[2024-01-24 11:43:25,079] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:43:25,082] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:43:25,082] [INFO] DQC Reference Directory: /var/lib/cwl/stg0f6cc6eb-6746-443d-8581-f74e3091a1a4/dqc_reference
[2024-01-24 11:43:30,062] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:43:30,063] [INFO] Task started: Prodigal
[2024-01-24 11:43:30,064] [INFO] Running command: gunzip -c /var/lib/cwl/stgc163eb2c-877b-4d05-a8b5-745a627f9d94/GCF_016735685.1_ASM1673568v1_genomic.fna.gz | prodigal -d GCF_016735685.1_ASM1673568v1_genomic.fna/cds.fna -a GCF_016735685.1_ASM1673568v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:43:38,898] [INFO] Task succeeded: Prodigal
[2024-01-24 11:43:38,899] [INFO] Task started: HMMsearch
[2024-01-24 11:43:38,899] [INFO] Running command: hmmsearch --tblout GCF_016735685.1_ASM1673568v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0f6cc6eb-6746-443d-8581-f74e3091a1a4/dqc_reference/reference_markers.hmm GCF_016735685.1_ASM1673568v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:43:39,183] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:43:39,184] [INFO] Found 6/6 markers.
[2024-01-24 11:43:39,213] [INFO] Query marker FASTA was written to GCF_016735685.1_ASM1673568v1_genomic.fna/markers.fasta
[2024-01-24 11:43:39,213] [INFO] Task started: Blastn
[2024-01-24 11:43:39,213] [INFO] Running command: blastn -query GCF_016735685.1_ASM1673568v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0f6cc6eb-6746-443d-8581-f74e3091a1a4/dqc_reference/reference_markers.fasta -out GCF_016735685.1_ASM1673568v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:43:40,300] [INFO] Task succeeded: Blastn
[2024-01-24 11:43:40,305] [INFO] Selected 18 target genomes.
[2024-01-24 11:43:40,305] [INFO] Target genome list was writen to GCF_016735685.1_ASM1673568v1_genomic.fna/target_genomes.txt
[2024-01-24 11:43:40,318] [INFO] Task started: fastANI
[2024-01-24 11:43:40,318] [INFO] Running command: fastANI --query /var/lib/cwl/stgc163eb2c-877b-4d05-a8b5-745a627f9d94/GCF_016735685.1_ASM1673568v1_genomic.fna.gz --refList GCF_016735685.1_ASM1673568v1_genomic.fna/target_genomes.txt --output GCF_016735685.1_ASM1673568v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:43:57,614] [INFO] Task succeeded: fastANI
[2024-01-24 11:43:57,615] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0f6cc6eb-6746-443d-8581-f74e3091a1a4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:43:57,615] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0f6cc6eb-6746-443d-8581-f74e3091a1a4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:43:57,630] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:43:57,631] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:43:57,631] [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
Schlegelella thermodepolymerans	strain=DSM 15344	GCA_002933415.1	215580	215580	type	True	80.5518	532	1006	95	below_threshold
Sphaerotilus sulfidivorans	strain=D-501	GCA_013426975.1	639200	639200	type	True	80.5505	552	1006	95	below_threshold
Schlegelella thermodepolymerans	strain=DSM 15344	GCA_015476235.1	215580	215580	type	True	80.5354	532	1006	95	below_threshold
Schlegelella thermodepolymerans	strain=DSM 15344	GCA_003349825.1	215580	215580	type	True	80.5259	534	1006	95	below_threshold
Sphaerotilus natans subsp. natans	strain=DSM 6575	GCA_000689195.1	882627	34103	type	True	80.5038	537	1006	95	below_threshold
Pelomonas saccharophila	strain=DSM 654	GCA_004342485.1	304	304	type	True	80.42	542	1006	95	below_threshold
Sphaerotilus natans	strain=ATCC 13338	GCA_900156335.1	34103	34103	type	True	80.4177	571	1006	95	below_threshold
Sphaerotilus hippei	strain=DSM 566	GCA_003201595.1	744406	744406	type	True	80.369	548	1006	95	below_threshold
Ideonella dechloratans	strain=CCUG 30977	GCA_021049305.1	36863	36863	type	True	80.3277	534	1006	95	below_threshold
Rubrivivax benzoatilyticus	strain=JA2	GCA_000190375.2	316997	316997	type	True	80.2548	542	1006	95	below_threshold
Azohydromonas caseinilytica	strain=G-1-1-14	GCA_012927045.1	2728836	2728836	type	True	80.1716	559	1006	95	below_threshold
Ideonella azotifigens	strain=DSM 21438	GCA_006519715.1	513160	513160	type	True	80.1174	431	1006	95	below_threshold
Ideonella benzenivorans	strain=B7	GCA_020387415.1	2831643	2831643	type	True	80.1072	503	1006	95	below_threshold
Azohydromonas australica	strain=DSM 1124	GCA_000430725.1	364039	364039	type	True	79.9819	589	1006	95	below_threshold
Mitsuaria chitinivorans	strain=HWN-4	GCA_002761755.1	2917965	2917965	type	True	79.7285	490	1006	95	below_threshold
Paucibacter toxinivorans	strain=DSM 16998	GCA_004362525.1	270368	270368	type	True	79.6874	543	1006	95	below_threshold
Aquabacterium soli	strain=SJQ9	GCA_003933735.1	2493092	2493092	type	True	79.6458	452	1006	95	below_threshold
Ramlibacter pinisoli	strain=MAH-25	GCA_009758015.1	2682844	2682844	type	True	79.0491	477	1006	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:43:57,633] [INFO] DFAST Taxonomy check result was written to GCF_016735685.1_ASM1673568v1_genomic.fna/tc_result.tsv
[2024-01-24 11:43:57,633] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:43:57,633] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:43:57,634] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0f6cc6eb-6746-443d-8581-f74e3091a1a4/dqc_reference/checkm_data
[2024-01-24 11:43:57,634] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:43:57,669] [INFO] Task started: CheckM
