[2024-01-24 13:46:41,079] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:46:41,081] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:46:41,081] [INFO] DQC Reference Directory: /var/lib/cwl/stg280b1576-9b07-472c-b117-496d5e592929/dqc_reference
[2024-01-24 13:46:42,368] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:46:42,369] [INFO] Task started: Prodigal
[2024-01-24 13:46:42,369] [INFO] Running command: gunzip -c /var/lib/cwl/stgfa87bf45-178f-43d8-b91a-592287b85a38/GCF_020387415.1_ASM2038741v1_genomic.fna.gz | prodigal -d GCF_020387415.1_ASM2038741v1_genomic.fna/cds.fna -a GCF_020387415.1_ASM2038741v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:46:57,164] [INFO] Task succeeded: Prodigal
[2024-01-24 13:46:57,165] [INFO] Task started: HMMsearch
[2024-01-24 13:46:57,165] [INFO] Running command: hmmsearch --tblout GCF_020387415.1_ASM2038741v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg280b1576-9b07-472c-b117-496d5e592929/dqc_reference/reference_markers.hmm GCF_020387415.1_ASM2038741v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:46:57,483] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:46:57,485] [INFO] Found 6/6 markers.
[2024-01-24 13:46:57,543] [INFO] Query marker FASTA was written to GCF_020387415.1_ASM2038741v1_genomic.fna/markers.fasta
[2024-01-24 13:46:57,544] [INFO] Task started: Blastn
[2024-01-24 13:46:57,544] [INFO] Running command: blastn -query GCF_020387415.1_ASM2038741v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg280b1576-9b07-472c-b117-496d5e592929/dqc_reference/reference_markers.fasta -out GCF_020387415.1_ASM2038741v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:46:58,553] [INFO] Task succeeded: Blastn
[2024-01-24 13:46:58,556] [INFO] Selected 12 target genomes.
[2024-01-24 13:46:58,557] [INFO] Target genome list was writen to GCF_020387415.1_ASM2038741v1_genomic.fna/target_genomes.txt
[2024-01-24 13:46:58,569] [INFO] Task started: fastANI
[2024-01-24 13:46:58,570] [INFO] Running command: fastANI --query /var/lib/cwl/stgfa87bf45-178f-43d8-b91a-592287b85a38/GCF_020387415.1_ASM2038741v1_genomic.fna.gz --refList GCF_020387415.1_ASM2038741v1_genomic.fna/target_genomes.txt --output GCF_020387415.1_ASM2038741v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:47:12,695] [INFO] Task succeeded: fastANI
[2024-01-24 13:47:12,696] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg280b1576-9b07-472c-b117-496d5e592929/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:47:12,697] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg280b1576-9b07-472c-b117-496d5e592929/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:47:12,718] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:47:12,718] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:47:12,719] [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
Ideonella benzenivorans	strain=B7	GCA_020387415.1	2831643	2831643	type	True	100.0	1486	1487	95	conclusive
Ideonella dechloratans	strain=CCUG 30977	GCA_008801845.1	36863	36863	type	True	88.4501	1106	1487	95	below_threshold
Ideonella dechloratans	strain=CCUG 30977	GCA_021049305.1	36863	36863	type	True	88.4394	1163	1487	95	below_threshold
Ideonella azotifigens	strain=DSM 21438	GCA_006519715.1	513160	513160	type	True	82.1644	635	1487	95	below_threshold
Ideonella livida	strain=TBM-1	GCA_010499455.1	2707176	2707176	type	True	81.2427	714	1487	95	below_threshold
Sphaerotilus sulfidivorans	strain=D-501	GCA_013426975.1	639200	639200	type	True	80.6691	640	1487	95	below_threshold
Schlegelella thermodepolymerans	strain=DSM 15344	GCA_015476235.1	215580	215580	type	True	80.5656	606	1487	95	below_threshold
Azohydromonas aeria	strain=CFCC 13393	GCA_009760915.1	2590212	2590212	type	True	79.9247	700	1487	95	below_threshold
Azohydromonas lata	strain=NBRC 102462	GCA_001571085.1	45677	45677	type	True	79.9236	668	1487	95	below_threshold
Schlegelella brevitalea	strain=DSM 7029	GCA_001017435.1	413882	413882	type	True	79.2413	561	1487	95	below_threshold
Xylophilus rhododendri	strain=KACC 21265	GCA_009906855.1	2697032	2697032	type	True	78.9163	598	1487	95	below_threshold
Roseospira goensis	strain=JA135	GCA_014197795.1	391922	391922	type	True	75.4474	179	1487	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:47:12,720] [INFO] DFAST Taxonomy check result was written to GCF_020387415.1_ASM2038741v1_genomic.fna/tc_result.tsv
[2024-01-24 13:47:12,720] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:47:12,721] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:47:12,721] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg280b1576-9b07-472c-b117-496d5e592929/dqc_reference/checkm_data
[2024-01-24 13:47:12,722] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:47:12,764] [INFO] Task started: CheckM
[2024-01-24 13:47:12,764] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_020387415.1_ASM2038741v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_020387415.1_ASM2038741v1_genomic.fna/checkm_input GCF_020387415.1_ASM2038741v1_genomic.fna/checkm_result
