[2023-03-18 22:25:04,422] [INFO] DFAST_QC pipeline started.
[2023-03-18 22:25:04,422] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 22:25:04,422] [INFO] DQC Reference Directory: /var/lib/cwl/stg889248e3-6960-425f-ae03-42c923f9fc07/dqc_reference
[2023-03-18 22:25:05,592] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 22:25:05,593] [INFO] Task started: Prodigal
[2023-03-18 22:25:05,593] [INFO] Running command: cat /var/lib/cwl/stgc722f15f-8db5-451b-85a5-2664e53d9c91/OceanDNA-b22250.fa | prodigal -d OceanDNA-b22250/cds.fna -a OceanDNA-b22250/protein.faa -g 11 -q > /dev/null
[2023-03-18 22:25:28,023] [INFO] Task succeeded: Prodigal
[2023-03-18 22:25:28,023] [INFO] Task started: HMMsearch
[2023-03-18 22:25:28,023] [INFO] Running command: hmmsearch --tblout OceanDNA-b22250/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg889248e3-6960-425f-ae03-42c923f9fc07/dqc_reference/reference_markers.hmm OceanDNA-b22250/protein.faa > /dev/null
[2023-03-18 22:25:28,240] [INFO] Task succeeded: HMMsearch
[2023-03-18 22:25:28,241] [INFO] Found 6/6 markers.
[2023-03-18 22:25:28,263] [INFO] Query marker FASTA was written to OceanDNA-b22250/markers.fasta
[2023-03-18 22:25:28,265] [INFO] Task started: Blastn
[2023-03-18 22:25:28,265] [INFO] Running command: blastn -query OceanDNA-b22250/markers.fasta -db /var/lib/cwl/stg889248e3-6960-425f-ae03-42c923f9fc07/dqc_reference/reference_markers.fasta -out OceanDNA-b22250/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 22:25:28,831] [INFO] Task succeeded: Blastn
[2023-03-18 22:25:28,831] [INFO] Selected 26 target genomes.
[2023-03-18 22:25:28,832] [INFO] Target genome list was writen to OceanDNA-b22250/target_genomes.txt
[2023-03-18 22:25:28,846] [INFO] Task started: fastANI
[2023-03-18 22:25:28,846] [INFO] Running command: fastANI --query /var/lib/cwl/stgc722f15f-8db5-451b-85a5-2664e53d9c91/OceanDNA-b22250.fa --refList OceanDNA-b22250/target_genomes.txt --output OceanDNA-b22250/fastani_result.tsv --threads 1
[2023-03-18 22:25:45,475] [INFO] Task succeeded: fastANI
[2023-03-18 22:25:45,476] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg889248e3-6960-425f-ae03-42c923f9fc07/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 22:25:45,476] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg889248e3-6960-425f-ae03-42c923f9fc07/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 22:25:45,485] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 22:25:45,485] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 22:25:45,485] [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	76.5697	62	1221	95	below_threshold
Algisphaera agarilytica	strain=DSM 103725	GCA_014207595.1	1385975	1385975	type	True	76.006	88	1221	95	below_threshold
Phycisphaera mikurensis	strain=DSM 103959	GCA_014207395.1	547188	547188	type	True	75.6074	117	1221	95	below_threshold
Phycisphaera mikurensis	strain=NBRC 102666	GCA_000284115.1	547188	547188	type	True	75.5862	119	1221	95	below_threshold
Humisphaera borealis	strain=M1803	GCA_015169395.1	2807512	2807512	type	True	75.4245	58	1221	95	below_threshold
Paludisphaera rhizosphaereae	strain=JC665	GCA_011065895.1	2711216	2711216	type	True	75.1091	69	1221	95	below_threshold
Nocardioides kribbensis	strain=DSM 16314	GCA_015070375.1	305517	305517	type	True	74.9887	70	1221	95	below_threshold
Tautonia plasticadhaerens	strain=ElP	GCA_007752535.1	2527974	2527974	type	True	74.9721	95	1221	95	below_threshold
Paludisphaera soli	strain=JC670	GCA_011064595.1	2712865	2712865	type	True	74.9674	98	1221	95	below_threshold
Nocardioides litoris	strain=DSM 103718	GCA_006346315.1	1926648	1926648	type	True	74.8371	82	1221	95	below_threshold
Agromyces cavernae	strain=SYSU K20354	GCA_021044935.1	2898659	2898659	type	True	74.8185	66	1221	95	below_threshold
Agromyces flavus	strain=CCM 7623	GCA_014635805.1	589382	589382	type	True	74.8012	85	1221	95	below_threshold
Gryllotalpicola ginsengisoli	strain=DSM 22003	GCA_000419445.1	444608	444608	type	True	74.7296	59	1221	95	below_threshold
Paraconexibacter algicola	strain=Seoho-28	GCA_003044185.1	2133960	2133960	type	True	74.7225	129	1221	95	below_threshold
Miltoncostaea marina	strain=SCSIO 60955	GCA_018141525.1	2843215	2843215	type	True	74.7149	78	1221	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 22:25:45,486] [INFO] DFAST Taxonomy check result was written to OceanDNA-b22250/tc_result.tsv
[2023-03-18 22:25:45,486] [INFO] ===== Taxonomy check completed =====
[2023-03-18 22:25:45,486] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 22:25:45,486] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg889248e3-6960-425f-ae03-42c923f9fc07/dqc_reference/checkm_data
