[2024-01-24 13:40:55,222] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:55,223] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:55,223] [INFO] DQC Reference Directory: /var/lib/cwl/stgf3f50fb7-8060-40fe-b7a8-e96faa25899b/dqc_reference
[2024-01-24 13:40:56,444] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:56,445] [INFO] Task started: Prodigal
[2024-01-24 13:40:56,445] [INFO] Running command: gunzip -c /var/lib/cwl/stg65936a21-9996-477f-a9c5-30b07e499a2d/GCF_003569765.1_ASM356976v1_genomic.fna.gz | prodigal -d GCF_003569765.1_ASM356976v1_genomic.fna/cds.fna -a GCF_003569765.1_ASM356976v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:41:09,791] [INFO] Task succeeded: Prodigal
[2024-01-24 13:41:09,791] [INFO] Task started: HMMsearch
[2024-01-24 13:41:09,791] [INFO] Running command: hmmsearch --tblout GCF_003569765.1_ASM356976v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf3f50fb7-8060-40fe-b7a8-e96faa25899b/dqc_reference/reference_markers.hmm GCF_003569765.1_ASM356976v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:41:10,161] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:41:10,162] [INFO] Found 6/6 markers.
[2024-01-24 13:41:10,211] [INFO] Query marker FASTA was written to GCF_003569765.1_ASM356976v1_genomic.fna/markers.fasta
[2024-01-24 13:41:10,212] [INFO] Task started: Blastn
[2024-01-24 13:41:10,212] [INFO] Running command: blastn -query GCF_003569765.1_ASM356976v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf3f50fb7-8060-40fe-b7a8-e96faa25899b/dqc_reference/reference_markers.fasta -out GCF_003569765.1_ASM356976v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:11,288] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:11,291] [INFO] Selected 18 target genomes.
[2024-01-24 13:41:11,291] [INFO] Target genome list was writen to GCF_003569765.1_ASM356976v1_genomic.fna/target_genomes.txt
[2024-01-24 13:41:11,295] [INFO] Task started: fastANI
[2024-01-24 13:41:11,295] [INFO] Running command: fastANI --query /var/lib/cwl/stg65936a21-9996-477f-a9c5-30b07e499a2d/GCF_003569765.1_ASM356976v1_genomic.fna.gz --refList GCF_003569765.1_ASM356976v1_genomic.fna/target_genomes.txt --output GCF_003569765.1_ASM356976v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:31,501] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:31,502] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf3f50fb7-8060-40fe-b7a8-e96faa25899b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:31,502] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf3f50fb7-8060-40fe-b7a8-e96faa25899b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:31,513] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:41:31,513] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:41:31,513] [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
Schlegelella thermodepolymerans	strain=DSM 15344	GCA_002933415.1	215580	215580	type	True	82.7347	774	1744	95	below_threshold
Schlegelella thermodepolymerans	strain=DSM 15344	GCA_015476235.1	215580	215580	type	True	82.7294	787	1744	95	below_threshold
Schlegelella thermodepolymerans	strain=DSM 15344	GCA_003349825.1	215580	215580	type	True	82.7021	789	1744	95	below_threshold
Sphaerotilus natans subsp. natans	strain=DSM 6575	GCA_000689195.1	882627	34103	type	True	81.5378	767	1744	95	below_threshold
Sphaerotilus sulfidivorans	strain=D-501	GCA_013426975.1	639200	639200	type	True	81.4839	767	1744	95	below_threshold
Sphaerotilus natans	strain=ATCC 13338	GCA_900156335.1	34103	34103	type	True	81.4454	806	1744	95	below_threshold
Rubrivivax benzoatilyticus	strain=JA2	GCA_000190375.2	316997	316997	type	True	81.2325	725	1744	95	below_threshold
Azohydromonas caseinilytica	strain=G-1-1-14	GCA_012927045.1	2728836	2728836	type	True	81.1133	926	1744	95	below_threshold
Azohydromonas aeria	strain=CFCC 13393	GCA_009760915.1	2590212	2590212	type	True	81.0842	975	1744	95	below_threshold
Azohydromonas australica	strain=DSM 1124	GCA_000430725.1	364039	364039	type	True	81.069	949	1744	95	below_threshold
Rubrivivax gelatinosus	strain=DSM 1709	GCA_016583525.1	28068	28068	suspected-type	True	80.9476	797	1744	95	below_threshold
