[2023-03-16 19:49:08,468] [INFO] DFAST_QC pipeline started.
[2023-03-16 19:49:08,468] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 19:49:08,468] [INFO] DQC Reference Directory: /var/lib/cwl/stgeaf6b422-1175-4299-87aa-d62b16fb043d/dqc_reference
[2023-03-16 19:49:09,566] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 19:49:09,566] [INFO] Task started: Prodigal
[2023-03-16 19:49:09,566] [INFO] Running command: cat /var/lib/cwl/stg1fd8c874-07fe-4375-a76c-2184a76ff9ea/OceanDNA-b33300.fa | prodigal -d OceanDNA-b33300/cds.fna -a OceanDNA-b33300/protein.faa -g 11 -q > /dev/null
[2023-03-16 19:49:19,498] [INFO] Task succeeded: Prodigal
[2023-03-16 19:49:19,498] [INFO] Task started: HMMsearch
[2023-03-16 19:49:19,499] [INFO] Running command: hmmsearch --tblout OceanDNA-b33300/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgeaf6b422-1175-4299-87aa-d62b16fb043d/dqc_reference/reference_markers.hmm OceanDNA-b33300/protein.faa > /dev/null
[2023-03-16 19:49:19,685] [INFO] Task succeeded: HMMsearch
[2023-03-16 19:49:19,686] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg1fd8c874-07fe-4375-a76c-2184a76ff9ea/OceanDNA-b33300.fa]
[2023-03-16 19:49:19,704] [INFO] Query marker FASTA was written to OceanDNA-b33300/markers.fasta
[2023-03-16 19:49:19,705] [INFO] Task started: Blastn
[2023-03-16 19:49:19,705] [INFO] Running command: blastn -query OceanDNA-b33300/markers.fasta -db /var/lib/cwl/stgeaf6b422-1175-4299-87aa-d62b16fb043d/dqc_reference/reference_markers.fasta -out OceanDNA-b33300/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 19:49:20,484] [INFO] Task succeeded: Blastn
[2023-03-16 19:49:20,489] [INFO] Selected 21 target genomes.
[2023-03-16 19:49:20,490] [INFO] Target genome list was writen to OceanDNA-b33300/target_genomes.txt
[2023-03-16 19:49:20,503] [INFO] Task started: fastANI
[2023-03-16 19:49:20,504] [INFO] Running command: fastANI --query /var/lib/cwl/stg1fd8c874-07fe-4375-a76c-2184a76ff9ea/OceanDNA-b33300.fa --refList OceanDNA-b33300/target_genomes.txt --output OceanDNA-b33300/fastani_result.tsv --threads 1
[2023-03-16 19:49:36,640] [INFO] Task succeeded: fastANI
[2023-03-16 19:49:36,641] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgeaf6b422-1175-4299-87aa-d62b16fb043d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 19:49:36,641] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgeaf6b422-1175-4299-87aa-d62b16fb043d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 19:49:36,653] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 19:49:36,653] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 19:49:36,653] [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
Acidovorax wautersii	strain=DSM 27981	GCA_900113035.1	1177982	1177982	type	True	82.5145	326	388	95	below_threshold
Acidovorax caeni	strain=R-24608	GCA_900116825.1	343013	343013	type	True	82.2009	269	388	95	below_threshold
Melaminivora alkalimesophila	strain=CY1	GCA_000282995.1	1165852	1165852	type	True	82.1767	219	388	95	below_threshold
Acidovorax caeni	strain=R-24608	GCA_001298675.1	343013	343013	type	True	82.1062	273	388	95	below_threshold
Melaminivora alkalimesophila	strain=DSM 26006	GCA_003182375.1	1165852	1165852	type	True	82.0194	282	388	95	below_threshold
Acidovorax anthurii	strain=CFPB 3232	GCA_003269065.1	78229	78229	type	True	81.9943	297	388	95	below_threshold
Melaminivora jejuensis	strain=KCTC 32230	GCA_017811175.1	1267217	1267217	type	True	81.7684	282	388	95	below_threshold
Acidovorax oryzae	strain=ATCC 19882	GCA_000687165.1	862720	862720	type	True	81.6002	294	388	95	below_threshold
Comamonas phosphati	strain=CGMCC 1.12294	GCA_014637085.1	1211803	1211803	type	True	81.5297	244	388	95	below_threshold
Delftia acidovorans	strain=FDAARGOS_997	GCA_016127415.1	80866	80866	type	True	81.5256	280	388	95	below_threshold
Delftia acidovorans	strain=NBRC 14950	GCA_001598795.1	80866	80866	type	True	81.4613	283	388	95	below_threshold
Acidovorax cattleyae	strain=DSM 17101	GCA_900104515.1	80868	80868	type	True	81.3994	300	388	95	below_threshold
Acidovorax facilis	strain=DSM 649	GCA_023913775.1	12917	12917	type	True	80.8701	300	388	95	below_threshold
Pseudorhodoferax aquiterrae	strain=KCTC 23314	GCA_014652235.1	747304	747304	type	True	80.2567	271	388	95	below_threshold
Diaphorobacter caeni	strain=NR2-3-3-1	GCA_015354245.1	2784387	2784387	type	True	80.1494	284	388	95	below_threshold
Simplicispira metamorpha	strain=NBRC 13960	GCA_003568725.1	80881	80881	type	True	80.0408	238	388	95	below_threshold
Diaphorobacter aerolatus	strain=KACC 16536	GCA_014489535.1	1288495	1288495	type	True	80.0351	243	388	95	below_threshold
Hydrogenophaga crocea	strain=BA0156	GCA_011388215.1	2716225	2716225	type	True	79.891	234	388	95	below_threshold
Ramlibacter agri	strain=G-1-2-2	GCA_012927085.1	2728837	2728837	type	True	79.3381	240	388	95	below_threshold
Ramlibacter pinisoli	strain=MAH-25	GCA_009758015.1	2682844	2682844	type	True	79.1883	244	388	95	below_threshold
Xylophilus ampelinus	strain=CFBP 1192	GCA_024832295.1	54067	54067	type	True	79.0271	196	388	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 19:49:36,654] [INFO] DFAST Taxonomy check result was written to OceanDNA-b33300/tc_result.tsv
