[2023-06-05 05:15:32,633] [INFO] DFAST_QC pipeline started.
[2023-06-05 05:15:32,634] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 05:15:32,634] [INFO] DQC Reference Directory: /var/lib/cwl/stg29cfc4bb-ae19-472c-ab1b-827f753a9dbc/dqc_reference
[2023-06-05 05:15:34,838] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 05:15:34,839] [INFO] Task started: Prodigal
[2023-06-05 05:15:34,840] [INFO] Running command: gunzip -c /var/lib/cwl/stg6d073e77-41ed-4fe3-957e-5574b1e562a1/GCA_010032545.1_ASM1003254v1_genomic.fna.gz | prodigal -d GCA_010032545.1_ASM1003254v1_genomic.fna/cds.fna -a GCA_010032545.1_ASM1003254v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 05:15:46,732] [INFO] Task succeeded: Prodigal
[2023-06-05 05:15:46,733] [INFO] Task started: HMMsearch
[2023-06-05 05:15:46,733] [INFO] Running command: hmmsearch --tblout GCA_010032545.1_ASM1003254v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg29cfc4bb-ae19-472c-ab1b-827f753a9dbc/dqc_reference/reference_markers.hmm GCA_010032545.1_ASM1003254v1_genomic.fna/protein.faa > /dev/null
[2023-06-05 05:15:47,040] [INFO] Task succeeded: HMMsearch
[2023-06-05 05:15:47,042] [INFO] Found 6/6 markers.
[2023-06-05 05:15:47,085] [INFO] Query marker FASTA was written to GCA_010032545.1_ASM1003254v1_genomic.fna/markers.fasta
[2023-06-05 05:15:47,085] [INFO] Task started: Blastn
[2023-06-05 05:15:47,085] [INFO] Running command: blastn -query GCA_010032545.1_ASM1003254v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg29cfc4bb-ae19-472c-ab1b-827f753a9dbc/dqc_reference/reference_markers.fasta -out GCA_010032545.1_ASM1003254v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 05:15:47,986] [INFO] Task succeeded: Blastn
[2023-06-05 05:15:47,991] [INFO] Selected 24 target genomes.
[2023-06-05 05:15:47,991] [INFO] Target genome list was writen to GCA_010032545.1_ASM1003254v1_genomic.fna/target_genomes.txt
[2023-06-05 05:15:47,993] [INFO] Task started: fastANI
[2023-06-05 05:15:47,994] [INFO] Running command: fastANI --query /var/lib/cwl/stg6d073e77-41ed-4fe3-957e-5574b1e562a1/GCA_010032545.1_ASM1003254v1_genomic.fna.gz --refList GCA_010032545.1_ASM1003254v1_genomic.fna/target_genomes.txt --output GCA_010032545.1_ASM1003254v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 05:16:08,873] [INFO] Task succeeded: fastANI
[2023-06-05 05:16:08,873] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg29cfc4bb-ae19-472c-ab1b-827f753a9dbc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 05:16:08,874] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg29cfc4bb-ae19-472c-ab1b-827f753a9dbc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 05:16:08,900] [INFO] Found 24 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 05:16:08,900] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-05 05:16:08,900] [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
Reyranella aquatilis	strain=KCTC 52223	GCA_020880995.1	2035356	2035356	type	True	82.7108	986	1249	95	below_threshold
Reyranella soli	strain=NBRC 108950	GCA_007992495.1	1230389	1230389	type	True	82.4277	964	1249	95	below_threshold
Reyranella massiliensis	strain=521	GCA_000312425.1	445220	445220	type	True	81.9577	915	1249	95	below_threshold
Vineibacter terrae	strain=CC-CFT640	GCA_008039615.1	2586908	2586908	type	True	78.6944	593	1249	95	below_threshold
Tistlia consotensis	strain=USBA 355	GCA_900177295.1	1321365	1321365	type	True	76.7161	313	1249	95	below_threshold
Oceanibaculum indicum	strain=P24	GCA_000299935.1	526216	526216	type	True	76.707	183	1249	95	below_threshold
Ferrovibrio terrae	strain=K5	GCA_007197755.1	2594003	2594003	type	True	76.7044	199	1249	95	below_threshold
