[2024-01-25 18:01:35,540] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:01:35,541] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:01:35,542] [INFO] DQC Reference Directory: /var/lib/cwl/stg5fdfbed6-41e2-427d-a4c6-df50e39bf78c/dqc_reference
[2024-01-25 18:01:36,676] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:01:36,677] [INFO] Task started: Prodigal
[2024-01-25 18:01:36,677] [INFO] Running command: gunzip -c /var/lib/cwl/stg35e7c2a7-c242-4565-8e82-53ff723585b4/GCF_000282995.1_CRZ1_genomic.fna.gz | prodigal -d GCF_000282995.1_CRZ1_genomic.fna/cds.fna -a GCF_000282995.1_CRZ1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:01:43,609] [INFO] Task succeeded: Prodigal
[2024-01-25 18:01:43,610] [INFO] Task started: HMMsearch
[2024-01-25 18:01:43,610] [INFO] Running command: hmmsearch --tblout GCF_000282995.1_CRZ1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5fdfbed6-41e2-427d-a4c6-df50e39bf78c/dqc_reference/reference_markers.hmm GCF_000282995.1_CRZ1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:01:43,825] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:01:43,826] [INFO] Found 6/6 markers.
[2024-01-25 18:01:43,854] [INFO] Query marker FASTA was written to GCF_000282995.1_CRZ1_genomic.fna/markers.fasta
[2024-01-25 18:01:43,854] [INFO] Task started: Blastn
[2024-01-25 18:01:43,854] [INFO] Running command: blastn -query GCF_000282995.1_CRZ1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5fdfbed6-41e2-427d-a4c6-df50e39bf78c/dqc_reference/reference_markers.fasta -out GCF_000282995.1_CRZ1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:01:44,901] [INFO] Task succeeded: Blastn
[2024-01-25 18:01:44,904] [INFO] Selected 18 target genomes.
[2024-01-25 18:01:44,904] [INFO] Target genome list was writen to GCF_000282995.1_CRZ1_genomic.fna/target_genomes.txt
[2024-01-25 18:01:44,913] [INFO] Task started: fastANI
[2024-01-25 18:01:44,913] [INFO] Running command: fastANI --query /var/lib/cwl/stg35e7c2a7-c242-4565-8e82-53ff723585b4/GCF_000282995.1_CRZ1_genomic.fna.gz --refList GCF_000282995.1_CRZ1_genomic.fna/target_genomes.txt --output GCF_000282995.1_CRZ1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:02:00,472] [INFO] Task succeeded: fastANI
[2024-01-25 18:02:00,472] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5fdfbed6-41e2-427d-a4c6-df50e39bf78c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:02:00,472] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5fdfbed6-41e2-427d-a4c6-df50e39bf78c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:02:00,484] [INFO] Found 18 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 18:02:00,484] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:02:00,484] [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
Melaminivora alkalimesophila	strain=CY1	GCA_000282995.1	1165852	1165852	type	True	100.0	629	645	95	conclusive
Melaminivora alkalimesophila	strain=DSM 26006	GCA_003182375.1	1165852	1165852	type	True	99.9537	624	645	95	conclusive
Melaminivora jejuensis	strain=KCTC 32230	GCA_017811175.1	1267217	1267217	type	True	85.92	527	645	95	below_threshold
Acidovorax wautersii	strain=DSM 27981	GCA_900113035.1	1177982	1177982	type	True	82.7429	468	645	95	below_threshold
Acidovorax citrulli	strain=DSM 17060	GCA_900100305.1	80869	80869	type	True	82.2698	449	645	95	below_threshold
Acidovorax oryzae	strain=ATCC 19882	GCA_000687165.1	862720	862720	type	True	82.0364	448	645	95	below_threshold
Acidovorax caeni	strain=R-24608	GCA_900116825.1	343013	343013	type	True	82.0341	438	645	95	below_threshold
Ramlibacter tataouinensis	strain=TTB310	GCA_000215705.1	94132	94132	type	True	81.7425	387	645	95	below_threshold
Comamonas phosphati	strain=CGMCC 1.12294	GCA_014637085.1	1211803	1211803	type	True	81.6093	397	645	95	below_threshold
Pseudorhodoferax aquiterrae	strain=KCTC 23314	GCA_014652235.1	747304	747304	type	True	81.3517	421	645	95	below_threshold
Ramlibacter rhizophilus	strain=CCTCC AB2015357	GCA_004681965.1	1781167	1781167	type	True	81.1584	365	645	95	below_threshold
Hydrogenophaga crocea	strain=BA0156	GCA_011388215.1	2716225	2716225	type	True	81.0336	394	645	95	below_threshold
Xylophilus ampelinus	strain=CFBP 1192	GCA_024832295.1	54067	54067	type	True	80.8727	364	645	95	below_threshold
Ramlibacter pinisoli	strain=MAH-25	GCA_009758015.1	2682844	2682844	type	True	80.8685	383	645	95	below_threshold
Pseudorhodoferax soli	strain=DSM 21634	GCA_003337555.1	545864	545864	type	True	80.7534	422	645	95	below_threshold
