[2023-06-29 02:29:03,241] [INFO] DFAST_QC pipeline started.
[2023-06-29 02:29:03,245] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 02:29:03,245] [INFO] DQC Reference Directory: /var/lib/cwl/stg3b286e31-9a78-43e2-8bc4-587d1d03e831/dqc_reference
[2023-06-29 02:29:05,816] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 02:29:05,818] [INFO] Task started: Prodigal
[2023-06-29 02:29:05,818] [INFO] Running command: gunzip -c /var/lib/cwl/stga337fbc6-ca43-42c5-880a-ed25c8af4bf3/GCA_020201335.1_ASM2020133v1_genomic.fna.gz | prodigal -d GCA_020201335.1_ASM2020133v1_genomic.fna/cds.fna -a GCA_020201335.1_ASM2020133v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 02:29:11,229] [INFO] Task succeeded: Prodigal
[2023-06-29 02:29:11,230] [INFO] Task started: HMMsearch
[2023-06-29 02:29:11,230] [INFO] Running command: hmmsearch --tblout GCA_020201335.1_ASM2020133v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3b286e31-9a78-43e2-8bc4-587d1d03e831/dqc_reference/reference_markers.hmm GCA_020201335.1_ASM2020133v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 02:29:11,450] [INFO] Task succeeded: HMMsearch
[2023-06-29 02:29:11,452] [INFO] Found 6/6 markers.
[2023-06-29 02:29:11,474] [INFO] Query marker FASTA was written to GCA_020201335.1_ASM2020133v1_genomic.fna/markers.fasta
[2023-06-29 02:29:11,475] [INFO] Task started: Blastn
[2023-06-29 02:29:11,475] [INFO] Running command: blastn -query GCA_020201335.1_ASM2020133v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3b286e31-9a78-43e2-8bc4-587d1d03e831/dqc_reference/reference_markers.fasta -out GCA_020201335.1_ASM2020133v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 02:29:12,310] [INFO] Task succeeded: Blastn
[2023-06-29 02:29:12,316] [INFO] Selected 33 target genomes.
[2023-06-29 02:29:12,316] [INFO] Target genome list was writen to GCA_020201335.1_ASM2020133v1_genomic.fna/target_genomes.txt
[2023-06-29 02:29:12,320] [INFO] Task started: fastANI
[2023-06-29 02:29:12,320] [INFO] Running command: fastANI --query /var/lib/cwl/stga337fbc6-ca43-42c5-880a-ed25c8af4bf3/GCA_020201335.1_ASM2020133v1_genomic.fna.gz --refList GCA_020201335.1_ASM2020133v1_genomic.fna/target_genomes.txt --output GCA_020201335.1_ASM2020133v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 02:29:32,569] [INFO] Task succeeded: fastANI
[2023-06-29 02:29:32,569] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3b286e31-9a78-43e2-8bc4-587d1d03e831/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 02:29:32,570] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3b286e31-9a78-43e2-8bc4-587d1d03e831/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 02:29:32,589] [INFO] Found 20 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 02:29:32,590] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 02:29:32,590] [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
Arenimonas composti	strain=DSM 18010	GCA_000426365.1	370776	370776	type	True	76.7107	88	570	95	below_threshold
Thioalkalivibrio nitratireducens	strain=DSM 14787	GCA_000321415.2	186931	186931	type	True	76.6123	62	570	95	below_threshold
Pseudoxanthomonas helianthi	strain=110414	GCA_017939625.1	1453541	1453541	type	True	76.5513	71	570	95	below_threshold
Thioalkalivibrio paradoxus	strain=ARh 1	GCA_000227685.3	108010	108010	type	True	76.5258	78	570	95	below_threshold
Plasticicumulans lactativorans	strain=DSM 25287	GCA_004341245.1	1133106	1133106	type	True	76.5077	111	570	95	below_threshold
