[2023-06-17 01:44:47,978] [INFO] DFAST_QC pipeline started.
[2023-06-17 01:44:47,982] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 01:44:47,983] [INFO] DQC Reference Directory: /var/lib/cwl/stga9588ca4-2b43-475c-8246-faaa29ab6f85/dqc_reference
[2023-06-17 01:44:49,896] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 01:44:49,897] [INFO] Task started: Prodigal
[2023-06-17 01:44:49,897] [INFO] Running command: gunzip -c /var/lib/cwl/stg78508d8a-fb80-4f70-a521-fab30172e8c7/GCA_028287355.1_ASM2828735v1_genomic.fna.gz | prodigal -d GCA_028287355.1_ASM2828735v1_genomic.fna/cds.fna -a GCA_028287355.1_ASM2828735v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 01:44:57,030] [INFO] Task succeeded: Prodigal
[2023-06-17 01:44:57,030] [INFO] Task started: HMMsearch
[2023-06-17 01:44:57,030] [INFO] Running command: hmmsearch --tblout GCA_028287355.1_ASM2828735v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga9588ca4-2b43-475c-8246-faaa29ab6f85/dqc_reference/reference_markers.hmm GCA_028287355.1_ASM2828735v1_genomic.fna/protein.faa > /dev/null
[2023-06-17 01:44:57,254] [INFO] Task succeeded: HMMsearch
[2023-06-17 01:44:57,255] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg78508d8a-fb80-4f70-a521-fab30172e8c7/GCA_028287355.1_ASM2828735v1_genomic.fna.gz]
[2023-06-17 01:44:57,286] [INFO] Query marker FASTA was written to GCA_028287355.1_ASM2828735v1_genomic.fna/markers.fasta
[2023-06-17 01:44:57,287] [INFO] Task started: Blastn
[2023-06-17 01:44:57,287] [INFO] Running command: blastn -query GCA_028287355.1_ASM2828735v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga9588ca4-2b43-475c-8246-faaa29ab6f85/dqc_reference/reference_markers.fasta -out GCA_028287355.1_ASM2828735v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 01:44:58,020] [INFO] Task succeeded: Blastn
[2023-06-17 01:44:58,025] [INFO] Selected 15 target genomes.
[2023-06-17 01:44:58,026] [INFO] Target genome list was writen to GCA_028287355.1_ASM2828735v1_genomic.fna/target_genomes.txt
[2023-06-17 01:44:58,048] [INFO] Task started: fastANI
[2023-06-17 01:44:58,049] [INFO] Running command: fastANI --query /var/lib/cwl/stg78508d8a-fb80-4f70-a521-fab30172e8c7/GCA_028287355.1_ASM2828735v1_genomic.fna.gz --refList GCA_028287355.1_ASM2828735v1_genomic.fna/target_genomes.txt --output GCA_028287355.1_ASM2828735v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 01:45:10,125] [INFO] Task succeeded: fastANI
[2023-06-17 01:45:10,125] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga9588ca4-2b43-475c-8246-faaa29ab6f85/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 01:45:10,126] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga9588ca4-2b43-475c-8246-faaa29ab6f85/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 01:45:10,136] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 01:45:10,136] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-17 01:45:10,136] [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
Gemmatirosa kalamazoonensis	strain=KBS708	GCA_000522985.1	861299	861299	type	True	77.7515	397	800	95	below_threshold
Gemmatimonas groenlandica	strain=TET16	GCA_013004105.1	2732249	2732249	type	True	76.387	132	800	95	below_threshold
Gemmatimonas aurantiaca	strain=T-27	GCA_000010305.1	173480	173480	type	True	76.2567	99	800	95	below_threshold
Gemmatimonas phototrophica	strain=AP64	GCA_000695095.2	1379270	1379270	type	True	76.0081	93	800	95	below_threshold
Frateuria terrea	strain=CGMCC 1.7053	GCA_900115705.1	529704	529704	type	True	75.0922	59	800	95	below_threshold
Azospirillum rugosum	strain=IMMIB AFH-6	GCA_017876155.1	416170	416170	type	True	74.8922	117	800	95	below_threshold
Agromyces kandeliae	strain=Q22	GCA_009674665.1	2666141	2666141	type	True	74.8882	94	800	95	below_threshold
Kribbella sindirgiensis	strain=DSM 27082	GCA_004331435.1	1124744	1124744	type	True	74.8094	87	800	95	below_threshold
Cellulosimicrobium funkei	strain=NBRC 104118	GCA_001570825.1	264251	264251	suspected-type	True	74.775	135	800	95	below_threshold
Mangrovactinospora gilvigriseus	strain=MUSC 26	GCA_001879105.1	1428644	1428644	type	True	74.7647	113	800	95	below_threshold
Thioalbus denitrificans	strain=DSM 26407	GCA_003337735.1	547122	547122	type	True	74.7644	64	800	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-17 01:45:10,139] [INFO] DFAST Taxonomy check result was written to GCA_028287355.1_ASM2828735v1_genomic.fna/tc_result.tsv
[2023-06-17 01:45:10,139] [INFO] ===== Taxonomy check completed =====
[2023-06-17 01:45:10,140] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 01:45:10,140] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga9588ca4-2b43-475c-8246-faaa29ab6f85/dqc_reference/checkm_data
[2023-06-17 01:45:10,142] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 01:45:10,173] [INFO] Task started: CheckM
[2023-06-17 01:45:10,174] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_028287355.1_ASM2828735v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_028287355.1_ASM2828735v1_genomic.fna/checkm_input GCA_028287355.1_ASM2828735v1_genomic.fna/checkm_result
[2023-06-17 01:45:37,740] [INFO] Task succeeded: CheckM
[2023-06-17 01:45:37,746] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 67.71%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-17 01:45:37,768] [INFO] ===== Completeness check finished =====
[2023-06-17 01:45:37,769] [INFO] ===== Start GTDB Search =====
[2023-06-17 01:45:37,769] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_028287355.1_ASM2828735v1_genomic.fna/markers.fasta)
[2023-06-17 01:45:37,770] [INFO] Task started: Blastn
[2023-06-17 01:45:37,770] [INFO] Running command: blastn -query GCA_028287355.1_ASM2828735v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga9588ca4-2b43-475c-8246-faaa29ab6f85/dqc_reference/reference_markers_gtdb.fasta -out GCA_028287355.1_ASM2828735v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 01:45:38,868] [INFO] Task succeeded: Blastn
[2023-06-17 01:45:38,872] [INFO] Selected 17 target genomes.
