[2024-01-24 11:43:53,219] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:43:53,221] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:43:53,221] [INFO] DQC Reference Directory: /var/lib/cwl/stg2ff10ef2-2a26-481f-9b92-314ce38ad3f5/dqc_reference
[2024-01-24 11:43:54,471] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:43:54,472] [INFO] Task started: Prodigal
[2024-01-24 11:43:54,472] [INFO] Running command: gunzip -c /var/lib/cwl/stgfbad9cd2-1a49-495c-bcad-12ebd9c6924f/GCF_004362405.1_ASM436240v1_genomic.fna.gz | prodigal -d GCF_004362405.1_ASM436240v1_genomic.fna/cds.fna -a GCF_004362405.1_ASM436240v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:44:08,368] [INFO] Task succeeded: Prodigal
[2024-01-24 11:44:08,368] [INFO] Task started: HMMsearch
[2024-01-24 11:44:08,368] [INFO] Running command: hmmsearch --tblout GCF_004362405.1_ASM436240v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2ff10ef2-2a26-481f-9b92-314ce38ad3f5/dqc_reference/reference_markers.hmm GCF_004362405.1_ASM436240v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:44:08,613] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:44:08,614] [INFO] Found 6/6 markers.
[2024-01-24 11:44:08,649] [INFO] Query marker FASTA was written to GCF_004362405.1_ASM436240v1_genomic.fna/markers.fasta
[2024-01-24 11:44:08,649] [INFO] Task started: Blastn
[2024-01-24 11:44:08,650] [INFO] Running command: blastn -query GCF_004362405.1_ASM436240v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2ff10ef2-2a26-481f-9b92-314ce38ad3f5/dqc_reference/reference_markers.fasta -out GCF_004362405.1_ASM436240v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:44:09,648] [INFO] Task succeeded: Blastn
[2024-01-24 11:44:09,651] [INFO] Selected 17 target genomes.
[2024-01-24 11:44:09,651] [INFO] Target genome list was writen to GCF_004362405.1_ASM436240v1_genomic.fna/target_genomes.txt
[2024-01-24 11:44:09,655] [INFO] Task started: fastANI
[2024-01-24 11:44:09,656] [INFO] Running command: fastANI --query /var/lib/cwl/stgfbad9cd2-1a49-495c-bcad-12ebd9c6924f/GCF_004362405.1_ASM436240v1_genomic.fna.gz --refList GCF_004362405.1_ASM436240v1_genomic.fna/target_genomes.txt --output GCF_004362405.1_ASM436240v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:44:28,254] [INFO] Task succeeded: fastANI
[2024-01-24 11:44:28,254] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2ff10ef2-2a26-481f-9b92-314ce38ad3f5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:44:28,255] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2ff10ef2-2a26-481f-9b92-314ce38ad3f5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:44:28,268] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:44:28,269] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:44:28,269] [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
Pelomonas saccharophila	strain=DSM 654	GCA_004342485.1	304	304	type	True	81.1151	790	1442	95	below_threshold
Paucibacter toxinivorans	strain=DSM 16998	GCA_004362525.1	270368	270368	type	True	81.0954	844	1442	95	below_threshold
Roseateles depolymerans	strain=DSM 11813	GCA_003387155.1	76731	76731	type	True	80.8537	716	1442	95	below_threshold
Pelomonas puraquae	strain=CCUG 52769	GCA_002205845.1	431059	431059	type	True	80.8359	752	1442	95	below_threshold
Mitsuaria chitinivorans	strain=HWN-4	GCA_002761755.1	2917965	2917965	type	True	80.788	732	1442	95	below_threshold
Ideonella dechloratans	strain=CCUG 30977	GCA_021049305.1	36863	36863	type	True	80.6333	642	1442	95	below_threshold
Ideonella dechloratans	strain=CCUG 30977	GCA_008801845.1	36863	36863	type	True	80.6013	631	1442	95	below_threshold
Roseateles terrae	strain=CECT 7247	GCA_014192155.1	431060	431060	type	True	80.3522	700	1442	95	below_threshold
Ideonella benzenivorans	strain=B7	GCA_020387415.1	2831643	2831643	type	True	79.944	614	1442	95	below_threshold
Inhella proteolytica	strain=1Y17	GCA_016093275.1	2795029	2795029	type	True	79.9271	691	1442	95	below_threshold
Ideonella azotifigens	strain=DSM 21438	GCA_006519715.1	513160	513160	type	True	79.7286	514	1442	95	below_threshold
Azohydromonas caseinilytica	strain=G-1-1-14	GCA_012927045.1	2728836	2728836	type	True	79.6881	639	1442	95	below_threshold
Azohydromonas australica	strain=DSM 1124	GCA_000430725.1	364039	364039	type	True	79.6695	640	1442	95	below_threshold
Ideonella livida	strain=TBM-1	GCA_010499455.1	2707176	2707176	type	True	79.5125	614	1442	95	below_threshold
Aquabacterium olei	strain=NBRC 110486	GCA_003100395.1	1296669	1296669	type	True	79.4887	475	1442	95	below_threshold
Azohydromonas aeria	strain=CFCC 13393	GCA_009760915.1	2590212	2590212	type	True	79.4863	645	1442	95	below_threshold
Schlegelella brevitalea	strain=DSM 7029	GCA_001017435.1	413882	413882	type	True	78.7422	511	1442	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:44:28,270] [INFO] DFAST Taxonomy check result was written to GCF_004362405.1_ASM436240v1_genomic.fna/tc_result.tsv
[2024-01-24 11:44:28,271] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:44:28,271] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:44:28,271] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2ff10ef2-2a26-481f-9b92-314ce38ad3f5/dqc_reference/checkm_data
