[2023-03-17 10:48:45,645] [INFO] DFAST_QC pipeline started.
[2023-03-17 10:48:45,645] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 10:48:45,645] [INFO] DQC Reference Directory: /var/lib/cwl/stg172cfa12-7b29-4883-8780-a64b7fa1d0df/dqc_reference
[2023-03-17 10:48:46,754] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 10:48:46,755] [INFO] Task started: Prodigal
[2023-03-17 10:48:46,755] [INFO] Running command: cat /var/lib/cwl/stg690ee703-9873-4e13-a09a-02f6b3a03d3f/OceanDNA-b22117.fa | prodigal -d OceanDNA-b22117/cds.fna -a OceanDNA-b22117/protein.faa -g 11 -q > /dev/null
[2023-03-17 10:49:06,868] [INFO] Task succeeded: Prodigal
[2023-03-17 10:49:06,868] [INFO] Task started: HMMsearch
[2023-03-17 10:49:06,869] [INFO] Running command: hmmsearch --tblout OceanDNA-b22117/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg172cfa12-7b29-4883-8780-a64b7fa1d0df/dqc_reference/reference_markers.hmm OceanDNA-b22117/protein.faa > /dev/null
[2023-03-17 10:49:07,159] [INFO] Task succeeded: HMMsearch
[2023-03-17 10:49:07,159] [INFO] Found 6/6 markers.
[2023-03-17 10:49:07,181] [INFO] Query marker FASTA was written to OceanDNA-b22117/markers.fasta
[2023-03-17 10:49:07,181] [INFO] Task started: Blastn
[2023-03-17 10:49:07,181] [INFO] Running command: blastn -query OceanDNA-b22117/markers.fasta -db /var/lib/cwl/stg172cfa12-7b29-4883-8780-a64b7fa1d0df/dqc_reference/reference_markers.fasta -out OceanDNA-b22117/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 10:49:07,807] [INFO] Task succeeded: Blastn
[2023-03-17 10:49:07,808] [INFO] Selected 24 target genomes.
[2023-03-17 10:49:07,808] [INFO] Target genome list was writen to OceanDNA-b22117/target_genomes.txt
[2023-03-17 10:49:07,870] [INFO] Task started: fastANI
[2023-03-17 10:49:07,870] [INFO] Running command: fastANI --query /var/lib/cwl/stg690ee703-9873-4e13-a09a-02f6b3a03d3f/OceanDNA-b22117.fa --refList OceanDNA-b22117/target_genomes.txt --output OceanDNA-b22117/fastani_result.tsv --threads 1
[2023-03-17 10:49:24,871] [INFO] Task succeeded: fastANI
[2023-03-17 10:49:24,871] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg172cfa12-7b29-4883-8780-a64b7fa1d0df/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 10:49:24,871] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg172cfa12-7b29-4883-8780-a64b7fa1d0df/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 10:49:24,879] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 10:49:24,879] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 10:49:24,879] [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	76.3199	66	1081	95	below_threshold
Algisphaera agarilytica	strain=DSM 103725	GCA_014207595.1	1385975	1385975	type	True	76.3058	86	1081	95	below_threshold
Humisphaera borealis	strain=M1803	GCA_015169395.1	2807512	2807512	type	True	75.7188	62	1081	95	below_threshold
Phycisphaera mikurensis	strain=DSM 103959	GCA_014207395.1	547188	547188	type	True	75.5121	94	1081	95	below_threshold
Phycisphaera mikurensis	strain=NBRC 102666	GCA_000284115.1	547188	547188	type	True	75.5019	95	1081	95	below_threshold
Tautonia plasticadhaerens	strain=ElP	GCA_007752535.1	2527974	2527974	type	True	75.2202	88	1081	95	below_threshold
Paludisphaera soli	strain=JC670	GCA_011064595.1	2712865	2712865	type	True	75.1006	73	1081	95	below_threshold
Tautonia sociabilis	strain=GM2012	GCA_003977685.1	2080755	2080755	type	True	75.0683	63	1081	95	below_threshold
Nocardioides kribbensis	strain=DSM 16314	GCA_015070375.1	305517	305517	type	True	74.9795	62	1081	95	below_threshold
Miltoncostaea marina	strain=SCSIO 60955	GCA_018141525.1	2843215	2843215	type	True	74.8597	50	1081	95	below_threshold
Pseudokineococcus lusitanus	strain=CECT 7306	GCA_003751265.1	763993	763993	type	True	74.8211	61	1081	95	below_threshold
Glycomyces xiaoerkulensis	strain=TRM 41368	GCA_002798405.1	2038139	2038139	type	True	74.6755	51	1081	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 10:49:24,879] [INFO] DFAST Taxonomy check result was written to OceanDNA-b22117/tc_result.tsv
[2023-03-17 10:49:24,879] [INFO] ===== Taxonomy check completed =====
[2023-03-17 10:49:24,879] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 10:49:24,880] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg172cfa12-7b29-4883-8780-a64b7fa1d0df/dqc_reference/checkm_data
[2023-03-17 10:49:24,880] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 10:49:24,901] [INFO] Task started: CheckM
[2023-03-17 10:49:24,901] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b22117/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b22117/checkm_input OceanDNA-b22117/checkm_result
[2023-03-17 10:50:17,378] [INFO] Task succeeded: CheckM
[2023-03-17 10:50:17,378] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 10:50:17,381] [INFO] ===== Completeness check finished =====
[2023-03-17 10:50:17,381] [INFO] ===== Start GTDB Search =====
[2023-03-17 10:50:17,382] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b22117/markers.fasta)
[2023-03-17 10:50:17,383] [INFO] Task started: Blastn
[2023-03-17 10:50:17,383] [INFO] Running command: blastn -query OceanDNA-b22117/markers.fasta -db /var/lib/cwl/stg172cfa12-7b29-4883-8780-a64b7fa1d0df/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b22117/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 10:50:18,261] [INFO] Task succeeded: Blastn
[2023-03-17 10:50:18,262] [INFO] Selected 20 target genomes.
