[2023-03-14 14:21:29,838] [INFO] DFAST_QC pipeline started.
[2023-03-14 14:21:29,838] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 14:21:29,838] [INFO] DQC Reference Directory: /var/lib/cwl/stgba682132-47d8-46d5-8c58-c5b90e9d0510/dqc_reference
[2023-03-14 14:21:30,973] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 14:21:30,973] [INFO] Task started: Prodigal
[2023-03-14 14:21:30,973] [INFO] Running command: cat /var/lib/cwl/stgd90f4cdd-3a52-4a9b-a414-d34a51086091/OceanDNA-b22249.fa | prodigal -d OceanDNA-b22249/cds.fna -a OceanDNA-b22249/protein.faa -g 11 -q > /dev/null
[2023-03-14 14:21:56,087] [INFO] Task succeeded: Prodigal
[2023-03-14 14:21:56,088] [INFO] Task started: HMMsearch
[2023-03-14 14:21:56,088] [INFO] Running command: hmmsearch --tblout OceanDNA-b22249/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgba682132-47d8-46d5-8c58-c5b90e9d0510/dqc_reference/reference_markers.hmm OceanDNA-b22249/protein.faa > /dev/null
[2023-03-14 14:21:56,312] [INFO] Task succeeded: HMMsearch
[2023-03-14 14:21:56,313] [INFO] Found 6/6 markers.
[2023-03-14 14:21:56,333] [INFO] Query marker FASTA was written to OceanDNA-b22249/markers.fasta
[2023-03-14 14:21:56,333] [INFO] Task started: Blastn
[2023-03-14 14:21:56,333] [INFO] Running command: blastn -query OceanDNA-b22249/markers.fasta -db /var/lib/cwl/stgba682132-47d8-46d5-8c58-c5b90e9d0510/dqc_reference/reference_markers.fasta -out OceanDNA-b22249/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 14:21:56,950] [INFO] Task succeeded: Blastn
[2023-03-14 14:21:56,952] [INFO] Selected 28 target genomes.
[2023-03-14 14:21:56,952] [INFO] Target genome list was writen to OceanDNA-b22249/target_genomes.txt
[2023-03-14 14:21:57,010] [INFO] Task started: fastANI
[2023-03-14 14:21:57,010] [INFO] Running command: fastANI --query /var/lib/cwl/stgd90f4cdd-3a52-4a9b-a414-d34a51086091/OceanDNA-b22249.fa --refList OceanDNA-b22249/target_genomes.txt --output OceanDNA-b22249/fastani_result.tsv --threads 1
[2023-03-14 14:22:26,622] [INFO] Task succeeded: fastANI
[2023-03-14 14:22:26,622] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgba682132-47d8-46d5-8c58-c5b90e9d0510/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 14:22:26,622] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgba682132-47d8-46d5-8c58-c5b90e9d0510/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 14:22:26,632] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 14:22:26,632] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-14 14:22:26,632] [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
Algisphaera agarilytica	strain=DSM 103725	GCA_014207595.1	1385975	1385975	type	True	75.9079	85	1165	95	below_threshold
Mucisphaera calidilacus	strain=Pan265	GCA_007748075.1	2527982	2527982	type	True	75.8779	56	1165	95	below_threshold
Phycisphaera mikurensis	strain=DSM 103959	GCA_014207395.1	547188	547188	type	True	75.7378	103	1165	95	below_threshold
Phycisphaera mikurensis	strain=NBRC 102666	GCA_000284115.1	547188	547188	type	True	75.7374	105	1165	95	below_threshold
Paludisphaera rhizosphaereae	strain=JC665	GCA_011065895.1	2711216	2711216	type	True	75.3287	72	1165	95	below_threshold
Posidoniimonas corsicana	strain=KOR34	GCA_007859765.1	1938618	1938618	type	True	75.2241	72	1165	95	below_threshold
Paludisphaera soli	strain=JC670	GCA_011064595.1	2712865	2712865	type	True	75.1966	83	1165	95	below_threshold
Humisphaera borealis	strain=M1803	GCA_015169395.1	2807512	2807512	type	True	75.0772	65	1165	95	below_threshold
Pseudokineococcus marinus	strain=JCM 14547	GCA_013004605.1	351215	351215	type	True	75.0642	55	1165	95	below_threshold
Lutibaculum baratangense	strain=AMV1	GCA_000496075.1	1358440	1358440	type	True	74.8518	52	1165	95	below_threshold
Amnibacterium kyonggiense	strain=DSM 24782	GCA_004364555.1	595671	595671	type	True	74.7655	63	1165	95	below_threshold
Glycomyces paridis	strain=CPCC 204357	GCA_004912155.1	2126555	2126555	type	True	74.7607	79	1165	95	below_threshold
Tistlia consotensis	strain=DSM 21585	GCA_900188055.1	1321365	1321365	type	True	74.7425	96	1165	95	below_threshold
Aquibium microcysteis	strain=NIBR3	GCA_014495845.1	675281	675281	type	True	74.7344	54	1165	95	below_threshold
Tistlia consotensis	strain=USBA 355	GCA_900177295.1	1321365	1321365	type	True	74.727	93	1165	95	below_threshold
