[2023-06-13 11:50:37,631] [INFO] DFAST_QC pipeline started.
[2023-06-13 11:50:37,633] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 11:50:37,633] [INFO] DQC Reference Directory: /var/lib/cwl/stga8994161-e292-467d-98d6-1af45bbf621d/dqc_reference
[2023-06-13 11:50:39,047] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 11:50:39,048] [INFO] Task started: Prodigal
[2023-06-13 11:50:39,048] [INFO] Running command: gunzip -c /var/lib/cwl/stgde60772b-e778-459d-81af-c79197becb4b/GCA_022826185.1_ASM2282618v1_genomic.fna.gz | prodigal -d GCA_022826185.1_ASM2282618v1_genomic.fna/cds.fna -a GCA_022826185.1_ASM2282618v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 11:50:50,494] [INFO] Task succeeded: Prodigal
[2023-06-13 11:50:50,495] [INFO] Task started: HMMsearch
[2023-06-13 11:50:50,495] [INFO] Running command: hmmsearch --tblout GCA_022826185.1_ASM2282618v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga8994161-e292-467d-98d6-1af45bbf621d/dqc_reference/reference_markers.hmm GCA_022826185.1_ASM2282618v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 11:50:50,791] [INFO] Task succeeded: HMMsearch
[2023-06-13 11:50:50,792] [INFO] Found 6/6 markers.
[2023-06-13 11:50:50,839] [INFO] Query marker FASTA was written to GCA_022826185.1_ASM2282618v1_genomic.fna/markers.fasta
[2023-06-13 11:50:50,840] [INFO] Task started: Blastn
[2023-06-13 11:50:50,840] [INFO] Running command: blastn -query GCA_022826185.1_ASM2282618v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga8994161-e292-467d-98d6-1af45bbf621d/dqc_reference/reference_markers.fasta -out GCA_022826185.1_ASM2282618v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 11:50:51,733] [INFO] Task succeeded: Blastn
[2023-06-13 11:50:51,738] [INFO] Selected 39 target genomes.
[2023-06-13 11:50:51,738] [INFO] Target genome list was writen to GCA_022826185.1_ASM2282618v1_genomic.fna/target_genomes.txt
[2023-06-13 11:50:51,744] [INFO] Task started: fastANI
[2023-06-13 11:50:51,745] [INFO] Running command: fastANI --query /var/lib/cwl/stgde60772b-e778-459d-81af-c79197becb4b/GCA_022826185.1_ASM2282618v1_genomic.fna.gz --refList GCA_022826185.1_ASM2282618v1_genomic.fna/target_genomes.txt --output GCA_022826185.1_ASM2282618v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 11:51:24,371] [INFO] Task succeeded: fastANI
[2023-06-13 11:51:24,372] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga8994161-e292-467d-98d6-1af45bbf621d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 11:51:24,372] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga8994161-e292-467d-98d6-1af45bbf621d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 11:51:24,401] [INFO] Found 37 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 11:51:24,401] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 11:51:24,401] [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
Oceanibaculum pacificum	strain=MCCC 1A02656	GCA_001618175.1	580166	580166	type	True	76.7796	192	1345	95	below_threshold
Nisaea sediminum	strain=NBU1469	GCA_014904705.1	2775867	2775867	type	True	76.7339	196	1345	95	below_threshold
Oceanibaculum indicum	strain=P24	GCA_000299935.1	526216	526216	type	True	76.6967	206	1345	95	below_threshold
Oceanibaculum nanhaiense	strain=L54-1-50	GCA_002148795.1	1909734	1909734	type	True	76.6343	213	1345	95	below_threshold
Pelagibius marinus	strain=NBU2595	GCA_014925385.1	2762760	2762760	type	True	76.4535	228	1345	95	below_threshold
Stella humosa	strain=DSM 5900	GCA_003751345.1	94	94	type	True	76.4187	288	1345	95	below_threshold
Rhodobium orientis	strain=DSM 11290	GCA_016653375.1	34017	34017	type	True	76.3966	187	1345	95	below_threshold
Rhodovibrio salinarum	strain=DSM 9154	GCA_016583505.1	1087	1087	type	True	76.3937	124	1345	95	below_threshold
Rhodovibrio salinarum	strain=DSM 9154	GCA_000515255.1	1087	1087	type	True	76.3787	125	1345	95	below_threshold
