[2023-03-17 23:09:39,535] [INFO] DFAST_QC pipeline started.
[2023-03-17 23:09:39,535] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 23:09:39,535] [INFO] DQC Reference Directory: /var/lib/cwl/stg6331f0bf-f1f2-4568-9095-d651041d3a2e/dqc_reference
[2023-03-17 23:09:40,620] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 23:09:40,621] [INFO] Task started: Prodigal
[2023-03-17 23:09:40,621] [INFO] Running command: cat /var/lib/cwl/stg59539d7a-a454-4849-a740-297e95f53968/OceanDNA-b22246.fa | prodigal -d OceanDNA-b22246/cds.fna -a OceanDNA-b22246/protein.faa -g 11 -q > /dev/null
[2023-03-17 23:10:02,955] [INFO] Task succeeded: Prodigal
[2023-03-17 23:10:02,955] [INFO] Task started: HMMsearch
[2023-03-17 23:10:02,955] [INFO] Running command: hmmsearch --tblout OceanDNA-b22246/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6331f0bf-f1f2-4568-9095-d651041d3a2e/dqc_reference/reference_markers.hmm OceanDNA-b22246/protein.faa > /dev/null
[2023-03-17 23:10:03,147] [INFO] Task succeeded: HMMsearch
[2023-03-17 23:10:03,147] [INFO] Found 6/6 markers.
[2023-03-17 23:10:03,168] [INFO] Query marker FASTA was written to OceanDNA-b22246/markers.fasta
[2023-03-17 23:10:03,169] [INFO] Task started: Blastn
[2023-03-17 23:10:03,169] [INFO] Running command: blastn -query OceanDNA-b22246/markers.fasta -db /var/lib/cwl/stg6331f0bf-f1f2-4568-9095-d651041d3a2e/dqc_reference/reference_markers.fasta -out OceanDNA-b22246/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 23:10:03,796] [INFO] Task succeeded: Blastn
[2023-03-17 23:10:03,797] [INFO] Selected 25 target genomes.
[2023-03-17 23:10:03,797] [INFO] Target genome list was writen to OceanDNA-b22246/target_genomes.txt
[2023-03-17 23:10:03,805] [INFO] Task started: fastANI
[2023-03-17 23:10:03,805] [INFO] Running command: fastANI --query /var/lib/cwl/stg59539d7a-a454-4849-a740-297e95f53968/OceanDNA-b22246.fa --refList OceanDNA-b22246/target_genomes.txt --output OceanDNA-b22246/fastani_result.tsv --threads 1
[2023-03-17 23:10:19,216] [INFO] Task succeeded: fastANI
[2023-03-17 23:10:19,217] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6331f0bf-f1f2-4568-9095-d651041d3a2e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 23:10:19,217] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6331f0bf-f1f2-4568-9095-d651041d3a2e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 23:10:19,230] [INFO] Found 6 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 23:10:19,230] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 23:10:19,230] [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
Mucisphaera calidilacus	strain=Pan265	GCA_007748075.1	2527982	2527982	type	True	76.4947	58	1150	95	below_threshold
Algisphaera agarilytica	strain=DSM 103725	GCA_014207595.1	1385975	1385975	type	True	76.1618	71	1150	95	below_threshold
Phycisphaera mikurensis	strain=DSM 103959	GCA_014207395.1	547188	547188	type	True	75.9901	59	1150	95	below_threshold
Phycisphaera mikurensis	strain=NBRC 102666	GCA_000284115.1	547188	547188	type	True	75.9901	59	1150	95	below_threshold
Tistlia consotensis	strain=DSM 21585	GCA_900188055.1	1321365	1321365	type	True	74.68	60	1150	95	below_threshold
Tistlia consotensis	strain=USBA 355	GCA_900177295.1	1321365	1321365	type	True	74.6257	61	1150	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 23:10:19,230] [INFO] DFAST Taxonomy check result was written to OceanDNA-b22246/tc_result.tsv
[2023-03-17 23:10:19,230] [INFO] ===== Taxonomy check completed =====
[2023-03-17 23:10:19,230] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 23:10:19,230] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6331f0bf-f1f2-4568-9095-d651041d3a2e/dqc_reference/checkm_data
[2023-03-17 23:10:19,231] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 23:10:19,236] [INFO] Task started: CheckM
