[2023-06-29 12:22:18,671] [INFO] DFAST_QC pipeline started.
[2023-06-29 12:22:18,673] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 12:22:18,674] [INFO] DQC Reference Directory: /var/lib/cwl/stg3d886894-5925-429c-bfd9-4e71ae105acc/dqc_reference
[2023-06-29 12:22:19,876] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 12:22:19,876] [INFO] Task started: Prodigal
[2023-06-29 12:22:19,877] [INFO] Running command: gunzip -c /var/lib/cwl/stg28be03de-0813-4677-be3c-7f9100abaaee/GCA_021790775.1_ASM2179077v1_genomic.fna.gz | prodigal -d GCA_021790775.1_ASM2179077v1_genomic.fna/cds.fna -a GCA_021790775.1_ASM2179077v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 12:22:32,989] [INFO] Task succeeded: Prodigal
[2023-06-29 12:22:32,990] [INFO] Task started: HMMsearch
[2023-06-29 12:22:32,990] [INFO] Running command: hmmsearch --tblout GCA_021790775.1_ASM2179077v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3d886894-5925-429c-bfd9-4e71ae105acc/dqc_reference/reference_markers.hmm GCA_021790775.1_ASM2179077v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 12:22:33,231] [INFO] Task succeeded: HMMsearch
[2023-06-29 12:22:33,232] [INFO] Found 6/6 markers.
[2023-06-29 12:22:33,273] [INFO] Query marker FASTA was written to GCA_021790775.1_ASM2179077v1_genomic.fna/markers.fasta
[2023-06-29 12:22:33,274] [INFO] Task started: Blastn
[2023-06-29 12:22:33,274] [INFO] Running command: blastn -query GCA_021790775.1_ASM2179077v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3d886894-5925-429c-bfd9-4e71ae105acc/dqc_reference/reference_markers.fasta -out GCA_021790775.1_ASM2179077v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 12:22:34,206] [INFO] Task succeeded: Blastn
[2023-06-29 12:22:34,209] [INFO] Selected 28 target genomes.
[2023-06-29 12:22:34,210] [INFO] Target genome list was writen to GCA_021790775.1_ASM2179077v1_genomic.fna/target_genomes.txt
[2023-06-29 12:22:34,213] [INFO] Task started: fastANI
[2023-06-29 12:22:34,213] [INFO] Running command: fastANI --query /var/lib/cwl/stg28be03de-0813-4677-be3c-7f9100abaaee/GCA_021790775.1_ASM2179077v1_genomic.fna.gz --refList GCA_021790775.1_ASM2179077v1_genomic.fna/target_genomes.txt --output GCA_021790775.1_ASM2179077v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 12:22:59,217] [INFO] Task succeeded: fastANI
[2023-06-29 12:22:59,217] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3d886894-5925-429c-bfd9-4e71ae105acc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 12:22:59,218] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3d886894-5925-429c-bfd9-4e71ae105acc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 12:22:59,238] [INFO] Found 28 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 12:22:59,238] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 12:22:59,238] [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
Hypericibacter adhaerens	strain=R5959	GCA_008728835.1	2602016	2602016	type	True	77.9714	494	1610	95	below_threshold
Hypericibacter terrae	strain=R5913	GCA_008728855.1	2602015	2602015	type	True	77.9073	471	1610	95	below_threshold
Dongia mobilis	strain=CGMCC 1.7660	GCA_004363235.1	578943	578943	type	True	77.4722	312	1610	95	below_threshold
Oceanibaculum pacificum	strain=MCCC 1A02656	GCA_001618175.1	580166	580166	type	True	77.442	271	1610	95	below_threshold
Tistlia consotensis	strain=DSM 21585	GCA_900188055.1	1321365	1321365	type	True	77.2699	448	1610	95	below_threshold
Tistlia consotensis	strain=USBA 355	GCA_900177295.1	1321365	1321365	type	True	77.2645	452	1610	95	below_threshold
Oceanibaculum nanhaiense	strain=L54-1-50	GCA_002148795.1	1909734	1909734	type	True	77.2233	277	1610	95	below_threshold
Azospirillum ramasamyi	strain=M2T2B2	GCA_003233655.1	682998	682998	type	True	77.2113	320	1610	95	below_threshold
Azospirillum thermophilum	strain=CFH 70021	GCA_003130795.1	2202148	2202148	type	True	77.0869	367	1610	95	below_threshold
