[2024-01-24 14:31:01,563] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:31:01,567] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:31:01,567] [INFO] DQC Reference Directory: /var/lib/cwl/stg3742cb15-e61e-44d2-9d72-5c28385c5a0f/dqc_reference
[2024-01-24 14:31:04,074] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:31:04,076] [INFO] Task started: Prodigal
[2024-01-24 14:31:04,077] [INFO] Running command: gunzip -c /var/lib/cwl/stg648ec84a-2228-48af-8bda-bf61b6f99d2a/GCF_026712205.1_ASM2671220v1_genomic.fna.gz | prodigal -d GCF_026712205.1_ASM2671220v1_genomic.fna/cds.fna -a GCF_026712205.1_ASM2671220v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:31:20,129] [INFO] Task succeeded: Prodigal
[2024-01-24 14:31:20,129] [INFO] Task started: HMMsearch
[2024-01-24 14:31:20,129] [INFO] Running command: hmmsearch --tblout GCF_026712205.1_ASM2671220v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3742cb15-e61e-44d2-9d72-5c28385c5a0f/dqc_reference/reference_markers.hmm GCF_026712205.1_ASM2671220v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:31:20,504] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:31:20,505] [INFO] Found 6/6 markers.
[2024-01-24 14:31:20,552] [INFO] Query marker FASTA was written to GCF_026712205.1_ASM2671220v1_genomic.fna/markers.fasta
[2024-01-24 14:31:20,553] [INFO] Task started: Blastn
[2024-01-24 14:31:20,553] [INFO] Running command: blastn -query GCF_026712205.1_ASM2671220v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3742cb15-e61e-44d2-9d72-5c28385c5a0f/dqc_reference/reference_markers.fasta -out GCF_026712205.1_ASM2671220v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:31:21,689] [INFO] Task succeeded: Blastn
[2024-01-24 14:31:21,693] [INFO] Selected 20 target genomes.
[2024-01-24 14:31:21,693] [INFO] Target genome list was writen to GCF_026712205.1_ASM2671220v1_genomic.fna/target_genomes.txt
[2024-01-24 14:31:21,703] [INFO] Task started: fastANI
[2024-01-24 14:31:21,703] [INFO] Running command: fastANI --query /var/lib/cwl/stg648ec84a-2228-48af-8bda-bf61b6f99d2a/GCF_026712205.1_ASM2671220v1_genomic.fna.gz --refList GCF_026712205.1_ASM2671220v1_genomic.fna/target_genomes.txt --output GCF_026712205.1_ASM2671220v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:31:44,394] [INFO] Task succeeded: fastANI
[2024-01-24 14:31:44,395] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3742cb15-e61e-44d2-9d72-5c28385c5a0f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:31:44,396] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3742cb15-e61e-44d2-9d72-5c28385c5a0f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:31:44,415] [INFO] Found 20 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:31:44,415] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:31:44,415] [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	91.0384	1265	1683	95	below_threshold
Pelomonas puraquae	strain=CCUG 52769	GCA_002205845.1	431059	431059	type	True	85.7207	1155	1683	95	below_threshold
Mitsuaria chitinivorans	strain=HWN-4	GCA_002761755.1	2917965	2917965	type	True	81.3547	833	1683	95	below_threshold
Rubrivivax benzoatilyticus	strain=JA2	GCA_000190375.2	316997	316997	type	True	80.7704	681	1683	95	below_threshold
Rubrivivax benzoatilyticus	strain=JA2	GCA_000420125.1	316997	316997	type	True	80.7359	722	1683	95	below_threshold
Schlegelella thermodepolymerans	strain=DSM 15344	GCA_002933415.1	215580	215580	type	True	80.5261	619	1683	95	below_threshold
Schlegelella thermodepolymerans	strain=DSM 15344	GCA_015476235.1	215580	215580	type	True	80.4435	625	1683	95	below_threshold
Paucibacter toxinivorans	strain=DSM 16998	GCA_004362525.1	270368	270368	type	True	80.4367	814	1683	95	below_threshold
Ideonella dechloratans	strain=CCUG 30977	GCA_021049305.1	36863	36863	type	True	80.4062	661	1683	95	below_threshold
Roseateles depolymerans	strain=DSM 11813	GCA_003387155.1	76731	76731	type	True	80.3424	717	1683	95	below_threshold
Rubrivivax gelatinosus	strain=DSM 1709	GCA_016583525.1	28068	28068	suspected-type	True	80.3328	733	1683	95	below_threshold
Sphaerotilus natans subsp. natans	strain=DSM 6575	GCA_000689195.1	882627	34103	type	True	80.1543	646	1683	95	below_threshold
Sphaerotilus natans	strain=ATCC 13338	GCA_900156335.1	34103	34103	type	True	80.1187	678	1683	95	below_threshold
Sphaerotilus sulfidivorans	strain=D-501	GCA_013426975.1	639200	639200	type	True	80.0005	675	1683	95	below_threshold
Ideonella benzenivorans	strain=B7	GCA_020387415.1	2831643	2831643	type	True	79.9978	639	1683	95	below_threshold
Inhella proteolytica	strain=1Y17	GCA_016093275.1	2795029	2795029	type	True	79.9931	774	1683	95	below_threshold
Roseateles terrae	strain=CECT 7247	GCA_014192155.1	431060	431060	type	True	79.7032	674	1683	95	below_threshold
Aquabacterium soli	strain=SJQ9	GCA_003933735.1	2493092	2493092	type	True	79.3618	529	1683	95	below_threshold