Tistlia consotensis	strain=DSM 21585	GCA_900188055.1	1321365	1321365	type	True	76.7029	316	1249	95	below_threshold
Oceanibaculum pacificum	strain=MCCC 1A02656	GCA_001618175.1	580166	580166	type	True	76.6963	181	1249	95	below_threshold
Magnetospirillum moscoviense	strain=BB-1	GCA_001650635.1	1437059	1437059	type	True	76.6924	161	1249	95	below_threshold
Qipengyuania gaetbuli	strain=DSM 16225	GCA_009827315.1	266952	266952	type	True	76.6884	62	1249	95	below_threshold
Microvirga splendida	strain=BT325	GCA_016427565.1	2795727	2795727	type	True	76.6536	132	1249	95	below_threshold
Inquilinus limosus	strain=DSM 16000	GCA_000423185.1	171674	171674	type	True	76.5504	293	1249	95	below_threshold
Azospirillum oryzae	strain=COC8	GCA_008364795.1	286727	286727	type	True	76.4935	221	1249	95	below_threshold
Azospirillum thiophilum	strain=BV-S	GCA_001305595.1	528244	528244	type	True	76.4539	247	1249	95	below_threshold
Azospirillum thiophilum	strain=DSM 21654	GCA_000960825.1	528244	528244	type	True	76.4442	251	1249	95	below_threshold
Methylobrevis albus	strain=L22	GCA_015904235.1	2793297	2793297	type	True	76.4417	202	1249	95	below_threshold
Magnetospirillum caucaseum	strain=SO-1	GCA_000342045.1	1244869	1244869	type	True	76.3869	175	1249	95	below_threshold
Roseospira navarrensis	strain=DSM 15114	GCA_009601025.1	140058	140058	type	True	76.3764	131	1249	95	below_threshold
Oharaeibacter diazotrophicus	strain=DSM 102969	GCA_004362745.1	1920512	1920512	type	True	76.3338	241	1249	95	below_threshold
Magnetospirillum magnetotacticum	strain=MS-1	GCA_000829825.1	188	188	type	True	76.2033	124	1249	95	below_threshold
Pseudaminobacter soli	strain=HC19	GCA_014595955.1	2831468	2831468	type	True	76.1664	145	1249	95	below_threshold
Pseudaminobacter soli	strain=19-2017	GCA_018310375.1	2831468	2831468	type	True	76.1664	145	1249	95	below_threshold
Azospirillum halopraeferens	strain=DSM 3675	GCA_000429625.1	34010	34010	type	True	76.1034	247	1249	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 05:16:08,902] [INFO] DFAST Taxonomy check result was written to GCA_010032545.1_ASM1003254v1_genomic.fna/tc_result.tsv
[2023-06-05 05:16:08,903] [INFO] ===== Taxonomy check completed =====
[2023-06-05 05:16:08,903] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 05:16:08,903] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg29cfc4bb-ae19-472c-ab1b-827f753a9dbc/dqc_reference/checkm_data
[2023-06-05 05:16:08,904] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 05:16:08,946] [INFO] Task started: CheckM
[2023-06-05 05:16:08,946] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_010032545.1_ASM1003254v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_010032545.1_ASM1003254v1_genomic.fna/checkm_input GCA_010032545.1_ASM1003254v1_genomic.fna/checkm_result
[2023-06-05 05:16:46,763] [INFO] Task succeeded: CheckM
[2023-06-05 05:16:46,765] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 10.19%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 05:16:46,789] [INFO] ===== Completeness check finished =====
[2023-06-05 05:16:46,790] [INFO] ===== Start GTDB Search =====
[2023-06-05 05:16:46,790] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_010032545.1_ASM1003254v1_genomic.fna/markers.fasta)
[2023-06-05 05:16:46,790] [INFO] Task started: Blastn
[2023-06-05 05:16:46,790] [INFO] Running command: blastn -query GCA_010032545.1_ASM1003254v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg29cfc4bb-ae19-472c-ab1b-827f753a9dbc/dqc_reference/reference_markers_gtdb.fasta -out GCA_010032545.1_ASM1003254v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 05:16:48,369] [INFO] Task succeeded: Blastn
[2023-06-05 05:16:48,375] [INFO] Selected 28 target genomes.
