[2023-06-17 03:01:30,922] [INFO] DFAST_QC pipeline started.
[2023-06-17 03:01:30,924] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 03:01:30,924] [INFO] DQC Reference Directory: /var/lib/cwl/stg25e536f6-94b5-42d7-9520-961577300de8/dqc_reference
[2023-06-17 03:01:34,655] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 03:01:34,656] [INFO] Task started: Prodigal
[2023-06-17 03:01:34,657] [INFO] Running command: gunzip -c /var/lib/cwl/stg1a26f24b-1629-4e21-bbd7-dacd1c42635b/GCA_028291405.1_ASM2829140v1_genomic.fna.gz | prodigal -d GCA_028291405.1_ASM2829140v1_genomic.fna/cds.fna -a GCA_028291405.1_ASM2829140v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 03:01:50,023] [INFO] Task succeeded: Prodigal
[2023-06-17 03:01:50,024] [INFO] Task started: HMMsearch
[2023-06-17 03:01:50,024] [INFO] Running command: hmmsearch --tblout GCA_028291405.1_ASM2829140v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg25e536f6-94b5-42d7-9520-961577300de8/dqc_reference/reference_markers.hmm GCA_028291405.1_ASM2829140v1_genomic.fna/protein.faa > /dev/null
[2023-06-17 03:01:50,367] [INFO] Task succeeded: HMMsearch
[2023-06-17 03:01:50,369] [INFO] Found 6/6 markers.
[2023-06-17 03:01:50,423] [INFO] Query marker FASTA was written to GCA_028291405.1_ASM2829140v1_genomic.fna/markers.fasta
[2023-06-17 03:01:50,423] [INFO] Task started: Blastn
[2023-06-17 03:01:50,423] [INFO] Running command: blastn -query GCA_028291405.1_ASM2829140v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg25e536f6-94b5-42d7-9520-961577300de8/dqc_reference/reference_markers.fasta -out GCA_028291405.1_ASM2829140v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 03:01:51,406] [INFO] Task succeeded: Blastn
[2023-06-17 03:01:51,411] [INFO] Selected 28 target genomes.
[2023-06-17 03:01:51,412] [INFO] Target genome list was writen to GCA_028291405.1_ASM2829140v1_genomic.fna/target_genomes.txt
[2023-06-17 03:01:51,421] [INFO] Task started: fastANI
[2023-06-17 03:01:51,422] [INFO] Running command: fastANI --query /var/lib/cwl/stg1a26f24b-1629-4e21-bbd7-dacd1c42635b/GCA_028291405.1_ASM2829140v1_genomic.fna.gz --refList GCA_028291405.1_ASM2829140v1_genomic.fna/target_genomes.txt --output GCA_028291405.1_ASM2829140v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 03:02:18,747] [INFO] Task succeeded: fastANI
[2023-06-17 03:02:18,748] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg25e536f6-94b5-42d7-9520-961577300de8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 03:02:18,748] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg25e536f6-94b5-42d7-9520-961577300de8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 03:02:18,774] [INFO] Found 28 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 03:02:18,774] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-17 03:02:18,775] [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	77.525	459	1940	95	below_threshold
Hypericibacter adhaerens	strain=R5959	GCA_008728835.1	2602016	2602016	type	True	77.2719	365	1940	95	below_threshold
Skermanella pratensis	strain=W17	GCA_008843145.1	2233999	2233999	type	True	77.0869	321	1940	95	below_threshold
Stella humosa	strain=DSM 5900	GCA_003751345.1	94	94	type	True	77.0374	372	1940	95	below_threshold
Skermanella rosea	strain=KEMB 2255-458	GCA_016806835.2	1817965	1817965	type	True	77.0339	369	1940	95	below_threshold
Stella humosa	strain=ATCC 43930	GCA_006738645.1	94	94	type	True	77.0309	365	1940	95	below_threshold
Skermanella mucosa	strain=KEMB 2255-438	GCA_016765655.2	1789672	1789672	type	True	76.9643	364	1940	95	below_threshold
Skermanella stibiiresistens	strain=SB22	GCA_000576635.1	913326	913326	type	True	76.9497	323	1940	95	below_threshold
Azospirillum tabaci	strain=W712	GCA_014596085.1	2752310	2752310	type	True	76.9379	354	1940	95	below_threshold
