[2023-03-19 01:33:27,301] [INFO] DFAST_QC pipeline started.
[2023-03-19 01:33:27,301] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 01:33:27,302] [INFO] DQC Reference Directory: /var/lib/cwl/stg094db978-8766-4e5a-b1da-888f46edd100/dqc_reference
[2023-03-19 01:33:28,410] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 01:33:28,411] [INFO] Task started: Prodigal
[2023-03-19 01:33:28,411] [INFO] Running command: cat /var/lib/cwl/stg459131ec-d3d6-425c-b4c7-93a497e8a37e/OceanDNA-b33307.fa | prodigal -d OceanDNA-b33307/cds.fna -a OceanDNA-b33307/protein.faa -g 11 -q > /dev/null
[2023-03-19 01:33:50,193] [INFO] Task succeeded: Prodigal
[2023-03-19 01:33:50,193] [INFO] Task started: HMMsearch
[2023-03-19 01:33:50,193] [INFO] Running command: hmmsearch --tblout OceanDNA-b33307/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg094db978-8766-4e5a-b1da-888f46edd100/dqc_reference/reference_markers.hmm OceanDNA-b33307/protein.faa > /dev/null
[2023-03-19 01:33:50,407] [INFO] Task succeeded: HMMsearch
[2023-03-19 01:33:50,407] [INFO] Found 6/6 markers.
[2023-03-19 01:33:50,432] [INFO] Query marker FASTA was written to OceanDNA-b33307/markers.fasta
[2023-03-19 01:33:50,433] [INFO] Task started: Blastn
[2023-03-19 01:33:50,433] [INFO] Running command: blastn -query OceanDNA-b33307/markers.fasta -db /var/lib/cwl/stg094db978-8766-4e5a-b1da-888f46edd100/dqc_reference/reference_markers.fasta -out OceanDNA-b33307/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 01:33:51,322] [INFO] Task succeeded: Blastn
[2023-03-19 01:33:51,323] [INFO] Selected 17 target genomes.
[2023-03-19 01:33:51,323] [INFO] Target genome list was writen to OceanDNA-b33307/target_genomes.txt
[2023-03-19 01:33:51,334] [INFO] Task started: fastANI
[2023-03-19 01:33:51,335] [INFO] Running command: fastANI --query /var/lib/cwl/stg459131ec-d3d6-425c-b4c7-93a497e8a37e/OceanDNA-b33307.fa --refList OceanDNA-b33307/target_genomes.txt --output OceanDNA-b33307/fastani_result.tsv --threads 1
[2023-03-19 01:34:06,870] [INFO] Task succeeded: fastANI
[2023-03-19 01:34:06,871] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg094db978-8766-4e5a-b1da-888f46edd100/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 01:34:06,871] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg094db978-8766-4e5a-b1da-888f46edd100/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 01:34:06,882] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 01:34:06,882] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-19 01:34:06,882] [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
Hydrogenophaga crassostreae	strain=LPB0072	GCA_001761385.1	1763535	1763535	type	True	81.4687	677	1051	95	below_threshold
Hydrogenophaga crassostreae	strain=LPB0072	GCA_001640105.1	1763535	1763535	type	True	81.3973	675	1051	95	below_threshold
Hydrogenophaga aromaticivorans	strain=D2P1	GCA_013387465.1	2610898	2610898	type	True	80.4723	645	1051	95	below_threshold
Hydrogenophaga taeniospiralis	strain=NBRC 102512	GCA_001592305.1	65656	65656	type	True	80.429	614	1051	95	below_threshold
Hydrogenophaga palleronii	strain=NBRC 102513	GCA_001571225.1	65655	65655	type	True	80.0644	508	1051	95	below_threshold
Hydrogenophaga flava	strain=NBRC 102514	GCA_001571145.1	65657	65657	type	True	79.9629	593	1051	95	below_threshold
Hydrogenophaga pseudoflava	strain=NBRC 102511	GCA_001592285.1	47421	47421	type	True	79.9375	601	1051	95	below_threshold
Hydrogenophaga crocea	strain=BA0156	GCA_011388215.1	2716225	2716225	type	True	79.3789	481	1051	95	below_threshold
Hydrogenophaga borbori	strain=LA-38	GCA_003417535.1	2294117	2294117	type	True	79.3644	479	1051	95	below_threshold
Acidovorax delafieldii	strain=DSM 64	GCA_007993815.1	47920	47920	type	True	78.3688	368	1051	95	below_threshold
Curvibacter lanceolatus	strain=ATCC 14669	GCA_000381265.1	86182	86182	type	True	78.2642	376	1051	95	below_threshold
Variovorax boronicumulans	strain=NBRC 103145	GCA_001591345.1	436515	436515	type	True	78.2268	341	1051	95	below_threshold
Acidovorax facilis	strain=DSM 649	GCA_023913775.1	12917	12917	type	True	78.095	396	1051	95	below_threshold
Ramlibacter humi	strain=18x22-1	GCA_004681975.1	2530451	2530451	type	True	78.0537	320	1051	95	below_threshold
Brachymonas denitrificans	strain=DSM 15123	GCA_900110225.1	28220	28220	type	True	77.9985	217	1051	95	below_threshold
Ramlibacter agri	strain=G-1-2-2	GCA_012927085.1	2728837	2728837	type	True	77.7198	326	1051	95	below_threshold
Comamonas koreensis	strain=KCTC 12005	GCA_021026195.1	160825	160825	type	True	77.6261	253	1051	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 01:34:06,882] [INFO] DFAST Taxonomy check result was written to OceanDNA-b33307/tc_result.tsv
[2023-03-19 01:34:06,882] [INFO] ===== Taxonomy check completed =====