Virgisporangium aurantiacum	strain=NBRC 16421	GCA_016863635.1	175570	175570	type	True	74.6051	139	1165	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-14 14:22:26,633] [INFO] DFAST Taxonomy check result was written to OceanDNA-b22249/tc_result.tsv
[2023-03-14 14:22:26,633] [INFO] ===== Taxonomy check completed =====
[2023-03-14 14:22:26,633] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 14:22:26,633] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgba682132-47d8-46d5-8c58-c5b90e9d0510/dqc_reference/checkm_data
[2023-03-14 14:22:26,634] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 14:22:26,999] [INFO] Task started: CheckM
[2023-03-14 14:22:26,999] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b22249/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b22249/checkm_input OceanDNA-b22249/checkm_result
[2023-03-14 14:23:37,110] [INFO] Task succeeded: CheckM
[2023-03-14 14:23:37,111] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 14:23:37,120] [INFO] ===== Completeness check finished =====
[2023-03-14 14:23:37,120] [INFO] ===== Start GTDB Search =====
[2023-03-14 14:23:37,120] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b22249/markers.fasta)
[2023-03-14 14:23:37,121] [INFO] Task started: Blastn
[2023-03-14 14:23:37,121] [INFO] Running command: blastn -query OceanDNA-b22249/markers.fasta -db /var/lib/cwl/stgba682132-47d8-46d5-8c58-c5b90e9d0510/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b22249/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 14:23:38,198] [INFO] Task succeeded: Blastn
[2023-03-14 14:23:38,200] [INFO] Selected 13 target genomes.
[2023-03-14 14:23:38,200] [INFO] Target genome list was writen to OceanDNA-b22249/target_genomes_gtdb.txt
[2023-03-14 14:23:38,232] [INFO] Task started: fastANI
[2023-03-14 14:23:38,232] [INFO] Running command: fastANI --query /var/lib/cwl/stgd90f4cdd-3a52-4a9b-a414-d34a51086091/OceanDNA-b22249.fa --refList OceanDNA-b22249/target_genomes_gtdb.txt --output OceanDNA-b22249/fastani_result_gtdb.tsv --threads 1
[2023-03-14 14:23:46,144] [INFO] Task succeeded: fastANI
[2023-03-14 14:23:46,152] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-14 14:23:46,152] [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_002337215.1	s__UBA1926 sp002337215	99.9192	1123	1165	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_002480345.1	s__UBA1926 sp002480345	81.3982	691	1165	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	77.7566	208	1165	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	77.1936	192	1165	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__UBA6054	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017642965.1	s__UBA1924 sp017642965	77.1194	151	1165	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__UBA1924	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007124345.1	s__SLFH01 sp007124345	77.0711	122	1165	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__SLFH01	95.0	98.92	98.92	0.84	0.84	2	-
GCA_013285505.1	s__PNC22 sp013285505	77.0571	195	1165	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__PNC22	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003696675.1	s__UBA6054 sp003696675	77.0268	165	1165	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__UBA6054	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007693785.1	s__RECY01 sp007693785	76.6782	204	1165	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__RECY01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900696545.1	s__CAADGN01 sp900696545	76.4722	151	1165	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	76.3408	129	1165	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__J022	95.0	99.97	99.97	0.97	0.97	2	-
GCA_007693765.1	s__RECZ01 sp007693765	76.3332	137	1165	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__RECZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016125285.1	s__RI-212 sp016125285	75.7452	121	1165	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__Zrk34;g__RI-212	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-14 14:23:46,153] [INFO] GTDB search result was written to OceanDNA-b22249/result_gtdb.tsv
[2023-03-14 14:23:46,153] [INFO] ===== GTDB Search completed =====
[2023-03-14 14:23:46,155] [INFO] DFAST_QC result json was written to OceanDNA-b22249/dqc_result.json
[2023-03-14 14:23:46,155] [INFO] DFAST_QC completed!
[2023-03-14 14:23:46,156] [INFO] Total running time: 0h2m16s