,182] [INFO] Found 6 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 23:28:22,182] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 23:28:22,182] [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
Phycisphaera mikurensis	strain=NBRC 102666	GCA_000284115.1	547188	547188	type	True	75.1673	61	647	95	below_threshold
Phycisphaera mikurensis	strain=DSM 103959	GCA_014207395.1	547188	547188	type	True	75.1546	62	647	95	below_threshold
Tautonia plasticadhaerens	strain=ElP	GCA_007752535.1	2527974	2527974	type	True	74.8999	60	647	95	below_threshold
Tistlia consotensis	strain=USBA 355	GCA_900177295.1	1321365	1321365	type	True	74.8846	58	647	95	below_threshold
Tistlia consotensis	strain=DSM 21585	GCA_900188055.1	1321365	1321365	type	True	74.8766	59	647	95	below_threshold
Paludisphaera soli	strain=JC670	GCA_011064595.1	2712865	2712865	type	True	74.8084	67	647	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 23:28:22,182] [INFO] DFAST Taxonomy check result was written to OceanDNA-b22205/tc_result.tsv
[2023-03-18 23:28:22,182] [INFO] ===== Taxonomy check completed =====
[2023-03-18 23:28:22,182] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 23:28:22,182] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgda913b6b-2164-41f0-85ab-92e34be9329d/dqc_reference/checkm_data
[2023-03-18 23:28:22,183] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 23:28:22,188] [INFO] Task started: CheckM
[2023-03-18 23:28:22,188] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b22205/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b22205/checkm_input OceanDNA-b22205/checkm_result
[2023-03-18 23:28:57,690] [INFO] Task succeeded: CheckM
[2023-03-18 23:28:57,690] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.96%
Contamintation: 0.38%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 23:28:57,693] [INFO] ===== Completeness check finished =====
[2023-03-18 23:28:57,693] [INFO] ===== Start GTDB Search =====
[2023-03-18 23:28:57,693] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b22205/markers.fasta)
[2023-03-18 23:28:57,694] [INFO] Task started: Blastn
[2023-03-18 23:28:57,694] [INFO] Running command: blastn -query OceanDNA-b22205/markers.fasta -db /var/lib/cwl/stgda913b6b-2164-41f0-85ab-92e34be9329d/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b22205/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:28:58,564] [INFO] Task succeeded: Blastn
[2023-03-18 23:28:58,565] [INFO] Selected 11 target genomes.
[2023-03-18 23:28:58,565] [INFO] Target genome list was writen to OceanDNA-b22205/target_genomes_gtdb.txt
[2023-03-18 23:28:58,578] [INFO] Task started: fastANI
[2023-03-18 23:28:58,578] [INFO] Running command: fastANI --query /var/lib/cwl/stgef1abbf4-e8fa-4855-b6d5-313f19087c99/OceanDNA-b22205.fa --refList OceanDNA-b22205/target_genomes_gtdb.txt --output OceanDNA-b22205/fastani_result_gtdb.tsv --threads 1
[2023-03-18 23:29:04,878] [INFO] Task succeeded: fastANI
[2023-03-18 23:29:04,885] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 23:29:04,885] [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_002684855.1	s__UBA12014 sp002684855	98.7971	447	647	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__UBA12014	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002690755.1	s__UBA12014 sp002690755	84.0099	524	647	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__UBA12014	95.0	99.96	99.96	0.92	0.92	2	-
GCA_002684755.1	s__UBA12014 sp002684755	83.3499	434	647	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__UBA12014	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002683215.1	s__UBA12014 sp002683215	83.3156	412	647	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__UBA12014	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009936695.1	s__UBA12014 sp009936695	83.136	400	647	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__UBA12014	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002167845.2	s__UBA12014 sp002167845	79.2672	313	647	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__UBA12014	95.0	99.48	99.48	0.92	0.92	2	-
GCA_014237965.1	s__UBA12014 sp014237965	79.019	286	647	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__UBA12014	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002709295.1	s__GCA-002862325 sp002709295	78.4298	263	647	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__GCA-002862325	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002862325.1	s__GCA-002862325 sp002862325	78.0497	162	647	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__GCA-002862325	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905480395.1	s__UBA12014 sp905480395	77.5974	219	647	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__UBA12014	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 23:29:04,885] [INFO] GTDB search result was written to OceanDNA-b22205/result_gtdb.tsv
[2023-03-18 23:29:04,885] [INFO] ===== GTDB Search completed =====
[2023-03-18 23:29:04,886] [INFO] DFAST_QC result json was written to OceanDNA-b22205/dqc_result.json
[2023-03-18 23:29:04,887] [INFO] DFAST_QC completed!
[2023-03-18 23:29:04,887] [INFO] Total running time: 0h1m11s