[2023-06-05 05:16:48,375] [INFO] Target genome list was writen to GCA_010032545.1_ASM1003254v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 05:16:48,545] [INFO] Task started: fastANI
[2023-06-05 05:16:48,545] [INFO] Running command: fastANI --query /var/lib/cwl/stg6d073e77-41ed-4fe3-957e-5574b1e562a1/GCA_010032545.1_ASM1003254v1_genomic.fna.gz --refList GCA_010032545.1_ASM1003254v1_genomic.fna/target_genomes_gtdb.txt --output GCA_010032545.1_ASM1003254v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 05:17:16,511] [INFO] Task succeeded: fastANI
[2023-06-05 05:17:16,537] [INFO] Found 28 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 05:17:16,538] [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_010032545.1	s__Reyranella sp010032545	100.0	1237	1249	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_004296935.1	s__Reyranella sp004296935	85.9043	1026	1249	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001767945.1	s__Reyranella sp001767945	85.076	867	1249	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016191685.1	s__Reyranella sp016191685	84.9112	708	1249	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004296815.1	s__Reyranella sp004296815	83.2931	749	1249	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019039055.1	s__Reyranella sp019039055	82.947	971	1249	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001557035.1	s__Reyranella sp001557035	82.8776	861	1249	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002281855.1	s__Reyranella sp002281855	82.6947	939	1249	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	99.99	99.99	0.99	0.99	3	-
GCA_004297265.1	s__Reyranella sp004297265	82.6293	956	1249	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900110395.1	s__Reyranella sp900110395	82.4383	999	1249	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009377525.1	s__Reyranella sp009377525	82.3488	895	1249	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013290035.1	s__Reyranella sp013290035	82.3189	586	1249	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013205335.1	s__Reyranella sp013205335	82.2256	781	1249	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	81.9955	928	1249	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001897995.1	s__Reyranella sp001897995	81.9416	828	1249	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	99.19	98.73	0.86	0.86	3	-
GCF_000312425.1	s__Reyranella massiliensis	81.9324	919	1249	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005884705.1	s__Reyranella sp005884705	81.7828	609	1249	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018240745.1	s__Reyranella sp018240745	81.4244	835	1249	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007859315.1	s__SYSU-D60007 sp007859315	78.3842	549	1249	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__SYSU-D60007	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003576705.1	s__SYSU-D60015 sp003576705	77.1145	340	1249	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Ferrovibrionales;f__Ferrovibrionaceae;g__SYSU-D60015	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002796975.1	s__Ferrovibrio sp002796975	76.8435	189	1249	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Ferrovibrionales;f__Ferrovibrionaceae;g__Ferrovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017307375.1	s__JAFKFH01 sp017307375	76.7607	286	1249	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Ferrovibrionales;f__Ferrovibrionaceae;g__JAFKFH01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014197805.1	s__Rhodospirillum_A centenum	76.7091	179	1249	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_007197755.1	s__Ferrovibrio terrae	76.6811	201	1249	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Ferrovibrionales;f__Ferrovibrionaceae;g__Ferrovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000423185.1	s__Inquilinus limosus	76.5511	294	1249	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_018336035.1	s__Ferrovibrio sp018336035	76.4881	192	1249	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Ferrovibrionales;f__Ferrovibrionaceae;g__Ferrovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000009985.1	s__Phaeospirillum magneticum	76.3126	141	1249	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Phaeospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001939945.1	s__Aerophototrophica crusticola	76.0678	148	1249	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Aerophototrophica	95.0	99.94	99.94	0.97	0.97	2	-
--------------------------------------------------------------------------------
[2023-06-05 05:17:16,540] [INFO] GTDB search result was written to GCA_010032545.1_ASM1003254v1_genomic.fna/result_gtdb.tsv
[2023-06-05 05:17:16,540] [INFO] ===== GTDB Search completed =====
[2023-06-05 05:17:16,545] [INFO] DFAST_QC result json was written to GCA_010032545.1_ASM1003254v1_genomic.fna/dqc_result.json
[2023-06-05 05:17:16,546] [INFO] DFAST_QC completed!
[2023-06-05 05:17:16,546] [INFO] Total running time: 0h1m44s