Dokdonella fugitiva	strain=A3	GCA_004342425.1	328517	328517	type	True	76.4696	109	570	95	below_threshold
Thiohalobacter thiocyanaticus	strain=Hrh1	GCA_003932505.1	585455	585455	type	True	76.4149	51	570	95	below_threshold
Steroidobacter agaridevorans	strain=SA29-B	GCA_009932555.1	2695856	2695856	type	True	76.3666	60	570	95	below_threshold
Luteimonas lumbrici	strain=1.1416	GCA_006476065.1	2559601	2559601	type	True	76.3661	95	570	95	below_threshold
Frateuria terrea	strain=DSM 26515	GCA_900109025.1	529704	529704	type	True	76.276	62	570	95	below_threshold
Luteimonas viscosa	strain=XBU10	GCA_008244685.1	1132694	1132694	type	True	76.2614	85	570	95	below_threshold
Thioalbus denitrificans	strain=DSM 26407	GCA_003337735.1	547122	547122	type	True	76.2356	54	570	95	below_threshold
Frateuria terrea	strain=CGMCC 1.7053	GCA_900115705.1	529704	529704	type	True	76.2185	64	570	95	below_threshold
Sulfurivermis fontis	strain=JG42	GCA_004001245.1	1972068	1972068	type	True	76.2054	54	570	95	below_threshold
Stutzerimonas azotifigens	strain=DSM 17556	GCA_000425625.1	291995	291995	type	True	76.1801	63	570	95	below_threshold
Acidihalobacter prosperus	strain=DSM 5130	GCA_000754095.2	160660	160660	type	True	76.1599	58	570	95	below_threshold
Arhodomonas aquaeolei	strain=DSM 8974	GCA_000374645.1	2369	2369	type	True	76.0773	65	570	95	below_threshold
Thiohalocapsa marina	strain=DSM 19078	GCA_008632335.1	424902	424902	type	True	76.0717	50	570	95	below_threshold
Halofilum ochraceum	strain=XJ16	GCA_001614315.2	1611323	1611323	type	True	76.0641	51	570	95	below_threshold
Plasticicumulans acidivorans	strain=DSM 23606	GCA_003182095.1	886464	886464	type	True	75.9239	77	570	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 02:29:32,592] [INFO] DFAST Taxonomy check result was written to GCA_020201335.1_ASM2020133v1_genomic.fna/tc_result.tsv
[2023-06-29 02:29:32,593] [INFO] ===== Taxonomy check completed =====
[2023-06-29 02:29:32,594] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 02:29:32,594] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3b286e31-9a78-43e2-8bc4-587d1d03e831/dqc_reference/checkm_data
[2023-06-29 02:29:32,595] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 02:29:32,617] [INFO] Task started: CheckM
[2023-06-29 02:29:32,618] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_020201335.1_ASM2020133v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_020201335.1_ASM2020133v1_genomic.fna/checkm_input GCA_020201335.1_ASM2020133v1_genomic.fna/checkm_result
[2023-06-29 02:29:54,035] [INFO] Task succeeded: CheckM
[2023-06-29 02:29:54,037] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 78.79%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 02:29:54,057] [INFO] ===== Completeness check finished =====
[2023-06-29 02:29:54,058] [INFO] ===== Start GTDB Search =====
[2023-06-29 02:29:54,058] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_020201335.1_ASM2020133v1_genomic.fna/markers.fasta)
[2023-06-29 02:29:54,058] [INFO] Task started: Blastn
[2023-06-29 02:29:54,058] [INFO] Running command: blastn -query GCA_020201335.1_ASM2020133v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3b286e31-9a78-43e2-8bc4-587d1d03e831/dqc_reference/reference_markers_gtdb.fasta -out GCA_020201335.1_ASM2020133v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 02:29:55,575] [INFO] Task succeeded: Blastn
[2023-06-29 02:29:55,582] [INFO] Selected 32 target genomes.
