[2023-06-17 03:42:03,129] [INFO] DFAST_QC pipeline started.
[2023-06-17 03:42:03,131] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 03:42:03,132] [INFO] DQC Reference Directory: /var/lib/cwl/stg003f38e0-2641-4458-9862-808089b9fffb/dqc_reference
[2023-06-17 03:42:06,431] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 03:42:06,432] [INFO] Task started: Prodigal
[2023-06-17 03:42:06,433] [INFO] Running command: gunzip -c /var/lib/cwl/stgc16168cf-0321-4136-80bb-9bb96d61bf66/GCA_028871705.1_ASM2887170v1_genomic.fna.gz | prodigal -d GCA_028871705.1_ASM2887170v1_genomic.fna/cds.fna -a GCA_028871705.1_ASM2887170v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 03:42:14,044] [INFO] Task succeeded: Prodigal
[2023-06-17 03:42:14,045] [INFO] Task started: HMMsearch
[2023-06-17 03:42:14,045] [INFO] Running command: hmmsearch --tblout GCA_028871705.1_ASM2887170v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg003f38e0-2641-4458-9862-808089b9fffb/dqc_reference/reference_markers.hmm GCA_028871705.1_ASM2887170v1_genomic.fna/protein.faa > /dev/null
[2023-06-17 03:42:14,288] [INFO] Task succeeded: HMMsearch
[2023-06-17 03:42:14,290] [INFO] Found 6/6 markers.
[2023-06-17 03:42:14,327] [INFO] Query marker FASTA was written to GCA_028871705.1_ASM2887170v1_genomic.fna/markers.fasta
[2023-06-17 03:42:14,327] [INFO] Task started: Blastn
[2023-06-17 03:42:14,328] [INFO] Running command: blastn -query GCA_028871705.1_ASM2887170v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg003f38e0-2641-4458-9862-808089b9fffb/dqc_reference/reference_markers.fasta -out GCA_028871705.1_ASM2887170v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 03:42:15,342] [INFO] Task succeeded: Blastn
[2023-06-17 03:42:15,347] [INFO] Selected 32 target genomes.
[2023-06-17 03:42:15,348] [INFO] Target genome list was writen to GCA_028871705.1_ASM2887170v1_genomic.fna/target_genomes.txt
[2023-06-17 03:42:15,356] [INFO] Task started: fastANI
[2023-06-17 03:42:15,356] [INFO] Running command: fastANI --query /var/lib/cwl/stgc16168cf-0321-4136-80bb-9bb96d61bf66/GCA_028871705.1_ASM2887170v1_genomic.fna.gz --refList GCA_028871705.1_ASM2887170v1_genomic.fna/target_genomes.txt --output GCA_028871705.1_ASM2887170v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 03:42:38,822] [INFO] Task succeeded: fastANI
[2023-06-17 03:42:38,823] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg003f38e0-2641-4458-9862-808089b9fffb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 03:42:38,823] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg003f38e0-2641-4458-9862-808089b9fffb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 03:42:38,853] [INFO] Found 31 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 03:42:38,853] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-17 03:42:38,853] [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
Steroidobacter agariperforans	strain=KA5-B	GCA_004138335.1	268404	268404	type	True	76.8106	151	848	95	below_threshold
Povalibacter uvarum	strain=DSM 26723	GCA_014202975.1	732238	732238	type	True	76.7254	140	848	95	below_threshold
Steroidobacter gossypii	strain=S1-65	GCA_016801985.1	2805490	2805490	type	True	76.7048	152	848	95	below_threshold
Steroidobacter agaridevorans	strain=SA29-B	GCA_009932555.1	2695856	2695856	type	True	76.6002	166	848	95	below_threshold
Luteimonas lumbrici	strain=1.1416	GCA_006476065.1	2559601	2559601	type	True	76.5881	140	848	95	below_threshold
Steroidobacter cummioxidans	strain=35Y	GCA_003104955.1	1803913	1803913	type	True	76.4873	139	848	95	below_threshold
Fulvimonas soli	strain=DSM 14263	GCA_003148905.1	155197	155197	type	True	76.244	223	848	95	below_threshold
Fulvimonas soli	strain=LMG 19981	GCA_006352285.1	155197	155197	type	True	76.235	206	848	95	below_threshold
Thiohalobacter thiocyanaticus	strain=Hrh1	GCA_003932505.1	585455	585455	type	True	76.2291	95	848	95	below_threshold
Halomonas lactosivorans	strain=KCTC 52281	GCA_003254665.1	2185141	2185141	type	True	76.2255	94	848	95	below_threshold
Dokdonella koreensis	strain=DS-123	GCA_001632775.1	323415	323415	type	True	76.1289	174	848	95	below_threshold