Schlegelella brevitalea	strain=DSM 7029	GCA_001017435.1	413882	413882	type	True	79.3167	609	1683	95	below_threshold
Variovorax soli	strain=NBRC 106424	GCA_001591385.1	376815	376815	type	True	79.1851	577	1683	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:31:44,417] [INFO] DFAST Taxonomy check result was written to GCF_026712205.1_ASM2671220v1_genomic.fna/tc_result.tsv
[2024-01-24 14:31:44,418] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:31:44,418] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:31:44,419] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3742cb15-e61e-44d2-9d72-5c28385c5a0f/dqc_reference/checkm_data
[2024-01-24 14:31:44,420] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:31:44,474] [INFO] Task started: CheckM
[2024-01-24 14:31:44,474] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_026712205.1_ASM2671220v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_026712205.1_ASM2671220v1_genomic.fna/checkm_input GCF_026712205.1_ASM2671220v1_genomic.fna/checkm_result
[2024-01-24 14:32:39,984] [INFO] Task succeeded: CheckM
[2024-01-24 14:32:39,987] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:32:40,009] [INFO] ===== Completeness check finished =====
[2024-01-24 14:32:40,010] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:32:40,010] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_026712205.1_ASM2671220v1_genomic.fna/markers.fasta)
[2024-01-24 14:32:40,011] [INFO] Task started: Blastn
[2024-01-24 14:32:40,011] [INFO] Running command: blastn -query GCF_026712205.1_ASM2671220v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3742cb15-e61e-44d2-9d72-5c28385c5a0f/dqc_reference/reference_markers_gtdb.fasta -out GCF_026712205.1_ASM2671220v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:32:42,167] [INFO] Task succeeded: Blastn
[2024-01-24 14:32:42,171] [INFO] Selected 12 target genomes.
[2024-01-24 14:32:42,171] [INFO] Target genome list was writen to GCF_026712205.1_ASM2671220v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:32:42,180] [INFO] Task started: fastANI
[2024-01-24 14:32:42,180] [INFO] Running command: fastANI --query /var/lib/cwl/stg648ec84a-2228-48af-8bda-bf61b6f99d2a/GCF_026712205.1_ASM2671220v1_genomic.fna.gz --refList GCF_026712205.1_ASM2671220v1_genomic.fna/target_genomes_gtdb.txt --output GCF_026712205.1_ASM2671220v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:33:00,210] [INFO] Task succeeded: fastANI
[2024-01-24 14:33:00,227] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 14:33:00,227] [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_004342485.1	s__Pelomonas saccharophila	91.0561	1264	1683	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pelomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009996515.1	s__Pelomonas sp009996515	88.1303	1063	1683	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pelomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019237615.1	s__Pelomonas sp019237615	87.6805	1060	1683	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pelomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003963075.1	s__Pelomonas sp003963075	87.2677	1051	1683	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pelomonas	95.0	96.90	96.90	0.86	0.86	2	-
GCF_003550215.1	s__Pelomonas sp003550215	87.1799	1156	1683	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	87.0898	1143	1683	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pelomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001425055.1	s__Pelomonas sp001425055	86.8073	1162	1683	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pelomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016195825.1	s__Pelomonas sp016195825	86.7441	1112	1683	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pelomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001425705.1	s__Pelomonas sp001425705	86.5319	1177	1683	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pelomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016790285.1	s__Pelomonas sp016790285	85.8279	1056	1683	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pelomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002205845.1	s__Pelomonas puraquae	85.7368	1152	1683	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pelomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003963005.1	s__Pelomonas sp003963005	85.4694	1096	1683	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pelomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:33:00,230] [INFO] GTDB search result was written to GCF_026712205.1_ASM2671220v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:33:00,231] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:33:00,236] [INFO] DFAST_QC result json was written to GCF_026712205.1_ASM2671220v1_genomic.fna/dqc_result.json
[2024-01-24 14:33:00,236] [INFO] DFAST_QC completed!
[2024-01-24 14:33:00,237] [INFO] Total running time: 0h1m59s