Dongia mobilis	strain=CGMCC 1.7660	GCA_004363235.1	578943	578943	type	True	76.9226	226	1940	95	below_threshold
Azospirillum agricola	strain=CC-HIH038	GCA_017876095.1	1720247	1720247	type	True	76.9152	455	1940	95	below_threshold
Pelagibius marinus	strain=NBU2595	GCA_014925385.1	2762760	2762760	type	True	76.8258	283	1940	95	below_threshold
Azospirillum soli	strain=CC-LY788	GCA_017876165.1	1304799	1304799	type	True	76.7968	327	1940	95	below_threshold
Inquilinus limosus	strain=DSM 16000	GCA_000423185.1	171674	171674	type	True	76.7682	468	1940	95	below_threshold
Azospirillum rugosum	strain=IMMIB AFH-6	GCA_017876155.1	416170	416170	type	True	76.7039	384	1940	95	below_threshold
Nisaea acidiphila	strain=MEBiC11861	GCA_024662015.1	1862145	1862145	type	True	76.6926	206	1940	95	below_threshold
Blastochloris tepida	strain=GI	GCA_003966715.1	2233851	2233851	type	True	76.6245	251	1940	95	below_threshold
Bradyrhizobium forestalis	strain=INPA54B	GCA_002795245.1	1419263	1419263	type	True	76.5855	315	1940	95	below_threshold
Blastochloris sulfoviridis	strain=DSM 729	GCA_008630065.1	50712	50712	type	True	76.4565	240	1940	95	below_threshold
Rhodovastum atsumiense	strain=G2-11	GCA_937425535.1	504468	504468	type	True	76.4446	302	1940	95	below_threshold
Bradyrhizobium cajani	strain=1010	GCA_009759665.1	1928661	1928661	type	True	76.372	338	1940	95	below_threshold
Bradyrhizobium sacchari	strain=p9-20	GCA_002068095.1	1399419	1399419	type	True	76.3593	347	1940	95	below_threshold
Roseococcus pinisoli	strain=XZZS9	GCA_018413645.1	2835040	2835040	type	True	76.2038	248	1940	95	below_threshold
Rhabdaerophilum calidifontis	strain=SYSU G02060	GCA_008641065.1	2604328	2604328	type	True	76.1783	231	1940	95	below_threshold
Methylobacterium adhaesivum	strain=DSM 17169	GCA_022179065.1	333297	333297	type	True	76.1748	177	1940	95	below_threshold
Roseomonas oryzae	strain=KCTC 42542	GCA_008386565.1	1608942	1608942	type	True	76.1339	208	1940	95	below_threshold
Roseomonas rubea	strain=MO17	GCA_016106015.1	2748666	2748666	type	True	76.0345	263	1940	95	below_threshold
Marinicauda salina	strain=WD6-1	GCA_003122085.1	2135793	2135793	type	True	75.8073	206	1940	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-17 03:02:18,777] [INFO] DFAST Taxonomy check result was written to GCA_028291405.1_ASM2829140v1_genomic.fna/tc_result.tsv
[2023-06-17 03:02:18,780] [INFO] ===== Taxonomy check completed =====
[2023-06-17 03:02:18,780] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 03:02:18,780] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg25e536f6-94b5-42d7-9520-961577300de8/dqc_reference/checkm_data
[2023-06-17 03:02:18,781] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 03:02:18,844] [INFO] Task started: CheckM
[2023-06-17 03:02:18,844] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_028291405.1_ASM2829140v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_028291405.1_ASM2829140v1_genomic.fna/checkm_input GCA_028291405.1_ASM2829140v1_genomic.fna/checkm_result
[2023-06-17 03:03:05,047] [INFO] Task succeeded: CheckM
[2023-06-17 03:03:05,049] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-17 03:03:05,081] [INFO] ===== Completeness check finished =====
[2023-06-17 03:03:05,082] [INFO] ===== Start GTDB Search =====
[2023-06-17 03:03:05,082] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_028291405.1_ASM2829140v1_genomic.fna/markers.fasta)
[2023-06-17 03:03:05,083] [INFO] Task started: Blastn
[2023-06-17 03:03:05,083] [INFO] Running command: blastn -query GCA_028291405.1_ASM2829140v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg25e536f6-94b5-42d7-9520-961577300de8/dqc_reference/reference_markers_gtdb.fasta -out GCA_028291405.1_ASM2829140v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 03:03:06,962] [INFO] Task succeeded: Blastn
[2023-06-17 03:03:06,968] [INFO] Selected 27 target genomes.