Azotobacter beijerinckii	strain=DSM 378	GCA_900110885.1	170623	170623	type	True	76.0829	105	848	95	below_threshold
Luteimonas aquatica	strain=RIB1-20	GCA_022662575.1	450364	450364	type	True	76.0128	180	848	95	below_threshold
Pseudomonas sagittaria	strain=JCM 18195	GCA_900115715.1	1135990	1135990	type	True	75.9454	113	848	95	below_threshold
Azotobacter chroococcum subsp. isscasi	strain=P205	GCA_004327895.1	2528971	353	type	True	75.9361	121	848	95	below_threshold
Rhodocyclus purpureus	strain=DSM 168	GCA_016653115.1	1067	1067	type	True	75.8787	99	848	95	below_threshold
Vulcaniibacterium tengchongense	strain=DSM 25623	GCA_003814555.1	1273429	1273429	type	True	75.8521	198	848	95	below_threshold
Vulcaniibacterium tengchongense	strain=YIM 77520	GCA_008033455.1	1273429	1273429	type	True	75.8515	192	848	95	below_threshold
Pseudomonas aromaticivorans	strain=MAP12	GCA_019097855.1	2849492	2849492	type	True	75.8486	130	848	95	below_threshold
Halochromatium glycolicum	strain=DSM 11080	GCA_016584085.1	85075	85075	type	True	75.8448	98	848	95	below_threshold
Stutzerimonas azotifigens	strain=DSM 17556	GCA_000425625.1	291995	291995	type	True	75.8	120	848	95	below_threshold
Tahibacter caeni	strain=BUT-6	GCA_024609805.1	1453545	1453545	type	True	75.7964	191	848	95	below_threshold
Luteibacter yeojuensis	strain=DSM 17673	GCA_011742875.1	345309	345309	type	True	75.7609	106	848	95	below_threshold
Luteibacter jiangsuensis	strain=CGMCC 1.10133	GCA_011742555.1	637577	637577	type	True	75.7159	99	848	95	below_threshold
Salinisphaera halophila	strain=YIM 95161	GCA_003732545.1	1304158	1304158	type	True	75.6669	106	848	95	below_threshold
Thermithiobacillus tepidarius	strain=DSM 3134	GCA_000423825.1	929	929	type	True	75.6388	70	848	95	below_threshold
Pseudomonas sihuiensis	strain=KCTC 32246	GCA_900106015.1	1274359	1274359	type	True	75.6371	67	848	95	below_threshold
Stutzerimonas frequens	strain=DNSP21	GCA_002890935.1	2968969	2968969	type	True	75.5018	74	848	95	below_threshold
Pseudomonas hydrolytica	strain=DSWY01	GCA_021495345.2	2493633	2493633	type	True	75.4912	99	848	95	below_threshold
Stutzerimonas frequens	strain=DNSP21	GCA_024448335.1	2968969	2968969	type	True	75.4879	75	848	95	below_threshold
Stutzerimonas frequens	strain=FDAARGOS_877	GCA_016028515.1	2968969	2968969	type	True	75.4879	75	848	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-17 03:42:38,855] [INFO] DFAST Taxonomy check result was written to GCA_028871705.1_ASM2887170v1_genomic.fna/tc_result.tsv
[2023-06-17 03:42:38,856] [INFO] ===== Taxonomy check completed =====
[2023-06-17 03:42:38,856] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 03:42:38,856] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg003f38e0-2641-4458-9862-808089b9fffb/dqc_reference/checkm_data
[2023-06-17 03:42:38,857] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 03:42:38,891] [INFO] Task started: CheckM
[2023-06-17 03:42:38,891] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_028871705.1_ASM2887170v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_028871705.1_ASM2887170v1_genomic.fna/checkm_input GCA_028871705.1_ASM2887170v1_genomic.fna/checkm_result
[2023-06-17 03:43:06,469] [INFO] Task succeeded: CheckM
[2023-06-17 03:43:06,471] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 55.30%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-17 03:43:06,493] [INFO] ===== Completeness check finished =====
[2023-06-17 03:43:06,493] [INFO] ===== Start GTDB Search =====
[2023-06-17 03:43:06,494] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_028871705.1_ASM2887170v1_genomic.fna/markers.fasta)
[2023-06-17 03:43:06,494] [INFO] Task started: Blastn
[2023-06-17 03:43:06,494] [INFO] Running command: blastn -query GCA_028871705.1_ASM2887170v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg003f38e0-2641-4458-9862-808089b9fffb/dqc_reference/reference_markers_gtdb.fasta -out GCA_028871705.1_ASM2887170v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 03:43:08,419] [INFO] Task succeeded: Blastn
[2023-06-17 03:43:08,424] [INFO] Selected 13 target genomes.