Rhodobium orientis	strain=DSM 11290	GCA_014197785.1	34017	34017	type	True	76.378	186	1345	95	below_threshold
Nisaea acidiphila	strain=MEBiC11861	GCA_024662015.1	1862145	1862145	type	True	76.3626	168	1345	95	below_threshold
Thalassobaculum fulvum	strain=KCTC 42651	GCA_014652915.1	1633335	1633335	type	True	76.3532	285	1345	95	below_threshold
Rhodobium orientis	strain=DSM 11290	GCA_003258835.1	34017	34017	type	True	76.3011	190	1345	95	below_threshold
Azospirillum tabaci	strain=W712	GCA_014596085.1	2752310	2752310	type	True	76.3008	229	1345	95	below_threshold
Marivibrio halodurans	strain=CGMCC 1.15697	GCA_017963645.1	2039722	2039722	type	True	76.2464	173	1345	95	below_threshold
Roseococcus microcysteis	strain=NIBR12	GCA_014764365.1	2771361	2771361	type	True	76.2434	182	1345	95	below_threshold
Magnetospirillum marisnigri	strain=SP-1	GCA_001650715.1	1285242	1285242	type	True	76.2397	137	1345	95	below_threshold
Stappia albiluteola	strain=F7233	GCA_014050225.1	2758565	2758565	type	True	76.2354	122	1345	95	below_threshold
Azospirillum thermophilum	strain=CFH 70021	GCA_003130795.1	2202148	2202148	type	True	76.2085	282	1345	95	below_threshold
Inquilinus limosus	strain=DSM 16000	GCA_000423185.1	171674	171674	type	True	76.2041	284	1345	95	below_threshold
Tistlia consotensis	strain=DSM 21585	GCA_900188055.1	1321365	1321365	type	True	76.1872	326	1345	95	below_threshold
Magnetospirillum kuznetsovii	strain=LBB-42	GCA_003284725.1	2053833	2053833	type	True	76.1831	122	1345	95	below_threshold
Azospirillum rugosum	strain=IMMIB AFH-6	GCA_017876155.1	416170	416170	type	True	76.1432	267	1345	95	below_threshold
Roseomonas rhizosphaerae	strain=YW11	GCA_002631185.1	1335062	1335062	type	True	76.1373	241	1345	95	below_threshold
Aliidongia dinghuensis	strain=CGMCC 1.15725	GCA_014643535.1	1867774	1867774	type	True	76.1277	217	1345	95	below_threshold
Aestuariivirga litoralis	strain=KCTC 52945	GCA_003234965.1	2650924	2650924	type	True	76.1194	131	1345	95	below_threshold
Roseococcus thiosulfatophilus	strain=RB-3	GCA_017311575.1	35813	35813	type	True	76.0548	192	1345	95	below_threshold
Rhodovastum atsumiense	strain=G2-11	GCA_937425535.1	504468	504468	type	True	76.0063	217	1345	95	below_threshold
Limimonas halophila	strain=DSM 25584	GCA_900100655.1	1082479	1082479	type	True	75.9742	152	1345	95	below_threshold
Arenibaculum pallidiluteum	strain=SYSU D00532	GCA_017355985.1	2812559	2812559	type	True	75.9575	234	1345	95	below_threshold
Roseospira navarrensis	strain=DSM 15114	GCA_009601025.1	140058	140058	type	True	75.9426	163	1345	95	below_threshold
Roseococcus pinisoli	strain=XZZS9	GCA_018413645.1	2835040	2835040	type	True	75.775	178	1345	95	below_threshold
Mesorhizobium sediminum	strain=KCTC 42205	GCA_013240295.1	1849104	1849104	type	True	75.7604	145	1345	95	below_threshold
Roseomonas rosea	strain=DSM 14916	GCA_900141905.1	198092	198092	type	True	75.75	189	1345	95	below_threshold
Rubrimonas cliftonensis	strain=DSM 15345	GCA_900107585.1	89524	89524	type	True	75.7266	239	1345	95	below_threshold
Rhodovarius crocodyli	strain=CCP-6	GCA_004005855.1	1979269	1979269	type	True	75.6922	193	1345	95	below_threshold
Agrobacterium leguminum	strain=MOPV5	GCA_015704895.1	2792015	2792015	type	True	75.4366	79	1345	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 11:51:24,403] [INFO] DFAST Taxonomy check result was written to GCA_022826185.1_ASM2282618v1_genomic.fna/tc_result.tsv
[2023-06-13 11:51:24,404] [INFO] ===== Taxonomy check completed =====
[2023-06-13 11:51:24,404] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 11:51:24,404] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga8994161-e292-467d-98d6-1af45bbf621d/dqc_reference/checkm_data
[2023-06-13 11:51:24,405] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 11:51:24,452] [INFO] Task started: CheckM
