[2024-01-24 14:28:17,877] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:28:17,881] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:28:17,881] [INFO] DQC Reference Directory: /var/lib/cwl/stge909e3d4-ccba-4496-9ca1-35151f6cbb27/dqc_reference
[2024-01-24 14:28:20,485] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:28:20,486] [INFO] Task started: Prodigal
[2024-01-24 14:28:20,487] [INFO] Running command: gunzip -c /var/lib/cwl/stgcb3edd8e-ca88-4ae3-929b-6a730720e129/GCF_025717515.1_ASM2571751v1_genomic.fna.gz | prodigal -d GCF_025717515.1_ASM2571751v1_genomic.fna/cds.fna -a GCF_025717515.1_ASM2571751v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:28:41,598] [INFO] Task succeeded: Prodigal
[2024-01-24 14:28:41,598] [INFO] Task started: HMMsearch
[2024-01-24 14:28:41,598] [INFO] Running command: hmmsearch --tblout GCF_025717515.1_ASM2571751v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge909e3d4-ccba-4496-9ca1-35151f6cbb27/dqc_reference/reference_markers.hmm GCF_025717515.1_ASM2571751v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:28:41,924] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:28:41,925] [INFO] Found 6/6 markers.
[2024-01-24 14:28:41,982] [INFO] Query marker FASTA was written to GCF_025717515.1_ASM2571751v1_genomic.fna/markers.fasta
[2024-01-24 14:28:41,983] [INFO] Task started: Blastn
[2024-01-24 14:28:41,983] [INFO] Running command: blastn -query GCF_025717515.1_ASM2571751v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge909e3d4-ccba-4496-9ca1-35151f6cbb27/dqc_reference/reference_markers.fasta -out GCF_025717515.1_ASM2571751v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:28:42,959] [INFO] Task succeeded: Blastn
[2024-01-24 14:28:42,963] [INFO] Selected 21 target genomes.
[2024-01-24 14:28:42,964] [INFO] Target genome list was writen to GCF_025717515.1_ASM2571751v1_genomic.fna/target_genomes.txt
[2024-01-24 14:28:42,984] [INFO] Task started: fastANI
[2024-01-24 14:28:42,984] [INFO] Running command: fastANI --query /var/lib/cwl/stgcb3edd8e-ca88-4ae3-929b-6a730720e129/GCF_025717515.1_ASM2571751v1_genomic.fna.gz --refList GCF_025717515.1_ASM2571751v1_genomic.fna/target_genomes.txt --output GCF_025717515.1_ASM2571751v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:29:01,348] [INFO] Task succeeded: fastANI
[2024-01-24 14:29:01,349] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge909e3d4-ccba-4496-9ca1-35151f6cbb27/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:29:01,350] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge909e3d4-ccba-4496-9ca1-35151f6cbb27/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:29:01,371] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:29:01,371] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:29:01,371] [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
Paucibacter toxinivorans	strain=DSM 16998	GCA_004362525.1	270368	270368	type	True	79.5425	722	1900	95	below_threshold
Pelomonas saccharophila	strain=DSM 654	GCA_004342485.1	304	304	type	True	78.9357	640	1900	95	below_threshold
Mitsuaria chitinivorans	strain=HWN-4	GCA_002761755.1	2917965	2917965	type	True	78.6724	569	1900	95	below_threshold
Ideonella azotifigens	strain=DSM 21438	GCA_006519715.1	513160	513160	type	True	78.5784	377	1900	95	below_threshold
Pelomonas puraquae	strain=CCUG 52769	GCA_002205845.1	431059	431059	type	True	78.2877	594	1900	95	below_threshold
Roseateles terrae	strain=CECT 7247	GCA_014192155.1	431060	431060	type	True	78.2465	474	1900	95	below_threshold
Roseateles depolymerans	strain=DSM 11813	GCA_003387155.1	76731	76731	type	True	78.2152	497	1900	95	below_threshold
Sphaerotilus sulfidivorans	strain=D-501	GCA_013426975.1	639200	639200	type	True	78.1623	440	1900	95	below_threshold
Sphaerotilus hippei	strain=DSM 566	GCA_003201595.1	744406	744406	type	True	78.1477	418	1900	95	below_threshold
Ideonella dechloratans	strain=CCUG 30977	GCA_021049305.1	36863	36863	type	True	78.1297	415	1900	95	below_threshold
Sphaerotilus natans subsp. natans	strain=DSM 6575	GCA_000689195.1	882627	34103	type	True	78.0436	446	1900	95	below_threshold
Schlegelella thermodepolymerans	strain=DSM 15344	GCA_003349825.1	215580	215580	type	True	78.0281	386	1900	95	below_threshold
Sphaerotilus natans	strain=ATCC 13338	GCA_900156335.1	34103	34103	type	True	78.0238	459	1900	95	below_threshold
Schlegelella thermodepolymerans	strain=DSM 15344	GCA_015476235.1	215580	215580	type	True	77.996	385	1900	95	below_threshold
Inhella proteolytica	strain=1Y17	GCA_016093275.1	2795029	2795029	type	True	77.9839	486	1900	95	below_threshold
Schlegelella thermodepolymerans	strain=DSM 15344	GCA_002933415.1	215580	215580	type	True	77.9784	388	1900	95	below_threshold
