[2023-06-30 14:53:55,837] [INFO] DFAST_QC pipeline started.
[2023-06-30 14:53:55,840] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 14:53:55,840] [INFO] DQC Reference Directory: /var/lib/cwl/stg73c93460-5fcb-44f0-9cf1-9ba5fef02a40/dqc_reference
[2023-06-30 14:53:57,133] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 14:53:57,134] [INFO] Task started: Prodigal
[2023-06-30 14:53:57,135] [INFO] Running command: gunzip -c /var/lib/cwl/stgab967ad5-eeef-45fd-b1e1-8a7d556acd34/GCA_903894065.1_freshwater_MAG_---_Erken-D11_bin-0528_genomic.fna.gz | prodigal -d GCA_903894065.1_freshwater_MAG_---_Erken-D11_bin-0528_genomic.fna/cds.fna -a GCA_903894065.1_freshwater_MAG_---_Erken-D11_bin-0528_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 14:54:03,831] [INFO] Task succeeded: Prodigal
[2023-06-30 14:54:03,831] [INFO] Task started: HMMsearch
[2023-06-30 14:54:03,832] [INFO] Running command: hmmsearch --tblout GCA_903894065.1_freshwater_MAG_---_Erken-D11_bin-0528_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg73c93460-5fcb-44f0-9cf1-9ba5fef02a40/dqc_reference/reference_markers.hmm GCA_903894065.1_freshwater_MAG_---_Erken-D11_bin-0528_genomic.fna/protein.faa > /dev/null
[2023-06-30 14:54:04,072] [INFO] Task succeeded: HMMsearch
[2023-06-30 14:54:04,074] [INFO] Found 6/6 markers.
[2023-06-30 14:54:04,124] [INFO] Query marker FASTA was written to GCA_903894065.1_freshwater_MAG_---_Erken-D11_bin-0528_genomic.fna/markers.fasta
[2023-06-30 14:54:04,124] [INFO] Task started: Blastn
[2023-06-30 14:54:04,125] [INFO] Running command: blastn -query GCA_903894065.1_freshwater_MAG_---_Erken-D11_bin-0528_genomic.fna/markers.fasta -db /var/lib/cwl/stg73c93460-5fcb-44f0-9cf1-9ba5fef02a40/dqc_reference/reference_markers.fasta -out GCA_903894065.1_freshwater_MAG_---_Erken-D11_bin-0528_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 14:54:04,979] [INFO] Task succeeded: Blastn
[2023-06-30 14:54:04,985] [INFO] Selected 24 target genomes.
[2023-06-30 14:54:04,985] [INFO] Target genome list was writen to GCA_903894065.1_freshwater_MAG_---_Erken-D11_bin-0528_genomic.fna/target_genomes.txt
[2023-06-30 14:54:04,989] [INFO] Task started: fastANI
[2023-06-30 14:54:04,990] [INFO] Running command: fastANI --query /var/lib/cwl/stgab967ad5-eeef-45fd-b1e1-8a7d556acd34/GCA_903894065.1_freshwater_MAG_---_Erken-D11_bin-0528_genomic.fna.gz --refList GCA_903894065.1_freshwater_MAG_---_Erken-D11_bin-0528_genomic.fna/target_genomes.txt --output GCA_903894065.1_freshwater_MAG_---_Erken-D11_bin-0528_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 14:54:21,517] [INFO] Task succeeded: fastANI
[2023-06-30 14:54:21,518] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg73c93460-5fcb-44f0-9cf1-9ba5fef02a40/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 14:54:21,519] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg73c93460-5fcb-44f0-9cf1-9ba5fef02a40/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 14:54:21,542] [INFO] Found 24 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 14:54:21,542] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 14:54:21,542] [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
Rhodoferax saidenbachensis	strain=DSM 22694	GCA_001955715.1	1484693	1484693	type	True	79.3354	159	375	95	below_threshold
Rhodoferax saidenbachensis	strain=ED16	GCA_000498435.1	1484693	1484693	type	True	79.3351	159	375	95	below_threshold
Rhodoferax lacus	strain=IMCC26218	GCA_003415675.1	2184758	2184758	type	True	79.0503	154	375	95	below_threshold
Rhodoferax bucti	strain=GSA243-2	GCA_005876985.1	2576305	2576305	type	True	78.5708	123	375	95	below_threshold
Acidovorax soli	strain=DSM 25157	GCA_900107605.1	592050	592050	type	True	78.3605	103	375	95	below_threshold
Acidovorax delafieldii	strain=DSM 64	GCA_007993815.1	47920	47920	type	True	78.0379	109	375	95	below_threshold