[2023-06-13 11:51:24,452] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022826185.1_ASM2282618v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022826185.1_ASM2282618v1_genomic.fna/checkm_input GCA_022826185.1_ASM2282618v1_genomic.fna/checkm_result
[2023-06-13 11:52:00,272] [INFO] Task succeeded: CheckM
[2023-06-13 11:52:00,274] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 11:52:00,298] [INFO] ===== Completeness check finished =====
[2023-06-13 11:52:00,298] [INFO] ===== Start GTDB Search =====
[2023-06-13 11:52:00,299] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022826185.1_ASM2282618v1_genomic.fna/markers.fasta)
[2023-06-13 11:52:00,299] [INFO] Task started: Blastn
[2023-06-13 11:52:00,299] [INFO] Running command: blastn -query GCA_022826185.1_ASM2282618v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga8994161-e292-467d-98d6-1af45bbf621d/dqc_reference/reference_markers_gtdb.fasta -out GCA_022826185.1_ASM2282618v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 11:52:01,724] [INFO] Task succeeded: Blastn
[2023-06-13 11:52:01,730] [INFO] Selected 33 target genomes.
[2023-06-13 11:52:01,730] [INFO] Target genome list was writen to GCA_022826185.1_ASM2282618v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 11:52:01,741] [INFO] Task started: fastANI
[2023-06-13 11:52:01,741] [INFO] Running command: fastANI --query /var/lib/cwl/stgde60772b-e778-459d-81af-c79197becb4b/GCA_022826185.1_ASM2282618v1_genomic.fna.gz --refList GCA_022826185.1_ASM2282618v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022826185.1_ASM2282618v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 11:52:29,413] [INFO] Task succeeded: fastANI
[2023-06-13 11:52:29,440] [INFO] Found 33 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-13 11:52:29,441] [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_002238885.1	s__Bin95 sp002238885	86.2767	558	1345	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Bin95;f__Bin95;g__Bin95	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011523655.1	s__Bin65 sp011523655	77.3407	268	1345	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Bin65;f__Bin65;g__Bin65	95.0	95.25	95.16	0.87	0.83	5	-
GCA_011523425.1	s__WTGU01 sp011523425	76.913	245	1345	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA828;f__UBA828;g__WTGU01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003576685.1	s__SYSU-D60014 sp003576685	76.6739	184	1345	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Dongiales;f__Dongiaceae;g__SYSU-D60014	95.0	N/A	N/A	N/A	N/A	1	-
GCA_006739055.1	s__Stella vacuolata	76.6108	298	1345	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__ATCC43930;f__Stellaceae;g__Stella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009694185.1	s__SHVR01 sp009694185	76.5863	176	1345	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__SHVR01;f__SHVR01;g__SHVR01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014925385.1	s__WHTV01 sp014925385	76.453	228	1345	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Kiloniellales;f__Kiloniellaceae;g__WHTV01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016869975.1	s__JAFAZJ01 sp016869975	76.4272	251	1345	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__JAFAZJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_006738865.1	s__Stella sp006738865	76.404	298	1345	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__ATCC43930;f__Stellaceae;g__Stella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900110395.1	s__Reyranella sp900110395	76.3949	260	1345	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017305915.1	s__Reyranella sp017305915	76.3844	280	1345	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014652915.1	s__Thalassobaculum_A fulvum	76.3412	283	1345	