[2024-01-25 18:42:20,338] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:42:20,340] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:42:20,340] [INFO] DQC Reference Directory: /var/lib/cwl/stgb2682b5c-6243-4814-9d3c-598dac6d49ef/dqc_reference
[2024-01-25 18:42:21,453] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:42:21,454] [INFO] Task started: Prodigal
[2024-01-25 18:42:21,454] [INFO] Running command: gunzip -c /var/lib/cwl/stg1d6d61fa-ac0c-43e1-818d-6d89f4109c5c/GCF_009760915.1_ASM976091v1_genomic.fna.gz | prodigal -d GCF_009760915.1_ASM976091v1_genomic.fna/cds.fna -a GCF_009760915.1_ASM976091v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:42:42,878] [INFO] Task succeeded: Prodigal
[2024-01-25 18:42:42,879] [INFO] Task started: HMMsearch
[2024-01-25 18:42:42,879] [INFO] Running command: hmmsearch --tblout GCF_009760915.1_ASM976091v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb2682b5c-6243-4814-9d3c-598dac6d49ef/dqc_reference/reference_markers.hmm GCF_009760915.1_ASM976091v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:42:43,191] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:42:43,192] [INFO] Found 6/6 markers.
[2024-01-25 18:42:43,249] [INFO] Query marker FASTA was written to GCF_009760915.1_ASM976091v1_genomic.fna/markers.fasta
[2024-01-25 18:42:43,250] [INFO] Task started: Blastn
[2024-01-25 18:42:43,250] [INFO] Running command: blastn -query GCF_009760915.1_ASM976091v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb2682b5c-6243-4814-9d3c-598dac6d49ef/dqc_reference/reference_markers.fasta -out GCF_009760915.1_ASM976091v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:42:44,190] [INFO] Task succeeded: Blastn
[2024-01-25 18:42:44,193] [INFO] Selected 12 target genomes.
[2024-01-25 18:42:44,193] [INFO] Target genome list was writen to GCF_009760915.1_ASM976091v1_genomic.fna/target_genomes.txt
[2024-01-25 18:42:44,197] [INFO] Task started: fastANI
[2024-01-25 18:42:44,197] [INFO] Running command: fastANI --query /var/lib/cwl/stg1d6d61fa-ac0c-43e1-818d-6d89f4109c5c/GCF_009760915.1_ASM976091v1_genomic.fna.gz --refList GCF_009760915.1_ASM976091v1_genomic.fna/target_genomes.txt --output GCF_009760915.1_ASM976091v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:43:05,988] [INFO] Task succeeded: fastANI
[2024-01-25 18:43:05,989] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb2682b5c-6243-4814-9d3c-598dac6d49ef/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:43:05,989] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb2682b5c-6243-4814-9d3c-598dac6d49ef/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:43:05,998] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:43:05,999] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:43:05,999] [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
Azohydromonas aeria	strain=CFCC 13393	GCA_009760915.1	2590212	2590212	type	True	100.0	2490	2502	95	conclusive
Azohydromonas australica	strain=DSM 1124	GCA_000430725.1	364039	364039	type	True	87.5328	1653	2502	95	below_threshold
Azohydromonas caseinilytica	strain=G-1-1-14	GCA_012927045.1	2728836	2728836	type	True	87.5052	1553	2502	95	below_threshold
Azohydromonas lata	strain=NBRC 102462	GCA_001571085.1	45677	45677	type	True	86.5152	1496	2502	95	below_threshold
Sphaerotilus natans	strain=ATCC 13338	GCA_900156335.1	34103	34103	type	True	80.5464	883	2502	95	below_threshold
Schlegelella thermodepolymerans	strain=DSM 15344	GCA_015476235.1	215580	215580	type	True	80.5021	808	2502	95	below_threshold
Ideonella dechloratans	strain=CCUG 30977	GCA_021049305.1	36863	36863	type	True	80.1551	756	2502	95	below_threshold
Ideonella benzenivorans	strain=B7	GCA_020387415.1	2831643	2831643	type	True	79.7677	720	2502	95	below_threshold
Ideonella livida	strain=TBM-1	GCA_010499455.1	2707176	2707176	type	True	79.4077	812	2502	95	below_threshold
Hydrogenophaga crocea	strain=BA0156	GCA_011388215.1	2716225	2716225	type	True	79.3925	784	2502	95	below_threshold
Pelomonas saccharophila	strain=DSM 654	GCA_004342485.1	304	304	type	True	79.2242	843	2502	95	below_threshold
Schlegelella brevitalea	strain=DSM 7029	GCA_001017435.1	413882	413882	type	True	79.0105	721	2502	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:43:06,000] [INFO] DFAST Taxonomy check result was written to GCF_009760915.1_ASM976091v1_genomic.fna/tc_result.tsv
[2024-01-25 18:43:06,001] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:43:06,004] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:43:06,004] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb2682b5c-6243-4814-9d3c-598dac6d49ef/dqc_reference/checkm_data
