[2024-01-24 13:49:40,650] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:49:40,652] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:49:40,652] [INFO] DQC Reference Directory: /var/lib/cwl/stg798167c2-2723-414e-946c-82299ca9fe92/dqc_reference
[2024-01-24 13:49:42,002] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:42,002] [INFO] Task started: Prodigal
[2024-01-24 13:49:42,005] [INFO] Running command: gunzip -c /var/lib/cwl/stg0bd98f65-a7dc-4094-974d-7b6c186617b3/GCF_013003965.1_ASM1300396v1_genomic.fna.gz | prodigal -d GCF_013003965.1_ASM1300396v1_genomic.fna/cds.fna -a GCF_013003965.1_ASM1300396v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:49:57,791] [INFO] Task succeeded: Prodigal
[2024-01-24 13:49:57,792] [INFO] Task started: HMMsearch
[2024-01-24 13:49:57,792] [INFO] Running command: hmmsearch --tblout GCF_013003965.1_ASM1300396v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg798167c2-2723-414e-946c-82299ca9fe92/dqc_reference/reference_markers.hmm GCF_013003965.1_ASM1300396v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:49:58,160] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:49:58,161] [INFO] Found 6/6 markers.
[2024-01-24 13:49:58,206] [INFO] Query marker FASTA was written to GCF_013003965.1_ASM1300396v1_genomic.fna/markers.fasta
[2024-01-24 13:49:58,206] [INFO] Task started: Blastn
[2024-01-24 13:49:58,206] [INFO] Running command: blastn -query GCF_013003965.1_ASM1300396v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg798167c2-2723-414e-946c-82299ca9fe92/dqc_reference/reference_markers.fasta -out GCF_013003965.1_ASM1300396v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:59,273] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:59,304] [INFO] Selected 25 target genomes.
[2024-01-24 13:49:59,305] [INFO] Target genome list was writen to GCF_013003965.1_ASM1300396v1_genomic.fna/target_genomes.txt
[2024-01-24 13:49:59,320] [INFO] Task started: fastANI
[2024-01-24 13:49:59,321] [INFO] Running command: fastANI --query /var/lib/cwl/stg0bd98f65-a7dc-4094-974d-7b6c186617b3/GCF_013003965.1_ASM1300396v1_genomic.fna.gz --refList GCF_013003965.1_ASM1300396v1_genomic.fna/target_genomes.txt --output GCF_013003965.1_ASM1300396v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:50:20,415] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:20,415] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg798167c2-2723-414e-946c-82299ca9fe92/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:50:20,416] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg798167c2-2723-414e-946c-82299ca9fe92/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:50:20,435] [INFO] Found 25 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:50:20,435] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:50:20,435] [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
Usitatibacter rugosus	strain=0125_3	GCA_013003965.1	2732067	2732067	type	True	100.0	1521	1521	95	conclusive
Usitatibacter palustris	strain=Swamp67	GCA_013003985.1	2732487	2732487	type	True	81.4929	835	1521	95	below_threshold
Ferrigenium kumadai	strain=An22	GCA_018324385.1	1682490	1682490	type	True	77.4285	141	1521	95	below_threshold
Sulfuritortus calidifontis	strain=J1A	GCA_003967275.1	1914471	1914471	type	True	77.3896	174	1521	95	below_threshold
Ramlibacter algicola	strain=CrO1	GCA_016641735.1	2795217	2795217	type	True	77.2668	285	1521	95	below_threshold
Sulfuritortus calidifontis	strain=DSM 103923	GCA_004346085.1	1914471	1914471	type	True	77.1949	166	1521	95	below_threshold
Ramlibacter henchirensis	strain=DSM 14656	GCA_004682015.1	204072	204072	type	True	77.0531	286	1521	95	below_threshold
Thauera aminoaromatica	strain=S2	GCA_000310185.1	164330	164330	type	True	77.0311	263	1521	95	below_threshold
Ralstonia pseudosolanacearum	strain=LMG 9673	GCA_024925465.1	1310165	1310165	type	True	76.9717	265	1521	95	below_threshold
Crenobacter luteus	strain=DSM 27258	GCA_004345725.1	1452487	1452487	type	True	76.9306	227	1521	95	below_threshold
Chitinimonas koreensis	strain=DSM 17726	GCA_000428465.1	356302	356302	type	True	76.8922	303	1521	95	below_threshold
Ramlibacter alkalitolerans	strain=KACC 19305	GCA_016722765.1	2039631	2039631	type	True	76.8467	326	1521	95	below_threshold
Ralstonia pseudosolanacearum	strain=LMG 9673	GCA_919586305.1	1310165	1310165	type	True	76.8232	272	1521	95	below_threshold
Cupriavidus cauae	strain=MKL-01	GCA_008632125.1	2608999	2608999	type	True	76.7833	311	1521	95	below_threshold
Burkholderia perseverans	strain=INN12	GCA_022870505.1	2615214	2615214	type	True	76.7744	352	1521	95	below_threshold
Pandoraea pulmonicola	strain=DSM 16583	GCA_000815105.2	93221	93221	type	True	76.7298	218	1521	95	below_threshold
Aromatoleum petrolei	strain=ToN1	GCA_017894385.1	76116	76116	type	True	76.6893	244	1521	95	below_threshold
Aromatoleum tolulyticum	strain=ATCC 51758	GCA_900156155.1	34027	34027	type	True	76.6474	283	1521	95	below_threshold
Aromatoleum toluolicum	strain=T	GCA_012911005.2	90060	90060	type	True	76.5782	268	1521	95	below_threshold
Aromatoleum petrolei	strain=ToN1	GCA_012910985.1	76116	76116	type	True	76.556	233	1521	95	below_threshold
Pandoraea pulmonicola	strain=NCTC13159	GCA_900454575.1	93221	93221	type	True	76.5546	215	1521	95	below_threshold