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__Thalassobaculum_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016792605.1	s__JAEULC01 sp016792605	76.3181	200	1345	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__JAEULC01;f__JAEULC01;g__JAEULC01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016869145.1	s__VGEU01 sp016869145	76.3029	202	1345	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__MPNO01;f__VGEU01;g__VGEU01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000518365.1	s__URHD0088 sp000518365	76.2856	289	1345	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__ATCC43930;f__Stellaceae;g__URHD0088	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015232485.1	s__JADFZP01 sp015232485	76.2674	138	1345	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__JADFZP01	95.0	96.70	95.97	0.70	0.69	3	-
GCA_016870115.1	s__VGCH01 sp016870115	76.2494	147	1345	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__VGCH01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016765655.1	s__Skermanella mucosa	76.2346	250	1345	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Skermanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900177295.1	s__Tistlia consotensis	76.2142	327	1345	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_000423185.1	s__Inquilinus limosus	76.2106	286	1345	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_002195995.1	s__Inquilinus limosus_C	76.195	297	1345	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__DSM-16000;f__Inquilinaceae;g__Inquilinus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016869645.1	s__SHVW01 sp016869645	76.1426	221	1345	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__SHVW01;f__SHVW01;g__SHVW01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000202835.1	s__Acidiphilium multivorum	76.1086	175	1345	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acidiphilium	95.0	98.69	98.42	0.90	0.87	6	-
GCF_902712915.1	s__Acidiphilium sp002255515	76.0346	148	1345	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acidiphilium	95.0	99.59	99.19	0.97	0.94	3	-
GCF_002797515.1	s__Bradyrhizobium lablabi_B	75.9957	138	1345	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018130945.1	s__Bradyrhizobium manausense_C	75.973	166	1345	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900100655.1	s__Limimonas halophila	75.9728	154	1345	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Kiloniellales;f__Rhodovibrionaceae;g__Limimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013240295.1	s__Aquamicrobium_A sediminum	75.7789	143	1345	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aquamicrobium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900107585.1	s__Rubrimonas cliftonensis	75.7205	240	1345	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rubrimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016775475.1	s__Belnapia sp016775475	75.6617	263	1345	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Belnapia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004005855.1	s__Rhodovarius sp004005855	75.6615	198	1345	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Rhodovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900696695.1	s__Terricaulis sp900696695	75.6389	135	1345	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__TH1-2;g__Terricaulis	95.0	99.53	99.53	0.91	0.91	2	-
GCF_001982615.1	s__Roseomonas deserti	75.638	250	1345	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 11:52:29,444] [INFO] GTDB search result was written to GCA_022826185.1_ASM2282618v1_genomic.fna/result_gtdb.tsv
[2023-06-13 11:52:29,444] [INFO] ===== GTDB Search completed =====
[2023-06-13 11:52:29,451] [INFO] DFAST_QC result json was written to GCA_022826185.1_ASM2282618v1_genomic.fna/dqc_result.json
[2023-06-13 11:52:29,452] [INFO] DFAST_QC completed!
[2023-06-13 11:52:29,452] [INFO] Total running time: 0h1m52s