[2023-06-29 02:29:55,582] [INFO] Target genome list was writen to GCA_020201335.1_ASM2020133v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 02:29:55,596] [INFO] Task started: fastANI
[2023-06-29 02:29:55,596] [INFO] Running command: fastANI --query /var/lib/cwl/stga337fbc6-ca43-42c5-880a-ed25c8af4bf3/GCA_020201335.1_ASM2020133v1_genomic.fna.gz --refList GCA_020201335.1_ASM2020133v1_genomic.fna/target_genomes_gtdb.txt --output GCA_020201335.1_ASM2020133v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 02:30:11,756] [INFO] Task succeeded: fastANI
[2023-06-29 02:30:11,777] [INFO] Found 19 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 02:30:11,777] [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_011089885.1	s__XN24 sp011089885	76.9897	89	570	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__XN24;f__XN24;g__XN24	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016704655.1	s__RPQJ01 sp016704655	76.9361	76	570	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__RPQJ01	95.0	98.97	98.97	0.93	0.93	2	-
GCA_018241525.1	s__SZAS-83 sp018241525	76.9076	113	570	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__SZAS-83	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016716465.1	s__JADJWH01 sp016716465	76.8554	59	570	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__JADJWH01;f__JADJWH01;g__JADJWH01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011058255.1	s__XN24 sp011058255	76.6912	80	570	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__XN24;f__XN24;g__XN24	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016705325.1	s__RPQJ01 sp016705325	76.6628	78	570	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__RPQJ01	95.0	98.86	98.83	0.87	0.85	3	-
GCA_017744955.1	s__Dokdonella_A sp017744955	76.5718	96	570	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dokdonella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003819815.1	s__RPQJ01 sp003819815	76.5571	78	570	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__RPQJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004341245.1	s__Plasticicumulans_A lactativorans	76.5077	111	570	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Competibacterales;f__Competibacteraceae;g__Plasticicumulans_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004342425.1	s__Dokdonella_A fugitiva	76.4879	108	570	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dokdonella_A	95.0	99.45	99.45	0.96	0.96	2	-
GCA_018241455.1	s__FEN-1191 sp018241455	76.419	53	570	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__FEN-1191	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018240295.1	s__Plasticicumulans sp003962905	76.4172	107	570	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Competibacterales;f__Competibacteraceae;g__Plasticicumulans	95.0	98.50	98.50	0.84	0.84	2	-
GCA_014359565.1	s__Immundisolibacter sp014359565	76.2918	60	570	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Immundisolibacterales;f__Immundisolibacteraceae;g__Immundisolibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000420165.1	s__Thioalkalivibrio sp000420165	76.2587	50	570	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Thioalkalivibrionaceae;g__Thioalkalivibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004001245.1	s__Sulfurivermis fontis	76.2054	54	570	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiohalomonadales;f__Thiohalomonadaceae;g__Sulfurivermis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015494165.1	s__S144-34 sp015494165	76.1633	73	570	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__S144-34;f__S144-34;g__S144-34	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000025545.1	s__Thioalkalivibrio sp000025545	76.1278	52	570	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Thioalkalivibrionaceae;g__Thioalkalivibrio	95.0	97.34	97.34	0.93	0.93	2	-
GCF_003182095.1	s__Plasticicumulans acidivorans	75.9239	77	570	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Competibacterales;f__Competibacteraceae;g__Plasticicumulans	95.0	N/A	N/A	N/A	N/A	1	-
GCA_008015835.1	s__SCMT01 sp008015835	75.6692	61	570	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__SCMT01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 02:30:11,779] [INFO] GTDB search result was written to GCA_020201335.1_ASM2020133v1_genomic.fna/result_gtdb.tsv
[2023-06-29 02:30:11,779] [INFO] ===== GTDB Search completed =====
[2023-06-29 02:30:11,784] [INFO] DFAST_QC result json was written to GCA_020201335.1_ASM2020133v1_genomic.fna/dqc_result.json
[2023-06-29 02:30:11,784] [INFO] DFAST_QC completed!
[2023-06-29 02:30:11,784] [INFO] Total running time: 0h1m9s