[2024-01-25 18:11:35,724] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:11:35,726] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:11:35,726] [INFO] DQC Reference Directory: /var/lib/cwl/stge84344ce-0fc6-4be9-afdf-6324d1a17b5a/dqc_reference
[2024-01-25 18:11:36,882] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:11:36,882] [INFO] Task started: Prodigal
[2024-01-25 18:11:36,882] [INFO] Running command: gunzip -c /var/lib/cwl/stgedd23d9e-b90a-4ae7-83b4-3b9ae5380a15/GCF_000739875.1_ASM73987v1_genomic.fna.gz | prodigal -d GCF_000739875.1_ASM73987v1_genomic.fna/cds.fna -a GCF_000739875.1_ASM73987v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:11:48,388] [INFO] Task succeeded: Prodigal
[2024-01-25 18:11:48,389] [INFO] Task started: HMMsearch
[2024-01-25 18:11:48,389] [INFO] Running command: hmmsearch --tblout GCF_000739875.1_ASM73987v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge84344ce-0fc6-4be9-afdf-6324d1a17b5a/dqc_reference/reference_markers.hmm GCF_000739875.1_ASM73987v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:11:48,656] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:11:48,657] [INFO] Found 6/6 markers.
[2024-01-25 18:11:48,686] [INFO] Query marker FASTA was written to GCF_000739875.1_ASM73987v1_genomic.fna/markers.fasta
[2024-01-25 18:11:48,686] [INFO] Task started: Blastn
[2024-01-25 18:11:48,686] [INFO] Running command: blastn -query GCF_000739875.1_ASM73987v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge84344ce-0fc6-4be9-afdf-6324d1a17b5a/dqc_reference/reference_markers.fasta -out GCF_000739875.1_ASM73987v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:11:49,667] [INFO] Task succeeded: Blastn
[2024-01-25 18:11:49,669] [INFO] Selected 18 target genomes.
[2024-01-25 18:11:49,670] [INFO] Target genome list was writen to GCF_000739875.1_ASM73987v1_genomic.fna/target_genomes.txt
[2024-01-25 18:11:49,691] [INFO] Task started: fastANI
[2024-01-25 18:11:49,691] [INFO] Running command: fastANI --query /var/lib/cwl/stgedd23d9e-b90a-4ae7-83b4-3b9ae5380a15/GCF_000739875.1_ASM73987v1_genomic.fna.gz --refList GCF_000739875.1_ASM73987v1_genomic.fna/target_genomes.txt --output GCF_000739875.1_ASM73987v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:12:07,084] [INFO] Task succeeded: fastANI
[2024-01-25 18:12:07,084] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge84344ce-0fc6-4be9-afdf-6324d1a17b5a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:12:07,085] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge84344ce-0fc6-4be9-afdf-6324d1a17b5a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:12:07,095] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:12:07,096] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:12:07,096] [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
Comamonas aquatica	strain=NBRC 14918	GCA_000739875.1	225991	225991	type	True	100.0	1184	1191	95	conclusive
Comamonas terrigena	strain=NCTC1937	GCA_900461435.1	32013	32013	type	True	83.6451	852	1191	95	below_threshold
Comamonas kerstersii	strain=CCUG 15333	GCA_008801935.1	225992	225992	type	True	82.8854	757	1191	95	below_threshold
Comamonas terrae	strain=NBRC 106524	GCA_001544075.1	673548	673548	type	True	82.6221	747	1191	95	below_threshold
Comamonas phosphati	strain=CGMCC 1.12294	GCA_014637085.1	1211803	1211803	type	True	82.4939	709	1191	95	below_threshold
Comamonas thiooxydans	strain=DSM 17888	GCA_001418295.1	363952	363952	type	True	81.6221	691	1191	95	below_threshold
Comamonas thiooxydans	strain=DSM 17888	GCA_000964545.1	363952	363952	type	True	81.6161	693	1191	95	below_threshold
Comamonas thiooxydans	strain=DSM 17888	GCA_001517325.1	363952	363952	type	True	81.5973	694	1191	95	below_threshold
Comamonas avium	strain=Sa2CVA6	GCA_014836675.1	2762231	2762231	type	True	81.5885	762	1191	95	below_threshold
Comamonas testosteroni	strain=ATCC 11996	GCA_000241525.2	285	285	suspected-type	True	81.5753	706	1191	95	below_threshold
Comamonas fluminis	strain=CJ34	GCA_019186805.1	2796366	2796366	type	True	81.0221	643	1191	95	below_threshold
Acidovorax facilis	strain=DSM 649	GCA_023913775.1	12917	12917	type	True	80.4623	603	1191	95	below_threshold
Comamonas suwonensis	strain=EJ-4	GCA_012844455.2	2606214	2606214	type	True	80.4282	609	1191	95	below_threshold
Acidovorax radicis	strain=N35	GCA_000204195.2	758826	758826	type	True	80.2976	626	1191	95	below_threshold
Diaphorobacter caeni	strain=NR2-3-3-1	GCA_015354245.1	2784387	2784387	type	True	80.0918	561	1191	95	below_threshold
Hydrogenophaga crocea	strain=BA0156	GCA_011388215.1	2716225	2716225	type	True	79.7453	516	1191	95	below_threshold
Ramlibacter humi	strain=18x22-1	GCA_004681975.1	2530451	2530451	type	True	79.4896	515	1191	95	below_threshold