Ideonella benzenivorans	strain=B7	GCA_020387415.1	2831643	2831643	type	True	77.8284	413	1900	95	below_threshold
Aquabacterium parvum	strain=B6	GCA_001447195.1	70584	70584	type	True	77.7024	313	1900	95	below_threshold
Ideonella livida	strain=TBM-1	GCA_010499455.1	2707176	2707176	type	True	77.684	344	1900	95	below_threshold
Aquabacterium soli	strain=SJQ9	GCA_003933735.1	2493092	2493092	type	True	77.5955	328	1900	95	below_threshold
Hydrogenophaga crocea	strain=BA0156	GCA_011388215.1	2716225	2716225	type	True	77.2618	319	1900	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:29:01,373] [INFO] DFAST Taxonomy check result was written to GCF_025717515.1_ASM2571751v1_genomic.fna/tc_result.tsv
[2024-01-24 14:29:01,374] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:29:01,374] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:29:01,374] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge909e3d4-ccba-4496-9ca1-35151f6cbb27/dqc_reference/checkm_data
[2024-01-24 14:29:01,375] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:29:01,434] [INFO] Task started: CheckM
[2024-01-24 14:29:01,434] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025717515.1_ASM2571751v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025717515.1_ASM2571751v1_genomic.fna/checkm_input GCF_025717515.1_ASM2571751v1_genomic.fna/checkm_result
[2024-01-24 14:30:01,582] [INFO] Task succeeded: CheckM
[2024-01-24 14:30:01,584] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.96%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:30:01,608] [INFO] ===== Completeness check finished =====
[2024-01-24 14:30:01,609] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:30:01,609] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025717515.1_ASM2571751v1_genomic.fna/markers.fasta)
[2024-01-24 14:30:01,609] [INFO] Task started: Blastn
[2024-01-24 14:30:01,610] [INFO] Running command: blastn -query GCF_025717515.1_ASM2571751v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge909e3d4-ccba-4496-9ca1-35151f6cbb27/dqc_reference/reference_markers_gtdb.fasta -out GCF_025717515.1_ASM2571751v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:30:03,475] [INFO] Task succeeded: Blastn
[2024-01-24 14:30:03,479] [INFO] Selected 11 target genomes.
[2024-01-24 14:30:03,480] [INFO] Target genome list was writen to GCF_025717515.1_ASM2571751v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:30:03,490] [INFO] Task started: fastANI
[2024-01-24 14:30:03,490] [INFO] Running command: fastANI --query /var/lib/cwl/stgcb3edd8e-ca88-4ae3-929b-6a730720e129/GCF_025717515.1_ASM2571751v1_genomic.fna.gz --refList GCF_025717515.1_ASM2571751v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025717515.1_ASM2571751v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:30:16,540] [INFO] Task succeeded: fastANI
[2024-01-24 14:30:16,554] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 14:30:16,554] [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
GCA_018780415.1	s__Paucibacter_A sp018780415	84.3782	1129	1900	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_005503085.1	s__Paucibacter_A sp005503085	80.6751	818	1900	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	80.6419	825	1900	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_001477625.1	s__Paucibacter_A sp001477625	80.5256	833	1900	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	80.4237	874	1900	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_002255955.1	s__Paucibacter_A sp002255955	80.3958	870	1900	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_003852425.1	s__Paucibacter_A sp003852425	80.1861	830	1900	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_016467315.1	s__OAE585 sp016467315	79.3441	727	1900	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__OAE585	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903820745.1	s__Paucibacter_A sp903820745	79.3102	505	1900	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paucibacter_A	95.0	99.77	99.75	0.91	0.91	3	-
GCF_001984095.1	s__KK5 sp001984095	79.1916	663	1900	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__KK5	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019234815.1	s__WAJ17 sp019234815	79.1732	458	1900	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__WAJ17	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:30:16,556] [INFO] GTDB search result was written to GCF_025717515.1_ASM2571751v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:30:16,557] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:30:16,560] [INFO] DFAST_QC result json was written to GCF_025717515.1_ASM2571751v1_genomic.fna/dqc_result.json
[2024-01-24 14:30:16,560] [INFO] DFAST_QC completed!
[2024-01-24 14:30:16,561] [INFO] Total running time: 0h1m59s