[2023-06-17 01:45:38,872] [INFO] Target genome list was writen to GCA_028287355.1_ASM2828735v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 01:45:38,879] [INFO] Task started: fastANI
[2023-06-17 01:45:38,879] [INFO] Running command: fastANI --query /var/lib/cwl/stg78508d8a-fb80-4f70-a521-fab30172e8c7/GCA_028287355.1_ASM2828735v1_genomic.fna.gz --refList GCA_028287355.1_ASM2828735v1_genomic.fna/target_genomes_gtdb.txt --output GCA_028287355.1_ASM2828735v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 01:45:49,278] [INFO] Task succeeded: fastANI
[2023-06-17 01:45:49,297] [INFO] Found 16 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-17 01:45:49,297] [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_013361335.1	s__AG11 sp013361335	80.5533	453	800	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__Gemmatimonadaceae;g__AG11	95.0	99.60	99.48	0.90	0.83	7	-
GCA_003223455.1	s__AG11 sp003223455	79.1401	400	800	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__Gemmatimonadaceae;g__AG11	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014378185.1	s__AG11 sp014378185	78.6024	231	800	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__Gemmatimonadaceae;g__AG11	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002215645.1	s__AG11 sp002215645	78.4877	270	800	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__Gemmatimonadaceae;g__AG11	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013361745.1	s__JABFXC01 sp013361745	78.2868	185	800	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__Gemmatimonadaceae;g__JABFXC01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013361935.1	s__JABFXC01 sp013361935	78.2543	299	800	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__Gemmatimonadaceae;g__JABFXC01	95.0	99.88	99.88	0.94	0.92	3	-
GCF_000522985.1	s__Gemmatirosa kalamazoonesis	77.7368	398	800	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__Gemmatimonadaceae;g__Gemmatirosa	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011390885.1	s__JAABRT01 sp011390885	77.4006	237	800	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__Gemmatimonadaceae;g__JAABRT01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001724275.1	s__SCN-70-22 sp001724275	77.2092	231	800	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__Gemmatimonadaceae;g__SCN-70-22	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013360595.1	s__JABWBJ01 sp013360595	77.1446	113	800	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__Gemmatimonadaceae;g__JABWBJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016794735.1	s__SCN-70-22 sp016794735	76.865	128	800	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__Gemmatimonadaceae;g__SCN-70-22	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002483225.1	s__Gemmatimonas sp002483225	76.789	123	800	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__Gemmatimonadaceae;g__Gemmatimonas	95.0	97.70	97.70	0.96	0.96	2	-
GCA_013697785.1	s__FEN-1250 sp013697785	76.684	144	800	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__Gemmatimonadaceae;g__FEN-1250	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003222205.1	s__40CM-2-70-7 sp003222205	76.0935	99	800	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__GWC2-71-9;g__40CM-2-70-7	95.0	97.54	95.75	0.87	0.83	8	-
GCA_003221045.1	s__AG41 sp003221045	75.718	67	800	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__GWC2-71-9;g__AG41	95.0	98.20	98.20	0.96	0.96	2	-
GCF_009674665.1	s__Agromyces kandeliae	74.8837	95	800	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-17 01:45:49,299] [INFO] GTDB search result was written to GCA_028287355.1_ASM2828735v1_genomic.fna/result_gtdb.tsv
[2023-06-17 01:45:49,299] [INFO] ===== GTDB Search completed =====
[2023-06-17 01:45:49,303] [INFO] DFAST_QC result json was written to GCA_028287355.1_ASM2828735v1_genomic.fna/dqc_result.json
[2023-06-17 01:45:49,303] [INFO] DFAST_QC completed!
[2023-06-17 01:45:49,304] [INFO] Total running time: 0h1m1s