Xylophilus ampelinus	strain=CFBP 1192	GCA_024832295.1	54067	54067	type	True	79.1843	472	1191	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:12:07,097] [INFO] DFAST Taxonomy check result was written to GCF_000739875.1_ASM73987v1_genomic.fna/tc_result.tsv
[2024-01-25 18:12:07,098] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:12:07,098] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:12:07,098] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge84344ce-0fc6-4be9-afdf-6324d1a17b5a/dqc_reference/checkm_data
[2024-01-25 18:12:07,099] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:12:07,137] [INFO] Task started: CheckM
[2024-01-25 18:12:07,137] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000739875.1_ASM73987v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000739875.1_ASM73987v1_genomic.fna/checkm_input GCF_000739875.1_ASM73987v1_genomic.fna/checkm_result
[2024-01-25 18:12:53,639] [INFO] Task succeeded: CheckM
[2024-01-25 18:12:53,640] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:12:53,661] [INFO] ===== Completeness check finished =====
[2024-01-25 18:12:53,661] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:12:53,661] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000739875.1_ASM73987v1_genomic.fna/markers.fasta)
[2024-01-25 18:12:53,661] [INFO] Task started: Blastn
[2024-01-25 18:12:53,661] [INFO] Running command: blastn -query GCF_000739875.1_ASM73987v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge84344ce-0fc6-4be9-afdf-6324d1a17b5a/dqc_reference/reference_markers_gtdb.fasta -out GCF_000739875.1_ASM73987v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:12:55,749] [INFO] Task succeeded: Blastn
[2024-01-25 18:12:55,752] [INFO] Selected 16 target genomes.
[2024-01-25 18:12:55,752] [INFO] Target genome list was writen to GCF_000739875.1_ASM73987v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:12:55,771] [INFO] Task started: fastANI
[2024-01-25 18:12:55,772] [INFO] Running command: fastANI --query /var/lib/cwl/stgedd23d9e-b90a-4ae7-83b4-3b9ae5380a15/GCF_000739875.1_ASM73987v1_genomic.fna.gz --refList GCF_000739875.1_ASM73987v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000739875.1_ASM73987v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:13:10,246] [INFO] Task succeeded: fastANI
[2024-01-25 18:13:10,256] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:13:10,257] [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_000739875.1	s__Comamonas aquatica	100.0	1184	1191	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas	95.0	96.97	96.57	0.89	0.87	7	conclusive
GCF_902829245.1	s__Comamonas jiangduensis	83.9403	545	1191	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas	95.0	95.84	95.73	0.85	0.79	3	-
GCF_900461435.1	s__Comamonas terrigena	83.6461	851	1191	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas	95.0	97.97	95.46	0.95	0.91	7	-
GCF_008801935.1	s__Comamonas kerstersii	82.886	757	1191	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas	95.0	98.88	98.82	0.91	0.88	10	-
GCF_001544075.1	s__Comamonas terrae	82.6116	749	1191	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014637085.1	s__Comamonas phosphati	82.5035	708	1191	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019236485.1	s__Comamonas sp019236485	81.7545	534	1191	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000964545.1	s__Comamonas thiooxydans	81.606	694	1191	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas	95.0	97.51	95.23	0.90	0.87	29	-
GCF_014836675.1	s__Comamonas sp014836675	81.5937	762	1191	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas	95.0	98.72	98.72	0.93	0.93	2	-
GCF_000241525.1	s__Comamonas testosteroni	81.5853	705	1191	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas	95.0	99.74	98.70	0.99	0.94	6	-
GCA_009360615.1	s__Comamonas sp009360615	81.5445	633	1191	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000761245.1	s__Comamonas testosteroni_C	81.475	716	1191	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas	95.0	98.84	98.53	0.90	0.90	4	-
GCA_015478895.1	s__Comamonas sp015478895	81.3978	653	1191	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019186805.1	s__Comamonas sp019186805	81.0129	645	1191	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001422735.1	s__Acidovorax sp001422735	80.74	659	1191	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001476815.1	s__Pseudacidovorax intermedius_A	80.0093	564	1191	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudacidovorax	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:13:10,258] [INFO] GTDB search result was written to GCF_000739875.1_ASM73987v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:13:10,258] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:13:10,262] [INFO] DFAST_QC result json was written to GCF_000739875.1_ASM73987v1_genomic.fna/dqc_result.json
[2024-01-25 18:13:10,262] [INFO] DFAST_QC completed!
[2024-01-25 18:13:10,262] [INFO] Total running time: 0h1m35s