[2024-01-24 11:43:57,669] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016735685.1_ASM1673568v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016735685.1_ASM1673568v1_genomic.fna/checkm_input GCF_016735685.1_ASM1673568v1_genomic.fna/checkm_result
[2024-01-24 11:44:49,922] [INFO] Task succeeded: CheckM
[2024-01-24 11:44:49,923] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:44:49,941] [INFO] ===== Completeness check finished =====
[2024-01-24 11:44:49,941] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:44:49,942] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016735685.1_ASM1673568v1_genomic.fna/markers.fasta)
[2024-01-24 11:44:49,942] [INFO] Task started: Blastn
[2024-01-24 11:44:49,942] [INFO] Running command: blastn -query GCF_016735685.1_ASM1673568v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0f6cc6eb-6746-443d-8581-f74e3091a1a4/dqc_reference/reference_markers_gtdb.fasta -out GCF_016735685.1_ASM1673568v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:44:52,172] [INFO] Task succeeded: Blastn
[2024-01-24 11:44:52,177] [INFO] Selected 21 target genomes.
[2024-01-24 11:44:52,178] [INFO] Target genome list was writen to GCF_016735685.1_ASM1673568v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:44:52,215] [INFO] Task started: fastANI
[2024-01-24 11:44:52,215] [INFO] Running command: fastANI --query /var/lib/cwl/stgc163eb2c-877b-4d05-a8b5-745a627f9d94/GCF_016735685.1_ASM1673568v1_genomic.fna.gz --refList GCF_016735685.1_ASM1673568v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016735685.1_ASM1673568v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:45:11,886] [INFO] Task succeeded: fastANI
[2024-01-24 11:45:11,908] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:45:11,908] [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_016735685.1	s__SJAQ100 sp016735685	100.0	1006	1006	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__SJAQ100	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014145335.1	s__SJAQ100 sp014145335	91.7766	858	1006	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__SJAQ100	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902826655.1	s__Methylibium sp902826655	81.1558	559	1006	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Methylibium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004217215.1	s__Rivibacter subsaxonicus	80.984	591	1006	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rivibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017983795.1	s__Piscinibacter sp017983795	80.9126	547	1006	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Piscinibacter	95.0	97.66	96.21	0.89	0.79	4	-
GCF_001425905.1	s__Methylibium sp001425905	80.8818	580	1006	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Methylibium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018069875.1	s__Ideonella sp018069875	80.8423	578	1006	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ideonella	95.0	98.74	98.74	0.92	0.92	2	-
GCF_000015725.1	s__Methylibium petroleiphilum	80.7771	569	1006	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Methylibium	95.0	96.91	96.03	0.83	0.81	5	-
GCF_018069755.1	s__Ideonella sp018069755	80.6407	580	1006	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ideonella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008329925.1	s__Sphaerotilus sulfidivorans	80.5714	563	1006	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Sphaerotilus	95.0	99.98	99.98	1.00	1.00	2	-
GCF_017795745.1	s__Piscinibacter sp017795745	80.5471	562	1006	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Piscinibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903889735.1	s__Methylibium sp903889735	80.5126	399	1006	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Methylibium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004342485.1	s__Pelomonas saccharophila	80.4859	536	1006	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pelomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015476235.1	s__Schlegelella thermodepolymerans	80.4802	537	1006	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Schlegelella	95.0	99.89	99.68	0.98	0.95	4	-
GCF_000284255.1	s__Rubrivivax gelatinosus_A	80.2996	578	1006	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rubrivivax	95.0	98.28	98.28	0.94	0.94	2	-
GCA_009996515.1	s__Pelomonas sp009996515	80.0223	523	1006	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pelomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001426885.1	s__Pelomonas sp001426885	79.919	527	1006	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pelomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903938815.1	s__Rubrivivax sp903938815	79.8358	510	1006	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rubrivivax	95.0	99.66	99.41	0.96	0.94	10	-
GCF_002761755.1	s__Mitsuaria sp002761755	79.7272	490	1006	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Mitsuaria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900113225.1	s__Mitsuaria sp900113225	79.6816	527	1006	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Mitsuaria	95.0	98.36	98.28	0.95	0.95	4	-
GCF_002205645.1	s__Mitsuaria aquatilis	79.4484	524	1006	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Mitsuaria	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:45:11,910] [INFO] GTDB search result was written to GCF_016735685.1_ASM1673568v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:45:11,910] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:45:11,914] [INFO] DFAST_QC result json was written to GCF_016735685.1_ASM1673568v1_genomic.fna/dqc_result.json
[2024-01-24 11:45:11,915] [INFO] DFAST_QC completed!
[2024-01-24 11:45:11,915] [INFO] Total running time: 0h1m47s