[2023-06-17 01:29:09,194] [INFO] DFAST_QC pipeline started.
[2023-06-17 01:29:09,197] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 01:29:09,197] [INFO] DQC Reference Directory: /var/lib/cwl/stg7445b69a-6513-4920-8e54-384edbe30788/dqc_reference
[2023-06-17 01:29:10,515] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 01:29:10,521] [INFO] Task started: Prodigal
[2023-06-17 01:29:10,522] [INFO] Running command: gunzip -c /var/lib/cwl/stg30642210-a3d1-4465-88d9-100250099971/GCA_028866355.1_ASM2886635v1_genomic.fna.gz | prodigal -d GCA_028866355.1_ASM2886635v1_genomic.fna/cds.fna -a GCA_028866355.1_ASM2886635v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 01:29:16,490] [INFO] Task succeeded: Prodigal
[2023-06-17 01:29:16,490] [INFO] Task started: HMMsearch
[2023-06-17 01:29:16,491] [INFO] Running command: hmmsearch --tblout GCA_028866355.1_ASM2886635v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7445b69a-6513-4920-8e54-384edbe30788/dqc_reference/reference_markers.hmm GCA_028866355.1_ASM2886635v1_genomic.fna/protein.faa > /dev/null
[2023-06-17 01:29:16,743] [INFO] Task succeeded: HMMsearch
[2023-06-17 01:29:16,745] [INFO] Found 6/6 markers.
[2023-06-17 01:29:16,773] [INFO] Query marker FASTA was written to GCA_028866355.1_ASM2886635v1_genomic.fna/markers.fasta
[2023-06-17 01:29:16,773] [INFO] Task started: Blastn
[2023-06-17 01:29:16,773] [INFO] Running command: blastn -query GCA_028866355.1_ASM2886635v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7445b69a-6513-4920-8e54-384edbe30788/dqc_reference/reference_markers.fasta -out GCA_028866355.1_ASM2886635v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 01:29:17,613] [INFO] Task succeeded: Blastn
[2023-06-17 01:29:17,618] [INFO] Selected 32 target genomes.
[2023-06-17 01:29:17,619] [INFO] Target genome list was writen to GCA_028866355.1_ASM2886635v1_genomic.fna/target_genomes.txt
[2023-06-17 01:29:17,624] [INFO] Task started: fastANI
[2023-06-17 01:29:17,624] [INFO] Running command: fastANI --query /var/lib/cwl/stg30642210-a3d1-4465-88d9-100250099971/GCA_028866355.1_ASM2886635v1_genomic.fna.gz --refList GCA_028866355.1_ASM2886635v1_genomic.fna/target_genomes.txt --output GCA_028866355.1_ASM2886635v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 01:29:47,445] [INFO] Task succeeded: fastANI
[2023-06-17 01:29:47,446] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7445b69a-6513-4920-8e54-384edbe30788/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 01:29:47,447] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7445b69a-6513-4920-8e54-384edbe30788/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 01:29:47,472] [INFO] Found 32 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 01:29:47,472] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-17 01:29:47,472] [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
Aliidongia dinghuensis	strain=CGMCC 1.15725	GCA_014643535.1	1867774	1867774	type	True	77.4629	189	605	95	below_threshold
Inquilinus limosus	strain=DSM 16000	GCA_000423185.1	171674	171674	type	True	77.2644	154	605	95	below_threshold
Hypericibacter adhaerens	strain=R5959	GCA_008728835.1	2602016	2602016	type	True	77.0097	149	605	95	below_threshold
Oceanibaculum pacificum	strain=MCCC 1A02656	GCA_001618175.1	580166	580166	type	True	76.9762	122	605	95	below_threshold
Nisaea acidiphila	strain=MEBiC11861	GCA_024662015.1	1862145	1862145	type	True	76.9625	77	605	95	below_threshold
Azospirillum rugosum	strain=IMMIB AFH-6	GCA_017876155.1	416170	416170	type	True	76.8647	132	605	95	below_threshold
Stella humosa	strain=DSM 5900	GCA_003751345.1	94	94	type	True	76.8539	143	605	95	below_threshold
Stella humosa	strain=ATCC 43930	GCA_006738645.1	94	94	type	True	76.8395	143	605	95	below_threshold
Magnetospirillum moscoviense	strain=BB-1	GCA_001650635.1	1437059	1437059	type	True	76.8169	99	605	95	below_threshold
Thalassobaculum fulvum	strain=KCTC 42651	GCA_014652915.1	1633335	1633335	type	True	76.7663	149	605	95	below_threshold
Hypericibacter terrae	strain=R5913	GCA_008728855.1	2602015	2602015	type	True	76.7662	168	605	95	below_threshold