[2023-03-19 01:34:06,882] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 01:34:06,882] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg094db978-8766-4e5a-b1da-888f46edd100/dqc_reference/checkm_data
[2023-03-19 01:34:06,883] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 01:34:06,985] [INFO] Task started: CheckM
[2023-03-19 01:34:06,985] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b33307/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b33307/checkm_input OceanDNA-b33307/checkm_result
[2023-03-19 01:35:14,596] [INFO] Task succeeded: CheckM
[2023-03-19 01:35:14,597] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 84.76%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 01:35:14,600] [INFO] ===== Completeness check finished =====
[2023-03-19 01:35:14,600] [INFO] ===== Start GTDB Search =====
[2023-03-19 01:35:14,600] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b33307/markers.fasta)
[2023-03-19 01:35:14,601] [INFO] Task started: Blastn
[2023-03-19 01:35:14,601] [INFO] Running command: blastn -query OceanDNA-b33307/markers.fasta -db /var/lib/cwl/stg094db978-8766-4e5a-b1da-888f46edd100/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b33307/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 01:35:16,414] [INFO] Task succeeded: Blastn
[2023-03-19 01:35:16,415] [INFO] Selected 19 target genomes.
[2023-03-19 01:35:16,415] [INFO] Target genome list was writen to OceanDNA-b33307/target_genomes_gtdb.txt
[2023-03-19 01:35:16,434] [INFO] Task started: fastANI
[2023-03-19 01:35:16,435] [INFO] Running command: fastANI --query /var/lib/cwl/stg459131ec-d3d6-425c-b4c7-93a497e8a37e/OceanDNA-b33307.fa --refList OceanDNA-b33307/target_genomes_gtdb.txt --output OceanDNA-b33307/fastani_result_gtdb.tsv --threads 1
[2023-03-19 01:35:32,609] [INFO] Task succeeded: fastANI
[2023-03-19 01:35:32,620] [INFO] Found 19 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 01:35:32,620] [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
GCF_004795855.1	s__Hydrogenophaga sp004795855	83.7133	853	1051	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001761385.1	s__Hydrogenophaga crassostreae	81.4583	678	1051	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	100.00	100.00	1.00	1.00	2	-
GCA_002842215.1	s__Hydrogenophaga sp002842215	80.5676	630	1051	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001770905.1	s__Hydrogenophaga sp001770905	80.4794	613	1051	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	99.83	99.75	0.90	0.90	3	-
GCF_013387465.1	s__Hydrogenophaga aromaticivorans	80.4589	645	1051	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	96.00	95.64	0.87	0.82	12	-
GCF_001592305.1	s__Hydrogenophaga taeniospiralis	80.4582	611	1051	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018780075.1	s__Hydrogenophaga sp018780075	80.3178	596	1051	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011391495.1	s__Hydrogenophaga sp011391495	80.272	495	1051	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002001205.1	s__Hydrogenophaga sp002001205	80.075	601	1051	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001571225.1	s__Hydrogenophaga palleronii	80.0644	508	1051	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011390835.1	s__Hydrogenophaga sp011390835	80.0609	515	1051	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001713375.1	s__Hydrogenophaga sp001713375	79.9999	564	1051	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013823655.1	s__Hydrogenophaga sp013823655	79.9894	376	1051	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001571145.1	s__Hydrogenophaga flava	79.9716	592	1051	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013823505.1	s__Hydrogenophaga sp013823505	79.9375	484	1051	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001592285.1	s__Hydrogenophaga pseudoflava	79.9337	601	1051	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	97.77	97.69	0.91	0.91	4	-
GCA_018780385.1	s__Hydrogenophaga sp018780385	79.9306	522	1051	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016790705.1	s__Hydrogenophaga sp016790705	79.6718	444	1051	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011388215.1	s__Hydrogenophaga sp011388215	79.3686	482	1051	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	99.06	99.06	0.95	0.95	2	-
--------------------------------------------------------------------------------
[2023-03-19 01:35:32,620] [INFO] GTDB search result was written to OceanDNA-b33307/result_gtdb.tsv
[2023-03-19 01:35:32,620] [INFO] ===== GTDB Search completed =====
[2023-03-19 01:35:32,622] [INFO] DFAST_QC result json was written to OceanDNA-b33307/dqc_result.json
[2023-03-19 01:35:32,622] [INFO] DFAST_QC completed!
[2023-03-19 01:35:32,622] [INFO] Total running time: 0h2m5s