[2023-06-28 14:06:29,686] [INFO] DFAST_QC pipeline started.
[2023-06-28 14:06:29,688] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 14:06:29,688] [INFO] DQC Reference Directory: /var/lib/cwl/stg952e18ac-800e-4247-85ac-23ee643f2179/dqc_reference
[2023-06-28 14:06:30,891] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 14:06:30,891] [INFO] Task started: Prodigal
[2023-06-28 14:06:30,892] [INFO] Running command: gunzip -c /var/lib/cwl/stgfd6b9901-dd72-4ce2-bcbf-e117123dd922/GCA_020446325.1_ASM2044632v1_genomic.fna.gz | prodigal -d GCA_020446325.1_ASM2044632v1_genomic.fna/cds.fna -a GCA_020446325.1_ASM2044632v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 14:06:39,209] [INFO] Task succeeded: Prodigal
[2023-06-28 14:06:39,210] [INFO] Task started: HMMsearch
[2023-06-28 14:06:39,210] [INFO] Running command: hmmsearch --tblout GCA_020446325.1_ASM2044632v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg952e18ac-800e-4247-85ac-23ee643f2179/dqc_reference/reference_markers.hmm GCA_020446325.1_ASM2044632v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 14:06:39,413] [INFO] Task succeeded: HMMsearch
[2023-06-28 14:06:39,414] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgfd6b9901-dd72-4ce2-bcbf-e117123dd922/GCA_020446325.1_ASM2044632v1_genomic.fna.gz]
[2023-06-28 14:06:39,446] [INFO] Query marker FASTA was written to GCA_020446325.1_ASM2044632v1_genomic.fna/markers.fasta
[2023-06-28 14:06:39,447] [INFO] Task started: Blastn
[2023-06-28 14:06:39,447] [INFO] Running command: blastn -query GCA_020446325.1_ASM2044632v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg952e18ac-800e-4247-85ac-23ee643f2179/dqc_reference/reference_markers.fasta -out GCA_020446325.1_ASM2044632v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 14:06:40,205] [INFO] Task succeeded: Blastn
[2023-06-28 14:06:40,210] [INFO] Selected 17 target genomes.
[2023-06-28 14:06:40,210] [INFO] Target genome list was writen to GCA_020446325.1_ASM2044632v1_genomic.fna/target_genomes.txt
[2023-06-28 14:06:40,211] [INFO] Task started: fastANI
[2023-06-28 14:06:40,211] [INFO] Running command: fastANI --query /var/lib/cwl/stgfd6b9901-dd72-4ce2-bcbf-e117123dd922/GCA_020446325.1_ASM2044632v1_genomic.fna.gz --refList GCA_020446325.1_ASM2044632v1_genomic.fna/target_genomes.txt --output GCA_020446325.1_ASM2044632v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 14:06:53,425] [INFO] Task succeeded: fastANI
[2023-06-28 14:06:53,425] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg952e18ac-800e-4247-85ac-23ee643f2179/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 14:06:53,425] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg952e18ac-800e-4247-85ac-23ee643f2179/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 14:06:53,439] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 14:06:53,439] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 14:06:53,439] [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
Ottowia beijingensis	strain=GCS-AN-3	GCA_013423955.1	1207057	1207057	type	True	83.4635	420	584	95	below_threshold
Ottowia testudinis	strain=27C	GCA_017498525.1	2816950	2816950	type	True	81.8567	377	584	95	below_threshold
Ottowia oryzae	strain=KADR8-3	GCA_003008535.1	2109914	2109914	type	True	81.5144	358	584	95	below_threshold
Ramlibacter tataouinensis	strain=TTB310	GCA_000215705.1	94132	94132	type	True	80.8422	332	584	95	below_threshold
Ramlibacter humi	strain=18x22-1	GCA_004681975.1	2530451	2530451	type	True	80.4111	319	584	95	below_threshold
Melaminivora alkalimesophila	strain=CY1	GCA_000282995.1	1165852	1165852	type	True	80.4092	216	584	95	below_threshold
Hydrogenophaga crocea	strain=BA0156	GCA_011388215.1	2716225	2716225	type	True	80.401	346	584	95	below_threshold
Ramlibacter pinisoli	strain=MAH-25	GCA_009758015.1	2682844	2682844	type	True	80.2353	333	584	95	below_threshold
Pseudorhodoferax aquiterrae	strain=KCTC 23314	GCA_014652235.1	747304	747304	type	True	80.2098	345	584	95	below_threshold
Melaminivora alkalimesophila	strain=DSM 26006	GCA_003182375.1	1165852	1165852	type	True	80.136	285	584	95	below_threshold
Comamonas serinivorans	strain=DSM 26136	GCA_002158865.1	1082851	1082851	type	True	79.7393	256	584	95	below_threshold
Comamonas terrae	strain=NBRC 106524	GCA_001544075.1	673548	673548	type	True	79.5955	289	584	95	below_threshold
Delftia acidovorans	strain=FDAARGOS_997	GCA_016127415.1	80866	80866	type	True	79.4982	317	584	95	below_threshold
Diaphorobacter ruginosibacter	strain=DSM 27467	GCA_014395975.1	1715720	1715720	type	True	79.1277	249	584	95	below_threshold
Comamonas aquatica	strain=NBRC 14918	GCA_000739875.1	225991	225991	type	True	79.0734	246	584	95	below_threshold
Ideonella dechloratans	strain=CCUG 30977	GCA_021049305.1	36863	36863	type	True	79.04	256	584	95	below_threshold
