[2024-01-24 13:17:13,814] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:17:13,817] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:17:13,817] [INFO] DQC Reference Directory: /var/lib/cwl/stg1bf590f1-4e41-4ace-a531-76729b3f7f9a/dqc_reference
[2024-01-24 13:17:15,123] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:17:15,124] [INFO] Task started: Prodigal
[2024-01-24 13:17:15,124] [INFO] Running command: gunzip -c /var/lib/cwl/stg37eb0ceb-d578-47f5-864d-77dcecb66532/GCF_030409115.1_ASM3040911v1_genomic.fna.gz | prodigal -d GCF_030409115.1_ASM3040911v1_genomic.fna/cds.fna -a GCF_030409115.1_ASM3040911v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:17:29,757] [INFO] Task succeeded: Prodigal
[2024-01-24 13:17:29,758] [INFO] Task started: HMMsearch
[2024-01-24 13:17:29,758] [INFO] Running command: hmmsearch --tblout GCF_030409115.1_ASM3040911v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1bf590f1-4e41-4ace-a531-76729b3f7f9a/dqc_reference/reference_markers.hmm GCF_030409115.1_ASM3040911v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:17:30,098] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:17:30,100] [INFO] Found 6/6 markers.
[2024-01-24 13:17:30,142] [INFO] Query marker FASTA was written to GCF_030409115.1_ASM3040911v1_genomic.fna/markers.fasta
[2024-01-24 13:17:30,143] [INFO] Task started: Blastn
[2024-01-24 13:17:30,143] [INFO] Running command: blastn -query GCF_030409115.1_ASM3040911v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1bf590f1-4e41-4ace-a531-76729b3f7f9a/dqc_reference/reference_markers.fasta -out GCF_030409115.1_ASM3040911v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:17:31,201] [INFO] Task succeeded: Blastn
[2024-01-24 13:17:31,207] [INFO] Selected 17 target genomes.
[2024-01-24 13:17:31,207] [INFO] Target genome list was writen to GCF_030409115.1_ASM3040911v1_genomic.fna/target_genomes.txt
[2024-01-24 13:17:31,278] [INFO] Task started: fastANI
[2024-01-24 13:17:31,278] [INFO] Running command: fastANI --query /var/lib/cwl/stg37eb0ceb-d578-47f5-864d-77dcecb66532/GCF_030409115.1_ASM3040911v1_genomic.fna.gz --refList GCF_030409115.1_ASM3040911v1_genomic.fna/target_genomes.txt --output GCF_030409115.1_ASM3040911v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:17:50,364] [INFO] Task succeeded: fastANI
[2024-01-24 13:17:50,365] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1bf590f1-4e41-4ace-a531-76729b3f7f9a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:17:50,366] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1bf590f1-4e41-4ace-a531-76729b3f7f9a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:17:50,390] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:17:50,390] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:17:50,390] [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	81.2112	774	1439	95	below_threshold
Paucibacter toxinivorans	strain=DSM 16998	GCA_004362525.1	270368	270368	type	True	81.1261	850	1439	95	below_threshold
Roseateles depolymerans	strain=DSM 11813	GCA_003387155.1	76731	76731	type	True	80.9667	716	1439	95	below_threshold
Pelomonas puraquae	strain=CCUG 52769	GCA_002205845.1	431059	431059	type	True	80.7837	749	1439	95	below_threshold
Mitsuaria chitinivorans	strain=HWN-4	GCA_002761755.1	2917965	2917965	type	True	80.7593	731	1439	95	below_threshold
Ideonella dechloratans	strain=CCUG 30977	GCA_021049305.1	36863	36863	type	True	80.6803	653	1439	95	below_threshold
Ideonella dechloratans	strain=CCUG 30977	GCA_008801845.1	36863	36863	type	True	80.6169	632	1439	95	below_threshold
Roseateles terrae	strain=CECT 7247	GCA_014192155.1	431060	431060	type	True	80.3097	708	1439	95	below_threshold
Ideonella benzenivorans	strain=B7	GCA_020387415.1	2831643	2831643	type	True	80.0333	603	1439	95	below_threshold
Inhella proteolytica	strain=1Y17	GCA_016093275.1	2795029	2795029	type	True	79.974	689	1439	95	below_threshold
Ideonella azotifigens	strain=DSM 21438	GCA_006519715.1	513160	513160	type	True	79.8119	513	1439	95	below_threshold
Azohydromonas australica	strain=DSM 1124	GCA_000430725.1	364039	364039	type	True	79.6837	628	1439	95	below_threshold
Ideonella livida	strain=TBM-1	GCA_010499455.1	2707176	2707176	type	True	79.6819	601	1439	95	below_threshold
Azohydromonas caseinilytica	strain=G-1-1-14	GCA_012927045.1	2728836	2728836	type	True	79.651	642	1439	95	below_threshold
Azohydromonas aeria	strain=CFCC 13393	GCA_009760915.1	2590212	2590212	type	True	79.6088	630	1439	95	below_threshold
Aquabacterium olei	strain=NBRC 110486	GCA_003100395.1	1296669	1296669	type	True	79.4353	475	1439	95	below_threshold