Diaphorobacter caeni	strain=NR2-3-3-1	GCA_015354245.1	2784387	2784387	type	True	80.6075	407	645	95	below_threshold
Acidovorax facilis	strain=DSM 649	GCA_023913775.1	12917	12917	type	True	80.3034	432	645	95	below_threshold
Ottowia testudinis	strain=27C	GCA_017498525.1	2816950	2816950	type	True	80.1913	371	645	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:02:00,485] [INFO] DFAST Taxonomy check result was written to GCF_000282995.1_CRZ1_genomic.fna/tc_result.tsv
[2024-01-25 18:02:00,486] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:02:00,486] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:02:00,486] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5fdfbed6-41e2-427d-a4c6-df50e39bf78c/dqc_reference/checkm_data
[2024-01-25 18:02:00,487] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:02:00,518] [INFO] Task started: CheckM
[2024-01-25 18:02:00,518] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000282995.1_CRZ1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000282995.1_CRZ1_genomic.fna/checkm_input GCF_000282995.1_CRZ1_genomic.fna/checkm_result
[2024-01-25 18:02:26,112] [INFO] Task succeeded: CheckM
[2024-01-25 18:02:26,113] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.52%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:02:26,134] [INFO] ===== Completeness check finished =====
[2024-01-25 18:02:26,134] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:02:26,135] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000282995.1_CRZ1_genomic.fna/markers.fasta)
[2024-01-25 18:02:26,135] [INFO] Task started: Blastn
[2024-01-25 18:02:26,135] [INFO] Running command: blastn -query GCF_000282995.1_CRZ1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5fdfbed6-41e2-427d-a4c6-df50e39bf78c/dqc_reference/reference_markers_gtdb.fasta -out GCF_000282995.1_CRZ1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:02:28,351] [INFO] Task succeeded: Blastn
[2024-01-25 18:02:28,353] [INFO] Selected 9 target genomes.
[2024-01-25 18:02:28,354] [INFO] Target genome list was writen to GCF_000282995.1_CRZ1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:02:28,364] [INFO] Task started: fastANI
[2024-01-25 18:02:28,364] [INFO] Running command: fastANI --query /var/lib/cwl/stg35e7c2a7-c242-4565-8e82-53ff723585b4/GCF_000282995.1_CRZ1_genomic.fna.gz --refList GCF_000282995.1_CRZ1_genomic.fna/target_genomes_gtdb.txt --output GCF_000282995.1_CRZ1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:02:35,262] [INFO] Task succeeded: fastANI
[2024-01-25 18:02:35,269] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:02:35,270] [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_000282995.1	s__Melaminivora alkalimesophila	100.0	629	645	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Melaminivora	95.0	99.95	99.95	0.97	0.97	2	conclusive
GCF_003013695.1	s__Pulveribacter suum	86.1815	522	645	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pulveribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900103645.1	s__Oryzisolibacter propanilivorax	86.0148	520	645	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Oryzisolibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002434305.1	s__Pulveribacter sp002434305	85.9643	526	645	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pulveribacter	95.0	97.39	97.21	0.93	0.92	3	-
GCF_017811175.1	s__Melaminivora_A jejuensis	85.8982	528	645	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Melaminivora_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003008575.1	s__Melaminivora_A sp003008575	85.8598	529	645	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Melaminivora_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000204645.1	s__Alicycliphilus denitrificans	84.6203	506	645	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Alicycliphilus	95.0	97.26	95.80	0.83	0.76	8	-
GCF_000400995.2	s__MR-S7 sp000400995	84.2202	502	645	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__MR-S7	95.0	97.31	97.31	0.83	0.83	2	-
GCF_015070875.1	s__Ramlibacter sp015070875	80.5427	384	645	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ramlibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:02:35,275] [INFO] GTDB search result was written to GCF_000282995.1_CRZ1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:02:35,275] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:02:35,278] [INFO] DFAST_QC result json was written to GCF_000282995.1_CRZ1_genomic.fna/dqc_result.json
[2024-01-25 18:02:35,278] [INFO] DFAST_QC completed!
[2024-01-25 18:02:35,278] [INFO] Total running time: 0h0m60s