[2024-01-24 11:44:28,272] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:44:28,312] [INFO] Task started: CheckM
[2024-01-24 11:44:28,312] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004362405.1_ASM436240v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004362405.1_ASM436240v1_genomic.fna/checkm_input GCF_004362405.1_ASM436240v1_genomic.fna/checkm_result
[2024-01-24 11:45:17,907] [INFO] Task succeeded: CheckM
[2024-01-24 11:45:17,908] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:45:17,926] [INFO] ===== Completeness check finished =====
[2024-01-24 11:45:17,926] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:45:17,927] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004362405.1_ASM436240v1_genomic.fna/markers.fasta)
[2024-01-24 11:45:17,927] [INFO] Task started: Blastn
[2024-01-24 11:45:17,927] [INFO] Running command: blastn -query GCF_004362405.1_ASM436240v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2ff10ef2-2a26-481f-9b92-314ce38ad3f5/dqc_reference/reference_markers_gtdb.fasta -out GCF_004362405.1_ASM436240v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:45:19,901] [INFO] Task succeeded: Blastn
[2024-01-24 11:45:19,904] [INFO] Selected 17 target genomes.
[2024-01-24 11:45:19,904] [INFO] Target genome list was writen to GCF_004362405.1_ASM436240v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:45:19,915] [INFO] Task started: fastANI
[2024-01-24 11:45:19,916] [INFO] Running command: fastANI --query /var/lib/cwl/stgfbad9cd2-1a49-495c-bcad-12ebd9c6924f/GCF_004362405.1_ASM436240v1_genomic.fna.gz --refList GCF_004362405.1_ASM436240v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004362405.1_ASM436240v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:45:40,874] [INFO] Task succeeded: fastANI
[2024-01-24 11:45:40,888] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:45:40,888] [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_004362405.1	s__Kinneretia asaccharophila	100.0	1440	1442	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Kinneretia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_015624425.1	s__Kinneretia sp015624425	84.9672	1069	1442	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Kinneretia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005503085.1	s__Paucibacter_A sp005503085	83.3831	1014	1442	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paucibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015657635.1	s__Kinneretia sp015657635	82.4945	882	1442	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Kinneretia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013824165.1	s__Kinneretia sp013824165	82.3408	871	1442	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Kinneretia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014174515.1	s__WAJ17 sp014174515	82.33	826	1442	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__WAJ17	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002885975.1	s__Paucibacter_A aquatile	82.3079	877	1442	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paucibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014204525.1	s__Paucibacter_A oligotrophus	82.2537	878	1442	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paucibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009996515.1	s__Pelomonas sp009996515	81.4458	787	1442	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pelomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001984095.1	s__KK5 sp001984095	81.4337	773	1442	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__KK5	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004342485.1	s__Pelomonas saccharophila	81.0978	793	1442	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pelomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003550215.1	s__Pelomonas sp003550215	80.9401	804	1442	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pelomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003387155.1	s__Roseateles depolymerans	80.8095	721	1442	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Roseateles	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900113225.1	s__Mitsuaria sp900113225	80.7692	768	1442	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Mitsuaria	95.0	98.36	98.28	0.95	0.95	4	-
GCA_019234295.1	s__JAFALK01 sp019234295	80.6241	580	1442	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__JAFALK01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016467315.1	s__OAE585 sp016467315	80.6082	806	1442	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__OAE585	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012927045.1	s__Azohydromonas caseinilytica	79.6465	645	1442	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Azohydromonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:45:40,893] [INFO] GTDB search result was written to GCF_004362405.1_ASM436240v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:45:40,893] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:45:40,897] [INFO] DFAST_QC result json was written to GCF_004362405.1_ASM436240v1_genomic.fna/dqc_result.json
[2024-01-24 11:45:40,897] [INFO] DFAST_QC completed!
[2024-01-24 11:45:40,897] [INFO] Total running time: 0h1m48s