[2023-03-17 10:50:18,263] [INFO] Target genome list was writen to OceanDNA-b22117/target_genomes_gtdb.txt
[2023-03-17 10:50:18,338] [INFO] Task started: fastANI
[2023-03-17 10:50:18,338] [INFO] Running command: fastANI --query /var/lib/cwl/stg690ee703-9873-4e13-a09a-02f6b3a03d3f/OceanDNA-b22117.fa --refList OceanDNA-b22117/target_genomes_gtdb.txt --output OceanDNA-b22117/fastani_result_gtdb.tsv --threads 1
[2023-03-17 10:50:29,276] [INFO] Task succeeded: fastANI
[2023-03-17 10:50:29,287] [INFO] Found 20 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 10:50:29,288] [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_017642965.1	s__UBA1924 sp017642965	77.5212	121	1081	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	77.1677	131	1081	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__UBA6054	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002429045.1	s__UBA6054 sp002429045	77.1061	132	1081	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__UBA6054	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007693765.1	s__RECZ01 sp007693765	77.0124	149	1081	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__RECZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016742075.1	s__JACVCL01 sp016742075	76.9969	146	1081	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__JACVCL01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013285505.1	s__PNC22 sp013285505	76.9928	171	1081	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__PNC22	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017303565.1	s__JAFLCM01 sp017303565	76.8912	124	1081	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__JAFLCM01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011331335.1	s__DSSA01 sp011331335	76.8729	129	1081	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__DSSA01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007124345.1	s__SLFH01 sp007124345	76.8088	115	1081	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__SLFH01	95.0	98.92	98.92	0.84	0.84	2	-
GCA_007693965.1	s__RECQ01 sp007693965	76.76	140	1081	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__RECQ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002364005.1	s__UBA1924 sp002364005	76.7496	106	1081	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__UBA1924	95.0	99.92	99.89	0.95	0.91	4	-
GCA_007694925.1	s__SLFH01 sp007694925	76.7289	135	1081	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__SLFH01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007693785.1	s__RECY01 sp007693785	76.4905	133	1081	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__RECY01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002343325.1	s__UBA2396 sp002343325	76.4793	85	1081	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__UBA2396	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016709445.1	s__PNC22 sp016709445	76.4318	108	1081	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__PNC22	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002480345.1	s__UBA1926 sp002480345	76.4077	133	1081	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__UBA1926	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003511945.1	s__UBA11155 sp003511945	76.3931	110	1081	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__UBA11155	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013360695.1	s__JABWBC01 sp013360695	76.2407	123	1081	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__JABWBC01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011525805.1	s__UBA5793 sp011525805	76.2347	113	1081	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA5793;g__UBA5793	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011053195.1	s__GCA-2732755 sp011053195	76.1682	72	1081	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__GCA-2732755	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 10:50:29,288] [INFO] GTDB search result was written to OceanDNA-b22117/result_gtdb.tsv
[2023-03-17 10:50:29,288] [INFO] ===== GTDB Search completed =====
[2023-03-17 10:50:29,290] [INFO] DFAST_QC result json was written to OceanDNA-b22117/dqc_result.json
[2023-03-17 10:50:29,290] [INFO] DFAST_QC completed!
[2023-03-17 10:50:29,291] [INFO] Total running time: 0h1m44s