Azospirillum soli	strain=CC-LY788	GCA_017876165.1	1304799	1304799	type	True	76.6877	133	605	95	below_threshold
Tistlia consotensis	strain=DSM 21585	GCA_900188055.1	1321365	1321365	type	True	76.6428	178	605	95	below_threshold
Reyranella soli	strain=NBRC 108950	GCA_007992495.1	1230389	1230389	type	True	76.6349	151	605	95	below_threshold
Pelagibius marinus	strain=NBU2595	GCA_014925385.1	2762760	2762760	type	True	76.625	111	605	95	below_threshold
Tistlia consotensis	strain=USBA 355	GCA_900177295.1	1321365	1321365	type	True	76.6083	178	605	95	below_threshold
Skermanella stibiiresistens	strain=SB22	GCA_000576635.1	913326	913326	type	True	76.573	130	605	95	below_threshold
Azospirillum picis	strain=IMMIB TAR-3	GCA_017876115.1	488438	488438	type	True	76.5606	157	605	95	below_threshold
Elioraea tepida	strain=MS-P2	GCA_019203965.1	2843330	2843330	type	True	76.5126	82	605	95	below_threshold
Hansschlegelia beijingensis	strain=DSM 25481	GCA_014196425.1	1133344	1133344	type	True	76.4966	96	605	95	below_threshold
Reyranella aquatilis	strain=KCTC 52223	GCA_020880995.1	2035356	2035356	type	True	76.4915	132	605	95	below_threshold
Acidiphilium iwatense	strain=KCTC 23505	GCA_021556475.1	768198	768198	type	True	76.418	89	605	95	below_threshold
Azospirillum agricola	strain=CC-HIH038	GCA_017876095.1	1720247	1720247	type	True	76.3496	164	605	95	below_threshold
Arenibaculum pallidiluteum	strain=SYSU D00532	GCA_017355985.1	2812559	2812559	type	True	76.2569	123	605	95	below_threshold
Mesorhizobium waimense	strain=ICMP19557	GCA_003601975.1	1300307	1300307	type	True	76.2034	107	605	95	below_threshold
Rhodovastum atsumiense	strain=G2-11	GCA_937425535.1	504468	504468	type	True	76.0961	114	605	95	below_threshold
Mesorhizobium neociceri	strain=CCANP35	GCA_013520985.1	1307853	1307853	type	True	76.0672	101	605	95	below_threshold
Rhodoligotrophos defluvii	strain=lm1	GCA_005281615.1	2561934	2561934	type	True	75.9982	78	605	95	below_threshold
Rhodoplanes elegans	strain=DSM 11907	GCA_003258805.1	29408	29408	type	True	75.9661	125	605	95	below_threshold
Rhodoplanes elegans	strain=DSM 11907	GCA_016653355.1	29408	29408	type	True	75.966	145	605	95	below_threshold
Rhodovarius crocodyli	strain=CCP-6	GCA_004005855.1	1979269	1979269	type	True	75.8146	74	605	95	below_threshold
Roseococcus microcysteis	strain=NIBR12	GCA_014764365.1	2771361	2771361	type	True	75.647	73	605	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-17 01:29:47,474] [INFO] DFAST Taxonomy check result was written to GCA_028866355.1_ASM2886635v1_genomic.fna/tc_result.tsv
[2023-06-17 01:29:47,475] [INFO] ===== Taxonomy check completed =====
[2023-06-17 01:29:47,475] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 01:29:47,475] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7445b69a-6513-4920-8e54-384edbe30788/dqc_reference/checkm_data
[2023-06-17 01:29:47,476] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 01:29:47,509] [INFO] Task started: CheckM
[2023-06-17 01:29:47,509] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_028866355.1_ASM2886635v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_028866355.1_ASM2886635v1_genomic.fna/checkm_input GCA_028866355.1_ASM2886635v1_genomic.fna/checkm_result
[2023-06-17 01:30:11,009] [INFO] Task succeeded: CheckM
[2023-06-17 01:30:11,011] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 72.16%
Contamintation: 4.55%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-06-17 01:30:11,032] [INFO] ===== Completeness check finished =====
[2023-06-17 01:30:11,032] [INFO] ===== Start GTDB Search =====
[2023-06-17 01:30:11,033] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_028866355.1_ASM2886635v1_genomic.fna/markers.fasta)
[2023-06-17 01:30:11,033] [INFO] Task started: Blastn
[2023-06-17 01:30:11,033] [INFO] Running command: blastn -query GCA_028866355.1_ASM2886635v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7445b69a-6513-4920-8e54-384edbe30788/dqc_reference/reference_markers_gtdb.fasta -out GCA_028866355.1_ASM2886635v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 01:30:12,614] [INFO] Task succeeded: Blastn
[2023-06-17 01:30:12,619] [INFO] Selected 27 target genomes.