[2023-03-16 19:49:36,654] [INFO] ===== Taxonomy check completed =====
[2023-03-16 19:49:36,654] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 19:49:36,654] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgeaf6b422-1175-4299-87aa-d62b16fb043d/dqc_reference/checkm_data
[2023-03-16 19:49:36,655] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 19:49:36,704] [INFO] Task started: CheckM
[2023-03-16 19:49:36,704] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b33300/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b33300/checkm_input OceanDNA-b33300/checkm_result
[2023-03-16 19:50:05,482] [INFO] Task succeeded: CheckM
[2023-03-16 19:50:05,482] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 68.07%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 19:50:05,485] [INFO] ===== Completeness check finished =====
[2023-03-16 19:50:05,485] [INFO] ===== Start GTDB Search =====
[2023-03-16 19:50:05,486] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b33300/markers.fasta)
[2023-03-16 19:50:05,486] [INFO] Task started: Blastn
[2023-03-16 19:50:05,486] [INFO] Running command: blastn -query OceanDNA-b33300/markers.fasta -db /var/lib/cwl/stgeaf6b422-1175-4299-87aa-d62b16fb043d/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b33300/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 19:50:07,044] [INFO] Task succeeded: Blastn
[2023-03-16 19:50:07,046] [INFO] Selected 17 target genomes.
[2023-03-16 19:50:07,046] [INFO] Target genome list was writen to OceanDNA-b33300/target_genomes_gtdb.txt
[2023-03-16 19:50:07,065] [INFO] Task started: fastANI
[2023-03-16 19:50:07,065] [INFO] Running command: fastANI --query /var/lib/cwl/stg1fd8c874-07fe-4375-a76c-2184a76ff9ea/OceanDNA-b33300.fa --refList OceanDNA-b33300/target_genomes_gtdb.txt --output OceanDNA-b33300/fastani_result_gtdb.tsv --threads 1
[2023-03-16 19:50:20,045] [INFO] Task succeeded: fastANI
[2023-03-16 19:50:20,055] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 19:50:20,055] [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_003755025.1	s__Diaphorobacter nitroreducens	97.6205	370	388	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Diaphorobacter	95.0	98.11	97.62	0.91	0.81	15	conclusive
GCF_000204645.1	s__Alicycliphilus denitrificans	85.1401	340	388	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Alicycliphilus	95.0	97.26	95.80	0.83	0.76	8	-
GCF_000400995.2	s__MR-S7 sp000400995	85.0065	346	388	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__MR-S7	95.0	97.31	97.31	0.83	0.83	2	-
GCA_002434305.1	s__Pulveribacter sp002434305	83.5475	313	388	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pulveribacter	95.0	97.39	97.21	0.93	0.92	3	-
GCA_018242005.1	s__Alicycliphilus sp018242005	83.0672	311	388	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Alicycliphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001725235.1	s__Acidovorax_C sp001725235	82.9543	292	388	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax_C	95.0	98.36	96.90	0.87	0.83	3	-
GCF_014489595.1	s__Acidovorax_F monticola	82.8081	333	388	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax_F	95.0	97.51	97.51	0.93	0.93	2	-
GCF_900113035.1	s__Acidovorax_A wautersii	82.5396	325	388	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003604195.1	s__Giesbergeria lacusdiani	82.4914	283	388	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Giesbergeria	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018240985.1	s__Alicycliphilus sp018240985	82.4812	295	388	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Alicycliphilus	95.0	99.65	99.65	0.85	0.85	2	-
GCA_018240995.1	s__Alicycliphilus sp018240995	82.4048	265	388	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Alicycliphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003269065.1	s__Acidovorax_A anthurii	82.0715	294	388	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017811175.1	s__Melaminivora_A jejuensis	81.7684	282	388	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Melaminivora_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000176855.2	s__Acidovorax_A avenae	81.6326	297	388	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax_A	95.2137	96.92	95.92	0.74	0.51	18	-
GCF_900104515.1	s__Acidovorax_A cattleyae	81.4187	300	388	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax_A	95.0	99.69	99.69	0.82	0.82	2	-
GCA_016192425.1	s__Giesbergeria sp016192425	81.4118	257	388	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Giesbergeria	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017998575.1	s__JAGOCV01 sp017998575	79.6961	191	388	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__JAGOCV01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 19:50:20,056] [INFO] GTDB search result was written to OceanDNA-b33300/result_gtdb.tsv
[2023-03-16 19:50:20,056] [INFO] ===== GTDB Search completed =====
[2023-03-16 19:50:20,058] [INFO] DFAST_QC result json was written to OceanDNA-b33300/dqc_result.json
[2023-03-16 19:50:20,059] [INFO] DFAST_QC completed!
[2023-03-16 19:50:20,059] [INFO] Total running time: 0h1m12s