[2023-03-18 22:25:45,487] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 22:25:45,557] [INFO] Task started: CheckM
[2023-03-18 22:25:45,557] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b22250/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b22250/checkm_input OceanDNA-b22250/checkm_result
[2023-03-18 22:26:47,553] [INFO] Task succeeded: CheckM
[2023-03-18 22:26:47,554] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 22:26:47,643] [INFO] ===== Completeness check finished =====
[2023-03-18 22:26:47,643] [INFO] ===== Start GTDB Search =====
[2023-03-18 22:26:47,644] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b22250/markers.fasta)
[2023-03-18 22:26:47,645] [INFO] Task started: Blastn
[2023-03-18 22:26:47,645] [INFO] Running command: blastn -query OceanDNA-b22250/markers.fasta -db /var/lib/cwl/stg889248e3-6960-425f-ae03-42c923f9fc07/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b22250/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 22:26:48,495] [INFO] Task succeeded: Blastn
[2023-03-18 22:26:48,499] [INFO] Selected 15 target genomes.
[2023-03-18 22:26:48,499] [INFO] Target genome list was writen to OceanDNA-b22250/target_genomes_gtdb.txt
[2023-03-18 22:26:48,509] [INFO] Task started: fastANI
[2023-03-18 22:26:48,510] [INFO] Running command: fastANI --query /var/lib/cwl/stgc722f15f-8db5-451b-85a5-2664e53d9c91/OceanDNA-b22250.fa --refList OceanDNA-b22250/target_genomes_gtdb.txt --output OceanDNA-b22250/fastani_result_gtdb.tsv --threads 1
[2023-03-18 22:26:57,390] [INFO] Task succeeded: fastANI
[2023-03-18 22:26:57,400] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 22:26:57,400] [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_002480345.1	s__UBA1926 sp002480345	99.8558	1097	1221	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__UBA1926	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002337215.1	s__UBA1926 sp002337215	81.2904	734	1221	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__UBA1926	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002706885.1	s__GCA-2706885 sp002706885	78.147	214	1221	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__GCA-2706885	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002429045.1	s__UBA6054 sp002429045	77.5002	211	1221	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__UBA6054	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007694925.1	s__SLFH01 sp007694925	77.2297	186	1221	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__SLFH01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002364005.1	s__UBA1924 sp002364005	77.2262	167	1221	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__UBA1924	95.0	99.92	99.89	0.95	0.91	4	-
GCA_007124345.1	s__SLFH01 sp007124345	77.184	161	1221	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__SLFH01	95.0	98.92	98.92	0.84	0.84	2	-
GCA_007693785.1	s__RECY01 sp007693785	77.1088	225	1221	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__RECY01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003696675.1	s__UBA6054 sp003696675	77.103	192	1221	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__UBA6054	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013285505.1	s__PNC22 sp013285505	77.0711	209	1221	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__PNC22	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017642965.1	s__UBA1924 sp017642965	77.0383	179	1221	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__UBA1924	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014584315.1	s__CAADGN01 sp014584315	76.6641	169	1221	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__CAADGN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900696545.1	s__CAADGN01 sp900696545	76.5415	160	1221	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__CAADGN01	95.0	99.87	99.83	0.94	0.92	3	-
GCA_008363215.1	s__J022 sp008363215	76.495	170	1221	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__J022	95.0	99.97	99.97	0.97	0.97	2	-
--------------------------------------------------------------------------------
[2023-03-18 22:26:57,402] [INFO] GTDB search result was written to OceanDNA-b22250/result_gtdb.tsv
[2023-03-18 22:26:57,403] [INFO] ===== GTDB Search completed =====
[2023-03-18 22:26:57,406] [INFO] DFAST_QC result json was written to OceanDNA-b22250/dqc_result.json
[2023-03-18 22:26:57,406] [INFO] DFAST_QC completed!
[2023-03-18 22:26:57,406] [INFO] Total running time: 0h1m53s