Limnohabitans radicicola	strain=JUR4	GCA_014837235.1	2771427	2771427	type	True	77.997	80	375	95	below_threshold
Curvibacter lanceolatus	strain=ATCC 14669	GCA_000381265.1	86182	86182	type	True	77.9431	117	375	95	below_threshold
Acidovorax radicis	strain=N35	GCA_000204195.2	758826	758826	type	True	77.9011	110	375	95	below_threshold
Simplicispira suum	strain=SC1-8	GCA_003008595.1	2109915	2109915	type	True	77.8681	86	375	95	below_threshold
Rhodoferax ferrireducens	strain=DSM 15236	GCA_000013605.1	192843	192843	type	True	77.8593	101	375	95	below_threshold
Rhodoferax antarcticus	strain=DSM 24876	GCA_001955735.1	81479	81479	type	True	77.8558	74	375	95	below_threshold
Polaromonas jejuensis	strain=NBRC 106434	GCA_001598235.1	457502	457502	type	True	77.7974	108	375	95	below_threshold
Ramlibacter tataouinensis	strain=TTB310	GCA_000215705.1	94132	94132	type	True	77.6466	94	375	95	below_threshold
Acidovorax valerianellae	strain=DSM 16619	GCA_900102625.1	187868	187868	type	True	77.6126	100	375	95	below_threshold
Delftia acidovorans	strain=FDAARGOS_997	GCA_016127415.1	80866	80866	type	True	77.5866	87	375	95	below_threshold
Variovorax boronicumulans	strain=NBRC 103145	GCA_001591345.1	436515	436515	type	True	77.5699	89	375	95	below_threshold
Acidovorax caeni	strain=R-24608	GCA_001298675.1	343013	343013	type	True	77.4415	96	375	95	below_threshold
Acidovorax caeni	strain=R-24608	GCA_900116825.1	343013	343013	type	True	77.4344	95	375	95	below_threshold
Ramlibacter humi	strain=18x22-1	GCA_004681975.1	2530451	2530451	type	True	77.3695	94	375	95	below_threshold
Tepidicella baoligensis	strain=B18-50	GCA_013432195.1	2707016	2707016	type	True	77.2453	68	375	95	below_threshold
Variovorax beijingensis	strain=502	GCA_003951285.1	2496117	2496117	type	True	77.2254	98	375	95	below_threshold
Variovorax paradoxus	strain=NBRC 15149	GCA_001591365.1	34073	34073	suspected-type	True	77.1606	99	375	95	below_threshold
Rhodoferax aquaticus	strain=Gr-4	GCA_006974105.1	2527691	2527691	type	True	77.0477	76	375	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 14:54:21,545] [INFO] DFAST Taxonomy check result was written to GCA_903894065.1_freshwater_MAG_---_Erken-D11_bin-0528_genomic.fna/tc_result.tsv
[2023-06-30 14:54:21,546] [INFO] ===== Taxonomy check completed =====
[2023-06-30 14:54:21,546] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 14:54:21,547] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg73c93460-5fcb-44f0-9cf1-9ba5fef02a40/dqc_reference/checkm_data
[2023-06-30 14:54:21,549] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 14:54:21,580] [INFO] Task started: CheckM
[2023-06-30 14:54:21,581] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903894065.1_freshwater_MAG_---_Erken-D11_bin-0528_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903894065.1_freshwater_MAG_---_Erken-D11_bin-0528_genomic.fna/checkm_input GCA_903894065.1_freshwater_MAG_---_Erken-D11_bin-0528_genomic.fna/checkm_result
[2023-06-30 14:54:47,711] [INFO] Task succeeded: CheckM
[2023-06-30 14:54:47,712] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 67.30%
Contamintation: 17.51%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-06-30 14:54:47,738] [INFO] ===== Completeness check finished =====
[2023-06-30 14:54:47,739] [INFO] ===== Start GTDB Search =====
[2023-06-30 14:54:47,739] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903894065.1_freshwater_MAG_---_Erken-D11_bin-0528_genomic.fna/markers.fasta)
[2023-06-30 14:54:47,739] [INFO] Task started: Blastn
[2023-06-30 14:54:47,740] [INFO] Running command: blastn -query GCA_903894065.1_freshwater_MAG_---_Erken-D11_bin-0528_genomic.fna/markers.fasta -db /var/lib/cwl/stg73c93460-5fcb-44f0-9cf1-9ba5fef02a40/dqc_reference/reference_markers_gtdb.fasta -out GCA_903894065.1_freshwater_MAG_---_Erken-D11_bin-0528_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 14:54:49,324] [INFO] Task succeeded: Blastn
[2023-06-30 14:54:49,329] [INFO] Selected 25 target genomes.
