[2023-03-17 11:25:37,083] [INFO] DFAST_QC pipeline started.
[2023-03-17 11:25:37,083] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 11:25:37,084] [INFO] DQC Reference Directory: /var/lib/cwl/stgbf08100a-ea6a-43ed-b5c4-6b52a274ee43/dqc_reference
[2023-03-17 11:25:38,185] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 11:25:38,185] [INFO] Task started: Prodigal
[2023-03-17 11:25:38,186] [INFO] Running command: cat /var/lib/cwl/stgc33d8397-4a4c-4487-91b8-07ef8dc8d370/OceanDNA-b33393.fa | prodigal -d OceanDNA-b33393/cds.fna -a OceanDNA-b33393/protein.faa -g 11 -q > /dev/null
[2023-03-17 11:26:08,125] [INFO] Task succeeded: Prodigal
[2023-03-17 11:26:08,125] [INFO] Task started: HMMsearch
[2023-03-17 11:26:08,125] [INFO] Running command: hmmsearch --tblout OceanDNA-b33393/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbf08100a-ea6a-43ed-b5c4-6b52a274ee43/dqc_reference/reference_markers.hmm OceanDNA-b33393/protein.faa > /dev/null
[2023-03-17 11:26:08,375] [INFO] Task succeeded: HMMsearch
[2023-03-17 11:26:08,375] [INFO] Found 6/6 markers.
[2023-03-17 11:26:08,417] [INFO] Query marker FASTA was written to OceanDNA-b33393/markers.fasta
[2023-03-17 11:26:08,418] [INFO] Task started: Blastn
[2023-03-17 11:26:08,418] [INFO] Running command: blastn -query OceanDNA-b33393/markers.fasta -db /var/lib/cwl/stgbf08100a-ea6a-43ed-b5c4-6b52a274ee43/dqc_reference/reference_markers.fasta -out OceanDNA-b33393/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 11:26:09,329] [INFO] Task succeeded: Blastn
[2023-03-17 11:26:09,334] [INFO] Selected 28 target genomes.
[2023-03-17 11:26:09,334] [INFO] Target genome list was writen to OceanDNA-b33393/target_genomes.txt
[2023-03-17 11:26:09,351] [INFO] Task started: fastANI
[2023-03-17 11:26:09,352] [INFO] Running command: fastANI --query /var/lib/cwl/stgc33d8397-4a4c-4487-91b8-07ef8dc8d370/OceanDNA-b33393.fa --refList OceanDNA-b33393/target_genomes.txt --output OceanDNA-b33393/fastani_result.tsv --threads 1
[2023-03-17 11:26:38,232] [INFO] Task succeeded: fastANI
[2023-03-17 11:26:38,233] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbf08100a-ea6a-43ed-b5c4-6b52a274ee43/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 11:26:38,233] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbf08100a-ea6a-43ed-b5c4-6b52a274ee43/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 11:26:38,248] [INFO] Found 28 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 11:26:38,248] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 11:26:38,248] [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
Pelomonas saccharophila	strain=DSM 654	GCA_004342485.1	304	304	type	True	86.9537	1074	1605	95	below_threshold
Pelomonas puraquae	strain=CCUG 52769	GCA_002205845.1	431059	431059	type	True	85.7238	1123	1605	95	below_threshold
Mitsuaria chitinivorans	strain=HWN-4	GCA_002761755.1	2917965	2917965	type	True	81.0369	842	1605	95	below_threshold
Roseateles depolymerans	strain=DSM 11813	GCA_003387155.1	76731	76731	type	True	80.509	707	1605	95	below_threshold
Schlegelella thermodepolymerans	strain=DSM 15344	GCA_002933415.1	215580	215580	type	True	80.4905	616	1605	95	below_threshold
Schlegelella thermodepolymerans	strain=DSM 15344	GCA_003349825.1	215580	215580	type	True	80.4372	631	1605	95	below_threshold
Schlegelella thermodepolymerans	strain=DSM 15344	GCA_015476235.1	215580	215580	type	True	80.3985	637	1605	95	below_threshold
Ideonella dechloratans	strain=CCUG 30977	GCA_021049305.1	36863	36863	type	True	80.3118	684	1605	95	below_threshold
Rubrivivax benzoatilyticus	strain=JA2	GCA_000190375.2	316997	316997	type	True	80.2548	679	1605	95	below_threshold
Rubrivivax benzoatilyticus	strain=JA2	GCA_000420125.1	316997	316997	type	True	80.2391	694	1605	95	below_threshold
Rubrivivax gelatinosus	strain=DSM 1709	GCA_004340905.1	28068	28068	suspected-type	True	80.1638	735	1605	95	below_threshold
Paucibacter toxinivorans	strain=DSM 16998	GCA_004362525.1	270368	270368	type	True	80.1492	799	1605	95	below_threshold
Rubrivivax gelatinosus	strain=DSM 1709	GCA_016583525.1	28068	28068	suspected-type	True	80.1088	736	1605	95	below_threshold
Ideonella benzenivorans	strain=B7	GCA_020387415.1	2831643	2831643	type	True	80.0272	638	1605	95	below_threshold
Sphaerotilus sulfidivorans	strain=D-501	GCA_013426975.1	639200	639200	type	True	80.0184	678	1605	95	below_threshold
Inhella crocodyli	strain=CCP-18	GCA_004004565.1	2499851	2499851	type	True	79.9306	644	1605	95	below_threshold
Roseateles terrae	strain=CECT 7247	GCA_014192155.1	431060	431060	type	True	79.8935	661	1605	95	below_threshold
Rhizobacter gummiphilus	strain=NBRC 109400	GCA_002762215.1	946333	946333	type	True	79.6641	674	1605	95	below_threshold
Inhella inkyongensis	strain=IMCC1713	GCA_005952805.1	392593	392593	type	True	79.5485	554	1605	95	below_threshold
Inhella inkyongensis	strain=DSM 23958	GCA_014202795.1	392593	392593	type	True	79.448	561	1605	95	below_threshold
Ramlibacter pinisoli	strain=MAH-25	GCA_009758015.1	2682844	2682844	type	True	79.4061	595	1605	95	below_threshold
Variovorax soli	strain=NBRC 106424	GCA_001591385.1	376815	376815	type	True	79.396	596	1605	95	below_threshold
Schlegelella brevitalea	strain=DSM 7029	GCA_001017435.1	413882	413882	type	True	79.1272	608	1605	95	below_threshold
Massilia solisilvae	strain=JCM 31607	GCA_024753215.1	1811225	1811225	type	True	77.3569	466	1605	95	below_threshold
Massilia agilis	strain=JCM 31605	GCA_024756255.1	1811226	1811226	type	True	77.198	486	1605	95	below_threshold
Derxia gummosa	strain=DSM 723	GCA_000482785.1	203699	203699	type	True	77.0699	479	1605	95	below_threshold