[2023-06-17 03:43:08,424] [INFO] Target genome list was writen to GCA_028871705.1_ASM2887170v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 03:43:08,439] [INFO] Task started: fastANI
[2023-06-17 03:43:08,439] [INFO] Running command: fastANI --query /var/lib/cwl/stgc16168cf-0321-4136-80bb-9bb96d61bf66/GCA_028871705.1_ASM2887170v1_genomic.fna.gz --refList GCA_028871705.1_ASM2887170v1_genomic.fna/target_genomes_gtdb.txt --output GCA_028871705.1_ASM2887170v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 03:43:17,294] [INFO] Task succeeded: fastANI
[2023-06-17 03:43:17,312] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-17 03:43:17,312] [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_001914695.1	s__13-2-20CM-66-19 sp001914695	80.9902	431	848	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__13-2-20CM-66-19	95.0	98.00	96.94	0.81	0.73	19	-
GCA_005878835.1	s__13-2-20CM-66-19 sp005878835	80.952	488	848	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__13-2-20CM-66-19	95.0	98.03	96.96	0.89	0.85	6	-
GCA_005878095.1	s__13-2-20CM-66-19 sp005878095	80.9063	449	848	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__13-2-20CM-66-19	95.0	99.52	99.52	0.84	0.84	2	-
GCA_018241425.1	s__13-2-20CM-66-19 sp018241425	80.7545	498	848	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__13-2-20CM-66-19	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005877965.1	s__13-2-20CM-66-19 sp005877965	80.7484	366	848	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__13-2-20CM-66-19	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018240525.1	s__13-2-20CM-66-19 sp018240525	80.4222	486	848	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__13-2-20CM-66-19	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019235245.1	s__13-2-20CM-66-19 sp019235245	80.2844	414	848	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__13-2-20CM-66-19	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019242385.1	s__13-2-20CM-66-19 sp019242385	80.1033	291	848	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__13-2-20CM-66-19	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019247195.1	s__13-2-20CM-66-19 sp019247195	79.7515	399	848	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__13-2-20CM-66-19	95.0	99.26	99.26	0.88	0.88	2	-
GCA_018241445.1	s__13-2-20CM-66-19 sp018241445	79.5407	379	848	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__13-2-20CM-66-19	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003242685.1	s__ZC4RG24 sp003242685	79.0328	299	848	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__ZC4RG24	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019187185.1	s__CADEFQ01 sp019187185	78.3435	255	848	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__CADEFQ01	95.0	98.79	98.79	0.92	0.92	2	-
GCA_019187495.1	s__CADEFQ01 sp019187495	77.9658	266	848	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__CADEFQ01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-17 03:43:17,314] [INFO] GTDB search result was written to GCA_028871705.1_ASM2887170v1_genomic.fna/result_gtdb.tsv
[2023-06-17 03:43:17,314] [INFO] ===== GTDB Search completed =====
[2023-06-17 03:43:17,319] [INFO] DFAST_QC result json was written to GCA_028871705.1_ASM2887170v1_genomic.fna/dqc_result.json
[2023-06-17 03:43:17,319] [INFO] DFAST_QC completed!
[2023-06-17 03:43:17,319] [INFO] Total running time: 0h1m14s