[2023-06-30 14:54:49,329] [INFO] Target genome list was writen to GCA_903894065.1_freshwater_MAG_---_Erken-D11_bin-0528_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 14:54:49,341] [INFO] Task started: fastANI
[2023-06-30 14:54:49,341] [INFO] Running command: fastANI --query /var/lib/cwl/stgab967ad5-eeef-45fd-b1e1-8a7d556acd34/GCA_903894065.1_freshwater_MAG_---_Erken-D11_bin-0528_genomic.fna.gz --refList GCA_903894065.1_freshwater_MAG_---_Erken-D11_bin-0528_genomic.fna/target_genomes_gtdb.txt --output GCA_903894065.1_freshwater_MAG_---_Erken-D11_bin-0528_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 14:55:06,185] [INFO] Task succeeded: fastANI
[2023-06-30 14:55:06,216] [INFO] Found 24 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-30 14:55:06,216] [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_016703945.1	s__Rhodoferax sp016703945	80.9813	194	375	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903853895.1	s__Rhodoferax sp903853895	80.4524	203	375	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	99.86	99.86	0.86	0.86	2	-
GCF_017798165.1	s__Rhodoferax sp017798165	80.3714	191	375	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016705575.1	s__Rhodoferax sp016705575	80.1431	192	375	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	99.15	99.12	0.95	0.95	5	-
GCA_903945325.1	s__Rhodoferax sp903945325	79.653	187	375	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	99.68	99.56	0.89	0.88	4	-
GCA_903924955.1	s__Rhodoferax sp903924955	79.3577	171	375	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002943465.1	s__Rhodoferax sp002943465	79.0796	138	375	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016719405.1	s__Rhodoferax sp016719405	79.0684	129	375	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	98.38	98.38	0.86	0.86	2	-
GCF_003415675.1	s__Rhodoferax sp003415675	79.0625	153	375	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001770935.1	s__Rhodoferax sp001770935	79.0222	140	375	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001795455.1	s__Rhodoferax sp001795455	78.9733	148	375	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	99.98	99.98	0.98	0.98	3	-
GCA_903845935.1	s__Rhodoferax sp903845935	78.531	133	375	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	99.58	99.41	0.92	0.88	22	-
GCA_903863395.1	s__Rhodoferax sp903863395	78.4981	127	375	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	98.94	98.87	0.83	0.81	5	-
GCA_903897925.1	s__Rhodoferax sp903897925	78.1635	123	375	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	99.65	99.65	0.87	0.87	2	-
GCA_001797315.1	s__Hylemonella sp001797315	78.1308	121	375	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hylemonella	95.0	99.98	99.98	0.98	0.98	2	-
GCF_001428665.1	s__Acidovorax sp001428665	78.1131	118	375	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	97.34	97.34	0.92	0.92	2	-
GCA_903876045.1	s__Rhodoferax sp903876045	78.037	92	375	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	99.28	99.14	0.84	0.81	3	-
GCF_000282655.1	s__Polaromonas sp000282655	77.9324	104	375	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polaromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900103405.1	s__Polaromonas sp900103405	77.9256	109	375	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polaromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012927445.1	s__Rhodoferax sp012927445	77.8772	104	375	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	98.76	98.76	0.94	0.94	2	-
GCF_017948265.1	s__Rhodoferax sp017948265	77.756	74	375	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903948045.1	s__Rhodoferax sp903948045	77.4033	83	375	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001422365.1	s__Pseudorhodoferax sp001422365	77.2469	103	375	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudorhodoferax	95.0	98.81	98.81	0.87	0.87	3	-
GCA_002255935.1	s__Limnohabitans_A sp002255935	77.1592	90	375	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 14:55:06,219] [INFO] GTDB search result was written to GCA_903894065.1_freshwater_MAG_---_Erken-D11_bin-0528_genomic.fna/result_gtdb.tsv
[2023-06-30 14:55:06,219] [INFO] ===== GTDB Search completed =====
[2023-06-30 14:55:06,227] [INFO] DFAST_QC result json was written to GCA_903894065.1_freshwater_MAG_---_Erken-D11_bin-0528_genomic.fna/dqc_result.json
[2023-06-30 14:55:06,227] [INFO] DFAST_QC completed!
[2023-06-30 14:55:06,227] [INFO] Total running time: 0h1m10s