Comamonas terrigena	strain=NCTC1937	GCA_900461435.1	32013	32013	type	True	78.7507	253	584	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 14:06:53,441] [INFO] DFAST Taxonomy check result was written to GCA_020446325.1_ASM2044632v1_genomic.fna/tc_result.tsv
[2023-06-28 14:06:53,443] [INFO] ===== Taxonomy check completed =====
[2023-06-28 14:06:53,444] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 14:06:53,444] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg952e18ac-800e-4247-85ac-23ee643f2179/dqc_reference/checkm_data
[2023-06-28 14:06:53,445] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 14:06:53,481] [INFO] Task started: CheckM
[2023-06-28 14:06:53,482] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_020446325.1_ASM2044632v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_020446325.1_ASM2044632v1_genomic.fna/checkm_input GCA_020446325.1_ASM2044632v1_genomic.fna/checkm_result
[2023-06-28 14:07:20,737] [INFO] Task succeeded: CheckM
[2023-06-28 14:07:20,739] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.66%
Contamintation: 12.96%
Strain heterogeneity: 25.00%
--------------------------------------------------------------------------------
[2023-06-28 14:07:20,762] [INFO] ===== Completeness check finished =====
[2023-06-28 14:07:20,762] [INFO] ===== Start GTDB Search =====
[2023-06-28 14:07:20,762] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_020446325.1_ASM2044632v1_genomic.fna/markers.fasta)
[2023-06-28 14:07:20,762] [INFO] Task started: Blastn
[2023-06-28 14:07:20,763] [INFO] Running command: blastn -query GCA_020446325.1_ASM2044632v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg952e18ac-800e-4247-85ac-23ee643f2179/dqc_reference/reference_markers_gtdb.fasta -out GCA_020446325.1_ASM2044632v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 14:07:22,145] [INFO] Task succeeded: Blastn
[2023-06-28 14:07:22,149] [INFO] Selected 11 target genomes.
[2023-06-28 14:07:22,149] [INFO] Target genome list was writen to GCA_020446325.1_ASM2044632v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 14:07:22,153] [INFO] Task started: fastANI
[2023-06-28 14:07:22,153] [INFO] Running command: fastANI --query /var/lib/cwl/stgfd6b9901-dd72-4ce2-bcbf-e117123dd922/GCA_020446325.1_ASM2044632v1_genomic.fna.gz --refList GCA_020446325.1_ASM2044632v1_genomic.fna/target_genomes_gtdb.txt --output GCA_020446325.1_ASM2044632v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 14:07:29,435] [INFO] Task succeeded: fastANI
[2023-06-28 14:07:29,445] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 14:07:29,445] [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_013423955.1	s__Ottowia beijingensis	83.4628	420	584	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ottowia	95.0	97.71	97.71	0.88	0.88	2	-
GCA_016703145.1	s__Ottowia sp016703145	83.0619	387	584	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ottowia	95.0	99.21	99.21	0.89	0.89	2	-
GCA_016702555.1	s__Ottowia sp016702555	83.0268	401	584	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ottowia	95.0	99.62	99.62	0.96	0.96	2	-
GCA_017307865.1	s__Ottowia sp017307865	82.654	386	584	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ottowia	95.0	98.48	98.25	0.89	0.83	4	-
GCA_001897615.1	s__Ottowia sp001897615	82.5634	374	584	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ottowia	95.0	96.20	96.20	0.84	0.84	2	-
GCF_017498525.1	s__Ottowia sp017498525	81.8369	378	584	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ottowia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008017535.1	s__Ottowia sp008017535	81.7043	378	584	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ottowia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018241325.1	s__Ottowia sp018241325	81.4801	356	584	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ottowia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017997715.1	s__Ottowia sp017997715	81.2223	304	584	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ottowia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003859965.1	s__Ottowia sp003859965	80.61	288	584	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ottowia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017996515.1	s__Brachymonas sp017996515	77.3617	52	584	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Brachymonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 14:07:29,447] [INFO] GTDB search result was written to GCA_020446325.1_ASM2044632v1_genomic.fna/result_gtdb.tsv
[2023-06-28 14:07:29,448] [INFO] ===== GTDB Search completed =====
[2023-06-28 14:07:29,452] [INFO] DFAST_QC result json was written to GCA_020446325.1_ASM2044632v1_genomic.fna/dqc_result.json
[2023-06-28 14:07:29,452] [INFO] DFAST_QC completed!
[2023-06-28 14:07:29,452] [INFO] Total running time: 0h0m60s