[2023-06-17 03:03:06,969] [INFO] Target genome list was writen to GCA_028291405.1_ASM2829140v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 03:03:07,002] [INFO] Task started: fastANI
[2023-06-17 03:03:07,002] [INFO] Running command: fastANI --query /var/lib/cwl/stg1a26f24b-1629-4e21-bbd7-dacd1c42635b/GCA_028291405.1_ASM2829140v1_genomic.fna.gz --refList GCA_028291405.1_ASM2829140v1_genomic.fna/target_genomes_gtdb.txt --output GCA_028291405.1_ASM2829140v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 03:03:30,670] [INFO] Task succeeded: fastANI
[2023-06-17 03:03:30,692] [INFO] Found 27 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-17 03:03:30,693] [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_000518365.1	s__URHD0088 sp000518365	79.9507	731	1940	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__ATCC43930;f__Stellaceae;g__URHD0088	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018971215.1	s__REEB95 sp018971215	77.9298	280	1940	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__ATCC43930;f__Stellaceae;g__REEB95	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014643535.1	s__Aliidongia dinghuensis	77.517	460	1940	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__ATCC43930;f__Stellaceae;g__Aliidongia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005888425.1	s__AP-15 sp005888425	77.4917	219	1940	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_005888515.1	s__AP-15 sp005888515	77.4139	192	1940	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__ATCC43930;f__Stellaceae;g__AP-15	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003576685.1	s__SYSU-D60014 sp003576685	77.2039	313	1940	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_006738865.1	s__Stella sp006738865	77.1507	421	1940	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__ATCC43930;f__Stellaceae;g__Stella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016201015.1	s__JACQDQ01 sp016201015	77.144	341	1940	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__CACIAM-22H2;f__CACIAM-22H2;g__JACQDQ01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900177295.1	s__Tistlia consotensis	77.0466	506	1940	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Kiloniellales;f__DSM-21159;g__Tistlia	95.0	99.99	99.99	0.99	0.99	2	-
GCA_019241915.1	s__AP-15 sp019241915	77.0174	271	1940	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	77.0173	367	1940	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__ATCC43930;f__Stellaceae;g__Stella	95.0	100.00	100.00	1.00	1.00	2	-
GCA_016869645.1	s__SHVW01 sp016869645	77.0061	367	1940	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__SHVW01;f__SHVW01;g__SHVW01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004363235.1	s__Dongia mobilis	76.9439	224	1940	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Dongiales;f__Dongiaceae;g__Dongia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_006739055.1	s__Stella vacuolata	76.9313	424	1940	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__ATCC43930;f__Stellaceae;g__Stella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903897565.1	s__CAIXXC01 sp903897565	76.924	241	1940	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__ATCC43930;f__Stellaceae;g__CAIXXC01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005884705.1	s__Reyranella sp005884705	76.9106	254	1940	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016794165.1	s__Dongia sp016794165	76.7904	167	1940	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Dongiales;f__Dongiaceae;g__Dongia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000423185.1	s__Inquilinus limosus	76.7877	464	1940	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_014197805.1	s__Rhodospirillum_A centenum	76.7248	250	1940	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Rhodospirillum_A	95.0	100.00	100.00	1.00	1.00	2	-
GCA_016195085.1	s__JACQAG01 sp016195085	76.7171	286	1940	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__SHVZ01;f__SHVZ01;g__JACQAG01	95.0	99.88	99.88	0.96	0.96	2	-
GCA_019240125.1	s__AP-15 sp019240125	76.7075	269	1940	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__ATCC43930;f__Stellaceae;g__AP-15	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900110395.1	s__Reyranella sp900110395	76.6629	393	1940	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002795245.1	s__Bradyrhizobium forestalis	76.6054	311	1940	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016185205.1	s__Pseudolabrys sp016185205	76.3744	220	1940	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Pseudolabrys	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000333275.1	s__Nitrospirillum sp000333275	76.3466	199	1940	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Nitrospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002068095.1	s__Bradyrhizobium sacchari	76.3285	348	1940	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	99.98	99.98	0.99	0.99	3	-
GCF_008641065.1	s__Rhabdaerophilum calidifontis	76.1566	229	1940	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Rhabdaerophilum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-17 03:03:30,695] [INFO] GTDB search result was written to GCA_028291405.1_ASM2829140v1_genomic.fna/result_gtdb.tsv
[2023-06-17 03:03:30,695] [INFO] ===== GTDB Search completed =====
[2023-06-17 03:03:30,701] [INFO] DFAST_QC result json was written to GCA_028291405.1_ASM2829140v1_genomic.fna/dqc_result.json
[2023-06-17 03:03:30,701] [INFO] DFAST_QC completed!
[2023-06-17 03:03:30,701] [INFO] Total running time: 0h1m60s