Stella humosa	strain=ATCC 43930	GCA_006738645.1	94	94	type	True	77.0407	345	1610	95	below_threshold
Azospirillum thiophilum	strain=DSM 21654	GCA_000960825.1	528244	528244	type	True	77.0315	359	1610	95	below_threshold
Azospirillum thiophilum	strain=BV-S	GCA_001305595.1	528244	528244	type	True	77.021	358	1610	95	below_threshold
Stella humosa	strain=DSM 5900	GCA_003751345.1	94	94	type	True	77.0136	347	1610	95	below_threshold
Thalassobaculum fulvum	strain=KCTC 42651	GCA_014652915.1	1633335	1633335	type	True	77.0084	338	1610	95	below_threshold
Azospirillum agricola	strain=CC-HIH038	GCA_017876095.1	1720247	1720247	type	True	76.9417	382	1610	95	below_threshold
Azospirillum oleiclasticum	strain=RWY-5-1-1	GCA_013423485.1	2735135	2735135	type	True	76.9404	341	1610	95	below_threshold
Azospirillum oryzae	strain=COC8	GCA_008364795.1	286727	286727	type	True	76.9227	314	1610	95	below_threshold
Arenibaculum pallidiluteum	strain=SYSU D00532	GCA_017355985.1	2812559	2812559	type	True	76.8829	323	1610	95	below_threshold
Azospirillum rugosum	strain=IMMIB AFH-6	GCA_017876155.1	416170	416170	type	True	76.8232	344	1610	95	below_threshold
Magnetospirillum caucaseum	strain=SO-1	GCA_000342045.1	1244869	1244869	type	True	76.8027	210	1610	95	below_threshold
Azospirillum baldaniorum	strain=Sp245	GCA_000237365.1	1064539	1064539	type	True	76.7345	346	1610	95	below_threshold
Azospirillum baldaniorum	strain=Sp245	GCA_003119195.2	1064539	1064539	type	True	76.726	353	1610	95	below_threshold
Nisaea acidiphila	strain=MEBiC11861	GCA_024662015.1	1862145	1862145	type	True	76.6171	249	1610	95	below_threshold
Rhodoligotrophos defluvii	strain=lm1	GCA_005281615.1	2561934	2561934	type	True	76.4322	166	1610	95	below_threshold
Rhodovastum atsumiense	strain=G2-11	GCA_937425535.1	504468	504468	type	True	76.428	241	1610	95	below_threshold
Roseomonas rubea	strain=MO17	GCA_016106015.1	2748666	2748666	type	True	76.3092	171	1610	95	below_threshold
Roseococcus pinisoli	strain=XZZS9	GCA_018413645.1	2835040	2835040	type	True	76.0804	185	1610	95	below_threshold
Pararhodospirillum oryzae	strain=NBRC 107573	GCA_007992075.1	478448	478448	type	True	76.0282	113	1610	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 12:22:59,241] [INFO] DFAST Taxonomy check result was written to GCA_021790775.1_ASM2179077v1_genomic.fna/tc_result.tsv
[2023-06-29 12:22:59,241] [INFO] ===== Taxonomy check completed =====
[2023-06-29 12:22:59,241] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 12:22:59,242] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3d886894-5925-429c-bfd9-4e71ae105acc/dqc_reference/checkm_data
[2023-06-29 12:22:59,243] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 12:22:59,287] [INFO] Task started: CheckM
[2023-06-29 12:22:59,287] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_021790775.1_ASM2179077v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_021790775.1_ASM2179077v1_genomic.fna/checkm_input GCA_021790775.1_ASM2179077v1_genomic.fna/checkm_result
[2023-06-29 12:23:38,238] [INFO] Task succeeded: CheckM
[2023-06-29 12:23:38,245] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 12:23:38,262] [INFO] ===== Completeness check finished =====
[2023-06-29 12:23:38,262] [INFO] ===== Start GTDB Search =====
[2023-06-29 12:23:38,263] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_021790775.1_ASM2179077v1_genomic.fna/markers.fasta)
[2023-06-29 12:23:38,263] [INFO] Task started: Blastn
[2023-06-29 12:23:38,263] [INFO] Running command: blastn -query GCA_021790775.1_ASM2179077v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3d886894-5925-429c-bfd9-4e71ae105acc/dqc_reference/reference_markers_gtdb.fasta -out GCA_021790775.1_ASM2179077v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 12:23:40,125] [INFO] Task succeeded: Blastn
[2023-06-29 12:23:40,138] [INFO] Selected 23 target genomes.