[2024-01-24 13:48:59,953] [INFO] Task succeeded: CheckM
[2024-01-24 13:48:59,954] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:48:59,976] [INFO] ===== Completeness check finished =====
[2024-01-24 13:48:59,977] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:48:59,977] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_020387415.1_ASM2038741v1_genomic.fna/markers.fasta)
[2024-01-24 13:48:59,977] [INFO] Task started: Blastn
[2024-01-24 13:48:59,978] [INFO] Running command: blastn -query GCF_020387415.1_ASM2038741v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg280b1576-9b07-472c-b117-496d5e592929/dqc_reference/reference_markers_gtdb.fasta -out GCF_020387415.1_ASM2038741v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:01,688] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:01,693] [INFO] Selected 17 target genomes.
[2024-01-24 13:49:01,693] [INFO] Target genome list was writen to GCF_020387415.1_ASM2038741v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:49:01,744] [INFO] Task started: fastANI
[2024-01-24 13:49:01,745] [INFO] Running command: fastANI --query /var/lib/cwl/stgfa87bf45-178f-43d8-b91a-592287b85a38/GCF_020387415.1_ASM2038741v1_genomic.fna.gz --refList GCF_020387415.1_ASM2038741v1_genomic.fna/target_genomes_gtdb.txt --output GCF_020387415.1_ASM2038741v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:49:19,444] [INFO] Task succeeded: fastANI
[2024-01-24 13:49:19,460] [INFO] Found 17 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:49:19,460] [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_008801845.1	s__Ideonella dechloratans	88.4731	1104	1487	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ideonella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000333615.1	s__Ideonella sp000333615	88.1067	933	1487	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ideonella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018069875.1	s__Ideonella sp018069875	82.125	826	1487	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ideonella	95.0	98.74	98.74	0.92	0.92	2	-
GCA_017302485.1	s__Ideonella sp017302485	82.0764	522	1487	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ideonella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018069755.1	s__Ideonella sp018069755	81.8766	781	1487	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ideonella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010499455.1	s__Ideonella sp010499455	81.19	720	1487	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ideonella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016213265.1	s__Ideonella sp016213265	81.031	679	1487	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ideonella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016710065.1	s__Ideonella sp016710065	80.9957	707	1487	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ideonella	95.0	99.07	99.00	0.95	0.93	3	-
GCA_018780145.1	s__Ideonella sp018780145	80.9722	710	1487	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ideonella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017992055.1	s__Aquabacterium_A sp017992055	80.5872	762	1487	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_017302505.1	s__Rubrivivax sp017302505	80.2022	530	1487	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rubrivivax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003265685.1	s__Piscinibacter caeni	80.1976	698	1487	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Piscinibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001770815.1	s__Aquabacterium_A sp001770815	80.1932	649	1487	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquabacterium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004016515.1	s__Rubrivivax albus	80.0279	663	1487	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rubrivivax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014197795.1	s__Rhodospira goensis	75.4403	180	1487	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__Rhodospira	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003258945.1	s__Paracraurococcus frigidaeris	75.2049	227	1487	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Paracraurococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003565155.1	s__T1Sed10-7 sp003565155	74.7459	90	1487	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nitriliruptorales;f__Nitriliruptoraceae;g__T1Sed10-7	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:49:19,462] [INFO] GTDB search result was written to GCF_020387415.1_ASM2038741v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:49:19,463] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:49:19,468] [INFO] DFAST_QC result json was written to GCF_020387415.1_ASM2038741v1_genomic.fna/dqc_result.json
[2024-01-24 13:49:19,468] [INFO] DFAST_QC completed!
[2024-01-24 13:49:19,468] [INFO] Total running time: 0h2m38s