[2023-06-17 01:30:12,619] [INFO] Target genome list was writen to GCA_028866355.1_ASM2886635v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 01:30:12,625] [INFO] Task started: fastANI
[2023-06-17 01:30:12,625] [INFO] Running command: fastANI --query /var/lib/cwl/stg30642210-a3d1-4465-88d9-100250099971/GCA_028866355.1_ASM2886635v1_genomic.fna.gz --refList GCA_028866355.1_ASM2886635v1_genomic.fna/target_genomes_gtdb.txt --output GCA_028866355.1_ASM2886635v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 01:30:33,234] [INFO] Task succeeded: fastANI
[2023-06-17 01:30:33,262] [INFO] Found 27 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-17 01:30:33,262] [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_018971215.1	s__REEB95 sp018971215	86.2162	465	605	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__ATCC43930;f__Stellaceae;g__REEB95	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903828515.1	s__CAIKMD01 sp903828515	77.9993	236	605	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__ATCC43930;f__Stellaceae;g__CAIKMD01	95.0	99.99	99.96	1.00	0.99	5	-
GCA_000518365.1	s__URHD0088 sp000518365	77.8662	242	605	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__ATCC43930;f__Stellaceae;g__URHD0088	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903822185.1	s__CAIKMD01 sp903822185	77.4864	165	605	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__ATCC43930;f__Stellaceae;g__CAIKMD01	95.0	99.70	99.51	0.99	0.98	4	-
GCF_014643535.1	s__Aliidongia dinghuensis	77.4646	189	605	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__ATCC43930;f__Stellaceae;g__Aliidongia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016869515.1	s__VGDZ01 sp016869515	77.2633	138	605	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__VGDZ01;f__VGDZ01;g__VGDZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015654725.1	s__JAATGI01 sp015654725	77.1958	124	605	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__ATCC43930;f__Stellaceae;g__JAATGI01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016792605.1	s__JAEULC01 sp016792605	77.168	126	605	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__JAEULC01;f__JAEULC01;g__JAEULC01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005888425.1	s__AP-15 sp005888425	77.0167	103	605	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__ATCC43930;f__Stellaceae;g__AP-15	95.0	97.44	97.38	0.68	0.66	3	-
GCA_019241915.1	s__AP-15 sp019241915	77.0123	124	605	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__ATCC43930;f__Stellaceae;g__AP-15	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008728835.1	s__Hypericibacter adhaerens	77.0097	149	605	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Dongiales;f__Dongiaceae;g__Hypericibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_006738865.1	s__Stella sp006738865	76.9262	172	605	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__ATCC43930;f__Stellaceae;g__Stella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016793045.1	s__JAEUKZ01 sp016793045	76.9134	156	605	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__CACIAM-22H2;f__CACIAM-22H2;g__JAEUKZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016869285.1	s__SHVZ01 sp016869285	76.8967	136	605	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__SHVZ01;f__SHVZ01;g__SHVZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019240125.1	s__AP-15 sp019240125	76.8578	133	605	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__ATCC43930;f__Stellaceae;g__AP-15	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006738645.1	s__Stella humosa	76.8564	142	605	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__ATCC43930;f__Stellaceae;g__Stella	95.0	100.00	100.00	1.00	1.00	2	-
GCA_903941105.1	s__CAJANL01 sp903941105	76.7211	95	605	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__CAJANL01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014925385.1	s__WHTV01 sp014925385	76.6435	110	605	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Kiloniellales;f__Kiloniellaceae;g__WHTV01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900177295.1	s__Tistlia consotensis	76.5959	178	605	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Kiloniellales;f__DSM-21159;g__Tistlia	95.0	99.99	99.99	0.99	0.99	2	-
GCF_002195995.1	s__Inquilinus limosus_C	76.5516	160	605	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__DSM-16000;f__Inquilinaceae;g__Inquilinus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014196425.1	s__Hansschlegelia beijingensis	76.5234	95	605	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Methylopilaceae;g__Hansschlegelia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016712715.1	s__Dongia sp016712715	76.5232	82	605	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Dongiales;f__Dongiaceae;g__Dongia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016861165.1	s__BOKV01 sp016861165	76.4288	94	605	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__BOKV01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009377445.1	s__WHUA01 sp009377445	76.3983	125	605	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA8366;f__UBA8366;g__WHUA01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003952505.1	s__Mesorhizobium sp003952505	76.3787	110	605	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	99.46	98.78	0.92	0.87	11	-
GCF_008630155.1	s__Rhodovastum atsumiense	76.1075	110	605	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Rhodovastum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013520985.1	s__Mesorhizobium sp013520985	76.082	100	605	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-17 01:30:33,264] [INFO] GTDB search result was written to GCA_028866355.1_ASM2886635v1_genomic.fna/result_gtdb.tsv
[2023-06-17 01:30:33,265] [INFO] ===== GTDB Search completed =====
[2023-06-17 01:30:33,270] [INFO] DFAST_QC result json was written to GCA_028866355.1_ASM2886635v1_genomic.fna/dqc_result.json
[2023-06-17 01:30:33,270] [INFO] DFAST_QC completed!
[2023-06-17 01:30:33,270] [INFO] Total running time: 0h1m24s