Burkholderia ubonensis		GCA_902499185.1	101571	101571	type	True	76.4236	313	1521	95	below_threshold
Fulvimonas soli	strain=DSM 14263	GCA_003148905.1	155197	155197	type	True	76.3443	225	1521	95	below_threshold
Fulvimonas soli	strain=LMG 19981	GCA_006352285.1	155197	155197	type	True	76.263	218	1521	95	below_threshold
Dyella solisilvae	strain=DHG54	GCA_003351225.1	1920168	1920168	type	True	76.0876	141	1521	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:50:20,437] [INFO] DFAST Taxonomy check result was written to GCF_013003965.1_ASM1300396v1_genomic.fna/tc_result.tsv
[2024-01-24 13:50:20,438] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:50:20,438] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:50:20,438] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg798167c2-2723-414e-946c-82299ca9fe92/dqc_reference/checkm_data
[2024-01-24 13:50:20,439] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:50:20,485] [INFO] Task started: CheckM
[2024-01-24 13:50:20,486] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013003965.1_ASM1300396v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013003965.1_ASM1300396v1_genomic.fna/checkm_input GCF_013003965.1_ASM1300396v1_genomic.fna/checkm_result
[2024-01-24 13:51:14,483] [INFO] Task succeeded: CheckM
[2024-01-24 13:51:14,484] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:51:14,505] [INFO] ===== Completeness check finished =====
[2024-01-24 13:51:14,506] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:51:14,506] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013003965.1_ASM1300396v1_genomic.fna/markers.fasta)
[2024-01-24 13:51:14,507] [INFO] Task started: Blastn
[2024-01-24 13:51:14,507] [INFO] Running command: blastn -query GCF_013003965.1_ASM1300396v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg798167c2-2723-414e-946c-82299ca9fe92/dqc_reference/reference_markers_gtdb.fasta -out GCF_013003965.1_ASM1300396v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:51:16,323] [INFO] Task succeeded: Blastn
[2024-01-24 13:51:16,326] [INFO] Selected 11 target genomes.
[2024-01-24 13:51:16,327] [INFO] Target genome list was writen to GCF_013003965.1_ASM1300396v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:51:16,360] [INFO] Task started: fastANI
[2024-01-24 13:51:16,360] [INFO] Running command: fastANI --query /var/lib/cwl/stg0bd98f65-a7dc-4094-974d-7b6c186617b3/GCF_013003965.1_ASM1300396v1_genomic.fna.gz --refList GCF_013003965.1_ASM1300396v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013003965.1_ASM1300396v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:51:26,639] [INFO] Task succeeded: fastANI
[2024-01-24 13:51:26,658] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:51:26,659] [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
GCF_013003965.1	s__Usitatibacter rugosus	100.0	1521	1521	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Usitatibacteraceae;g__Usitatibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_001953215.1	s__Usitatibacter sp001953215	84.3733	1103	1521	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Usitatibacteraceae;g__Usitatibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013003985.1	s__Usitatibacter palustris	81.5021	835	1521	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Usitatibacteraceae;g__Usitatibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003105245.1	s__FEB-7 sp003105245	80.5422	508	1521	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Usitatibacteraceae;g__FEB-7	95.0	99.57	99.57	0.92	0.92	2	-
GCA_016711875.1	s__FEB-7 sp016711875	80.0339	648	1521	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Usitatibacteraceae;g__FEB-7	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011391275.1	s__FEB-7 sp011391275	79.9611	477	1521	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Usitatibacteraceae;g__FEB-7	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016709665.1	s__FEB-7 sp016709665	79.9582	694	1521	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Usitatibacteraceae;g__FEB-7	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012274175.1	s__Usitatibacter sp012274175	79.8925	438	1521	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Usitatibacteraceae;g__Usitatibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017880705.1	s__Usitatibacter sp017880705	79.7868	500	1521	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Usitatibacteraceae;g__Usitatibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016708825.1	s__FEB-7 sp016708825	79.6845	586	1521	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Usitatibacteraceae;g__FEB-7	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016790695.1	s__JAEUOS01 sp016790695	76.7154	339	1521	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__JAEUOS01;g__JAEUOS01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:51:26,661] [INFO] GTDB search result was written to GCF_013003965.1_ASM1300396v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:51:26,662] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:51:26,665] [INFO] DFAST_QC result json was written to GCF_013003965.1_ASM1300396v1_genomic.fna/dqc_result.json
[2024-01-24 13:51:26,666] [INFO] DFAST_QC completed!
[2024-01-24 13:51:26,666] [INFO] Total running time: 0h1m46s