[2023-06-29 12:23:40,138] [INFO] Target genome list was writen to GCA_021790775.1_ASM2179077v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 12:23:40,147] [INFO] Task started: fastANI
[2023-06-29 12:23:40,147] [INFO] Running command: fastANI --query /var/lib/cwl/stg28be03de-0813-4677-be3c-7f9100abaaee/GCA_021790775.1_ASM2179077v1_genomic.fna.gz --refList GCA_021790775.1_ASM2179077v1_genomic.fna/target_genomes_gtdb.txt --output GCA_021790775.1_ASM2179077v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 12:24:02,608] [INFO] Task succeeded: fastANI
[2023-06-29 12:24:02,625] [INFO] Found 23 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 12:24:02,625] [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_003576685.1	s__SYSU-D60014 sp003576685	99.9858	1599	1610	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Dongiales;f__Dongiaceae;g__SYSU-D60014	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_902826565.1	s__CADEFF01 sp902826565	78.1648	403	1610	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Dongiales;f__Dongiaceae;g__CADEFF01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008728835.1	s__Hypericibacter adhaerens	77.9711	494	1610	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Dongiales;f__Dongiaceae;g__Hypericibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008728855.1	s__Hypericibacter terrae	77.8742	475	1610	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	77.3903	344	1610	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__ATCC43930;f__Stellaceae;g__Stella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009885795.1	s__VFKA01 sp009885795	77.3433	312	1610	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Dongiales;f__Dongiaceae;g__VFKA01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016869645.1	s__SHVW01 sp016869645	77.3191	324	1610	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__SHVW01;f__SHVW01;g__SHVW01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005938675.2	s__Inquilinus sp005938675	77.3168	425	1610	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_900177295.1	s__Tistlia consotensis	77.2956	446	1610	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_006739055.1	s__Stella vacuolata	77.2597	368	1610	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__ATCC43930;f__Stellaceae;g__Stella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016869145.1	s__VGEU01 sp016869145	77.244	255	1610	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__MPNO01;f__VGEU01;g__VGEU01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003233655.1	s__Azospirillum ramasamyi	77.2107	320	1610	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000010725.1	s__Azospirillum lipoferum_B	77.1369	334	1610	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014652915.1	s__Thalassobaculum_A fulvum	77.0127	339	1610	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_016794075.1	s__SYSU-D60009 sp016794075	76.9907	282	1610	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Dongiales;f__Dongiaceae;g__SYSU-D60009	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902729435.1	s__Magnetospirillum sp902729435	76.9497	253	1610	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Magnetospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008364795.1	s__Azospirillum oryzae	76.9376	313	1610	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	98.65	97.30	0.92	0.84	3	-
GCA_015232025.1	s__JADFZP01 sp015232025	76.9329	183	1610	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__JADFZP01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014197805.1	s__Rhodospirillum_A centenum	76.8507	265	1610	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Rhodospirillum_A	95.0	100.00	100.00	1.00	1.00	2	-
GCF_902729425.1	s__Phaeospirillum sp902729425	76.8035	203	1610	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Phaeospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003336875.1	s__Oleisolibacter albus	76.7892	230	1610	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Oleisolibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903853455.1	s__Phaeospirillum sp903853455	76.6171	204	1610	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Phaeospirillum	95.0	99.97	99.97	0.98	0.98	2	-
GCA_016124535.1	s__RI-112 sp016124535	76.3539	224	1610	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__RI-112	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 12:24:02,628] [INFO] GTDB search result was written to GCA_021790775.1_ASM2179077v1_genomic.fna/result_gtdb.tsv
[2023-06-29 12:24:02,628] [INFO] ===== GTDB Search completed =====
[2023-06-29 12:24:02,633] [INFO] DFAST_QC result json was written to GCA_021790775.1_ASM2179077v1_genomic.fna/dqc_result.json
[2023-06-29 12:24:02,633] [INFO] DFAST_QC completed!
[2023-06-29 12:24:02,633] [INFO] Total running time: 0h1m44s