Schlegelella brevitalea	strain=DSM 7029	GCA_001017435.1	413882	413882	type	True	78.7682	505	1439	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:17:50,393] [INFO] DFAST Taxonomy check result was written to GCF_030409115.1_ASM3040911v1_genomic.fna/tc_result.tsv
[2024-01-24 13:17:50,394] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:17:50,394] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:17:50,394] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1bf590f1-4e41-4ace-a531-76729b3f7f9a/dqc_reference/checkm_data
[2024-01-24 13:17:50,396] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:17:50,437] [INFO] Task started: CheckM
[2024-01-24 13:17:50,438] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030409115.1_ASM3040911v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030409115.1_ASM3040911v1_genomic.fna/checkm_input GCF_030409115.1_ASM3040911v1_genomic.fna/checkm_result
[2024-01-24 13:18:45,910] [INFO] Task succeeded: CheckM
[2024-01-24 13:18:45,912] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:18:45,936] [INFO] ===== Completeness check finished =====
[2024-01-24 13:18:45,937] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:18:45,938] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030409115.1_ASM3040911v1_genomic.fna/markers.fasta)
[2024-01-24 13:18:45,938] [INFO] Task started: Blastn
[2024-01-24 13:18:45,938] [INFO] Running command: blastn -query GCF_030409115.1_ASM3040911v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1bf590f1-4e41-4ace-a531-76729b3f7f9a/dqc_reference/reference_markers_gtdb.fasta -out GCF_030409115.1_ASM3040911v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:18:47,968] [INFO] Task succeeded: Blastn
[2024-01-24 13:18:47,973] [INFO] Selected 17 target genomes.
[2024-01-24 13:18:47,974] [INFO] Target genome list was writen to GCF_030409115.1_ASM3040911v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:18:47,988] [INFO] Task started: fastANI
[2024-01-24 13:18:47,989] [INFO] Running command: fastANI --query /var/lib/cwl/stg37eb0ceb-d578-47f5-864d-77dcecb66532/GCF_030409115.1_ASM3040911v1_genomic.fna.gz --refList GCF_030409115.1_ASM3040911v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030409115.1_ASM3040911v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:19:09,724] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:09,741] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:19:09,741] [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	99.9967	1434	1439	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	84.9576	1069	1439	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	83.329	1028	1439	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	82.5089	869	1439	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	82.3884	857	1439	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	82.3524	819	1439	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__WAJ17	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014204525.1	s__Paucibacter_A oligotrophus	82.2975	879	1439	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_002885975.1	s__Paucibacter_A aquatile	82.2227	903	1439	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	81.5532	773	1439	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	81.4811	761	1439	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	81.1945	775	1439	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	81.0597	798	1439	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	80.9666	716	1439	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	80.8815	753	1439	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Mitsuaria	95.0	98.36	98.28	0.95	0.95	4	-
GCF_016467315.1	s__OAE585 sp016467315	80.6067	811	1439	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__OAE585	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019234295.1	s__JAFALK01 sp019234295	80.5503	583	1439	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__JAFALK01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012927045.1	s__Azohydromonas caseinilytica	79.6567	640	1439	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 13:19:09,743] [INFO] GTDB search result was written to GCF_030409115.1_ASM3040911v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:19:09,743] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:19:09,748] [INFO] DFAST_QC result json was written to GCF_030409115.1_ASM3040911v1_genomic.fna/dqc_result.json
[2024-01-24 13:19:09,748] [INFO] DFAST_QC completed!
[2024-01-24 13:19:09,748] [INFO] Total running time: 0h1m56s