Duganella aceris	strain=SAP-35	GCA_011090165.1	2703883	2703883	type	True	76.8323	573	1605	95	below_threshold
Duganella margarita	strain=FT109W	GCA_009857535.1	2692170	2692170	type	True	76.6148	451	1605	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 11:26:38,253] [INFO] DFAST Taxonomy check result was written to OceanDNA-b33393/tc_result.tsv
[2023-03-17 11:26:38,258] [INFO] ===== Taxonomy check completed =====
[2023-03-17 11:26:38,258] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 11:26:38,258] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbf08100a-ea6a-43ed-b5c4-6b52a274ee43/dqc_reference/checkm_data
[2023-03-17 11:26:38,259] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 11:26:38,272] [INFO] Task started: CheckM
[2023-03-17 11:26:38,272] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b33393/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b33393/checkm_input OceanDNA-b33393/checkm_result
[2023-03-17 11:28:05,077] [INFO] Task succeeded: CheckM
[2023-03-17 11:28:05,077] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 11:28:05,206] [INFO] ===== Completeness check finished =====
[2023-03-17 11:28:05,206] [INFO] ===== Start GTDB Search =====
[2023-03-17 11:28:05,206] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b33393/markers.fasta)
[2023-03-17 11:28:05,208] [INFO] Task started: Blastn
[2023-03-17 11:28:05,208] [INFO] Running command: blastn -query OceanDNA-b33393/markers.fasta -db /var/lib/cwl/stgbf08100a-ea6a-43ed-b5c4-6b52a274ee43/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b33393/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 11:28:06,939] [INFO] Task succeeded: Blastn
[2023-03-17 11:28:06,949] [INFO] Selected 17 target genomes.
[2023-03-17 11:28:06,949] [INFO] Target genome list was writen to OceanDNA-b33393/target_genomes_gtdb.txt
[2023-03-17 11:28:06,966] [INFO] Task started: fastANI
[2023-03-17 11:28:06,966] [INFO] Running command: fastANI --query /var/lib/cwl/stgc33d8397-4a4c-4487-91b8-07ef8dc8d370/OceanDNA-b33393.fa --refList OceanDNA-b33393/target_genomes_gtdb.txt --output OceanDNA-b33393/fastani_result_gtdb.tsv --threads 1
[2023-03-17 11:28:29,054] [INFO] Task succeeded: fastANI
[2023-03-17 11:28:29,064] [INFO] Found 17 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 11:28:29,064] [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_009996515.1	s__Pelomonas sp009996515	87.8503	1033	1605	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pelomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001426885.1	s__Pelomonas sp001426885	87.709	1158	1605	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pelomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004342485.1	s__Pelomonas saccharophila	87.0009	1070	1605	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pelomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019237615.1	s__Pelomonas sp019237615	86.9517	994	1605	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pelomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016195825.1	s__Pelomonas sp016195825	86.5994	1110	1605	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pelomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003550215.1	s__Pelomonas sp003550215	86.368	1108	1605	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pelomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016790285.1	s__Pelomonas sp016790285	86.3583	1065	1605	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pelomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001425165.1	s__Pelomonas sp001425165	86.1262	1122	1605	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pelomonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001425705.1	s__Pelomonas sp001425705	85.9442	1123	1605	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pelomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001425055.1	s__Pelomonas sp001425055	85.9068	1135	1605	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pelomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002205845.1	s__Pelomonas puraquae	85.7206	1124	1605	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pelomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003963075.1	s__Pelomonas sp003963075	85.698	930	1605	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pelomonas	95.0	96.90	96.90	0.86	0.86	2	-
GCA_004211245.1	s__Variovorax sp004211245	78.115	357	1605	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Variovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000482785.1	s__Derxia gummosa	77.056	482	1605	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Derxia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012513825.1	s__SCN-69-89 sp012513825	77.0138	282	1605	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__SCN-69-89	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013376005.1	s__Duganella sp013376005	76.9341	565	1605	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Duganella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011090165.1	s__Duganella aceris	76.8488	574	1605	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Duganella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 11:28:29,068] [INFO] GTDB search result was written to OceanDNA-b33393/result_gtdb.tsv
[2023-03-17 11:28:29,071] [INFO] ===== GTDB Search completed =====
[2023-03-17 11:28:29,078] [INFO] DFAST_QC result json was written to OceanDNA-b33393/dqc_result.json
[2023-03-17 11:28:29,078] [INFO] DFAST_QC completed!
[2023-03-17 11:28:29,079] [INFO] Total running time: 0h2m52s