[2024-01-25 18:43:06,008] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:43:06,097] [INFO] Task started: CheckM
[2024-01-25 18:43:06,097] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009760915.1_ASM976091v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009760915.1_ASM976091v1_genomic.fna/checkm_input GCF_009760915.1_ASM976091v1_genomic.fna/checkm_result
[2024-01-25 18:45:44,112] [INFO] Task succeeded: CheckM
[2024-01-25 18:45:44,113] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:45:44,132] [INFO] ===== Completeness check finished =====
[2024-01-25 18:45:44,133] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:45:44,133] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009760915.1_ASM976091v1_genomic.fna/markers.fasta)
[2024-01-25 18:45:44,134] [INFO] Task started: Blastn
[2024-01-25 18:45:44,134] [INFO] Running command: blastn -query GCF_009760915.1_ASM976091v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb2682b5c-6243-4814-9d3c-598dac6d49ef/dqc_reference/reference_markers_gtdb.fasta -out GCF_009760915.1_ASM976091v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:45:46,091] [INFO] Task succeeded: Blastn
[2024-01-25 18:45:46,094] [INFO] Selected 12 target genomes.
[2024-01-25 18:45:46,094] [INFO] Target genome list was writen to GCF_009760915.1_ASM976091v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:45:46,102] [INFO] Task started: fastANI
[2024-01-25 18:45:46,103] [INFO] Running command: fastANI --query /var/lib/cwl/stg1d6d61fa-ac0c-43e1-818d-6d89f4109c5c/GCF_009760915.1_ASM976091v1_genomic.fna.gz --refList GCF_009760915.1_ASM976091v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009760915.1_ASM976091v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:46:10,277] [INFO] Task succeeded: fastANI
[2024-01-25 18:46:10,286] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:46:10,287] [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_009760915.1	s__Azohydromonas aeria	100.0	2490	2502	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Azohydromonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000430725.1	s__Azohydromonas australica	87.5818	1648	2502	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Azohydromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012927045.1	s__Azohydromonas caseinilytica	87.5275	1550	2502	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Azohydromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001571085.1	s__Azohydromonas lata	86.5324	1494	2502	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Azohydromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014873965.1	s__VBDL01 sp014873965	80.6704	965	2502	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__VBDL01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013294065.1	s__Sphaerotilus sp013294065	80.5958	940	2502	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Sphaerotilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900156335.1	s__Sphaerotilus natans	80.5754	880	2502	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Sphaerotilus	95.0	99.99	99.99	1.00	1.00	2	-
GCF_000969605.1	s__Aquincola tertiaricarbonis	80.4807	1038	2502	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquincola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000799605.1	s__Rhizobacter sp000799605	79.5548	917	2502	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhizobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016213205.1	s__Aquabacterium_A sp016213205	79.4157	940	2502	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquabacterium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013289985.1	s__CAIMXF01 sp013289985	79.2769	816	2502	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__CAIMXF01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018241265.1	s__JAFEEF01 sp018241265	78.7798	750	2502	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__JAFEEF01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:46:10,288] [INFO] GTDB search result was written to GCF_009760915.1_ASM976091v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:46:10,288] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:46:10,292] [INFO] DFAST_QC result json was written to GCF_009760915.1_ASM976091v1_genomic.fna/dqc_result.json
[2024-01-25 18:46:10,292] [INFO] DFAST_QC completed!
[2024-01-25 18:46:10,292] [INFO] Total running time: 0h3m50s