[2023-03-17 23:10:19,236] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b22246/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b22246/checkm_input OceanDNA-b22246/checkm_result
[2023-03-17 23:11:21,459] [INFO] Task succeeded: CheckM
[2023-03-17 23:11:21,459] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-17 23:11:21,463] [INFO] ===== Completeness check finished =====
[2023-03-17 23:11:21,463] [INFO] ===== Start GTDB Search =====
[2023-03-17 23:11:21,463] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b22246/markers.fasta)
[2023-03-17 23:11:21,463] [INFO] Task started: Blastn
[2023-03-17 23:11:21,464] [INFO] Running command: blastn -query OceanDNA-b22246/markers.fasta -db /var/lib/cwl/stg6331f0bf-f1f2-4568-9095-d651041d3a2e/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b22246/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 23:11:22,357] [INFO] Task succeeded: Blastn
[2023-03-17 23:11:22,358] [INFO] Selected 13 target genomes.
[2023-03-17 23:11:22,358] [INFO] Target genome list was writen to OceanDNA-b22246/target_genomes_gtdb.txt
[2023-03-17 23:11:22,365] [INFO] Task started: fastANI
[2023-03-17 23:11:22,365] [INFO] Running command: fastANI --query /var/lib/cwl/stg59539d7a-a454-4849-a740-297e95f53968/OceanDNA-b22246.fa --refList OceanDNA-b22246/target_genomes_gtdb.txt --output OceanDNA-b22246/fastani_result_gtdb.tsv --threads 1
[2023-03-17 23:11:29,632] [INFO] Task succeeded: fastANI
[2023-03-17 23:11:29,639] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 23:11:29,640] [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_002364005.1	s__UBA1924 sp002364005	99.9501	1083	1150	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__UBA1924	95.0	99.92	99.89	0.95	0.91	4	conclusive
GCA_002337545.1	s__UBA1924 sp002337545	81.4064	603	1150	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__UBA1924	95.0	98.57	98.49	0.90	0.89	3	-
GCA_017642965.1	s__UBA1924 sp017642965	80.7992	664	1150	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__UBA1924	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003696675.1	s__UBA6054 sp003696675	77.725	248	1150	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__UBA6054	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015487555.1	s__UBA1924 sp015487555	77.71	263	1150	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__UBA1924	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002429045.1	s__UBA6054 sp002429045	77.5117	249	1150	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__UBA6054	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017640485.1	s__UBA1924 sp017640485	77.1562	191	1150	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__UBA1924	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016764015.1	s__UBA1924 sp016764015	76.6291	153	1150	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__UBA1924	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016709445.1	s__PNC22 sp016709445	76.5997	130	1150	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__PNC22	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016763115.1	s__UBA1924 sp016763115	76.5455	129	1150	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__UBA1924	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016742075.1	s__JACVCL01 sp016742075	76.4154	84	1150	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__JACVCL01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007693965.1	s__RECQ01 sp007693965	76.0489	95	1150	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__RECQ01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 23:11:29,640] [INFO] GTDB search result was written to OceanDNA-b22246/result_gtdb.tsv
[2023-03-17 23:11:29,640] [INFO] ===== GTDB Search completed =====
[2023-03-17 23:11:29,641] [INFO] DFAST_QC result json was written to OceanDNA-b22246/dqc_result.json
[2023-03-17 23:11:29,641] [INFO] DFAST_QC completed!
[2023-03-17 23:11:29,641] [INFO] Total running time: 0h1m50s