Schlegelella brevitalea	strain=DSM 7029	GCA_001017435.1	413882	413882	type	True	80.6396	771	1744	95	below_threshold
Ideonella dechloratans	strain=CCUG 30977	GCA_008801845.1	36863	36863	type	True	80.3569	605	1744	95	below_threshold
Ideonella dechloratans	strain=CCUG 30977	GCA_021049305.1	36863	36863	type	True	80.3353	628	1744	95	below_threshold
Azohydromonas lata	strain=NBRC 102462	GCA_001571085.1	45677	45677	type	True	80.292	822	1744	95	below_threshold
Ideonella benzenivorans	strain=B7	GCA_020387415.1	2831643	2831643	type	True	80.17	589	1744	95	below_threshold
Hydrogenophaga crocea	strain=BA0156	GCA_011388215.1	2716225	2716225	type	True	79.9475	686	1744	95	below_threshold
Ideonella livida	strain=TBM-1	GCA_010499455.1	2707176	2707176	type	True	79.5525	605	1744	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:31,523] [INFO] DFAST Taxonomy check result was written to GCF_003569765.1_ASM356976v1_genomic.fna/tc_result.tsv
[2024-01-24 13:41:31,523] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:31,523] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:31,524] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf3f50fb7-8060-40fe-b7a8-e96faa25899b/dqc_reference/checkm_data
[2024-01-24 13:41:31,525] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:31,574] [INFO] Task started: CheckM
[2024-01-24 13:41:31,574] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003569765.1_ASM356976v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003569765.1_ASM356976v1_genomic.fna/checkm_input GCF_003569765.1_ASM356976v1_genomic.fna/checkm_result
[2024-01-24 13:42:49,358] [INFO] Task succeeded: CheckM
[2024-01-24 13:42:49,359] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:42:49,373] [INFO] ===== Completeness check finished =====
[2024-01-24 13:42:49,373] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:42:49,373] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003569765.1_ASM356976v1_genomic.fna/markers.fasta)
[2024-01-24 13:42:49,374] [INFO] Task started: Blastn
[2024-01-24 13:42:49,374] [INFO] Running command: blastn -query GCF_003569765.1_ASM356976v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf3f50fb7-8060-40fe-b7a8-e96faa25899b/dqc_reference/reference_markers_gtdb.fasta -out GCF_003569765.1_ASM356976v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:42:51,633] [INFO] Task succeeded: Blastn
[2024-01-24 13:42:51,636] [INFO] Selected 21 target genomes.
[2024-01-24 13:42:51,636] [INFO] Target genome list was writen to GCF_003569765.1_ASM356976v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:42:51,673] [INFO] Task started: fastANI
[2024-01-24 13:42:51,674] [INFO] Running command: fastANI --query /var/lib/cwl/stg65936a21-9996-477f-a9c5-30b07e499a2d/GCF_003569765.1_ASM356976v1_genomic.fna.gz --refList GCF_003569765.1_ASM356976v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003569765.1_ASM356976v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:43:17,156] [INFO] Task succeeded: fastANI
[2024-01-24 13:43:17,168] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:43:17,168] [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_003569765.1	s__Aquabacterium_B tepidiphilum	100.0	1738	1744	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquabacterium_B	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_015476235.1	s__Schlegelella thermodepolymerans	82.713	789	1744	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Schlegelella	95.0	99.89	99.68	0.98	0.95	4	-
GCA_017983795.1	s__Piscinibacter sp017983795	81.676	797	1744	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Piscinibacter	95.0	97.66	96.21	0.89	0.79	4	-
GCA_003265685.1	s__Piscinibacter caeni	81.6659	884	1744	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Piscinibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016706565.1	s__Piscinibacter sp016706565	81.6603	791	1744	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Piscinibacter	95.0	98.34	98.34	0.95	0.95	2	-
GCF_003574675.1	s__Calidifontimicrobium sediminis	81.5847	744	1744	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Calidifontimicrobium	95.0	96.54	96.54	0.86	0.86	2	-
GCF_013294065.1	s__Sphaerotilus sp013294065	81.5306	850	1744	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Sphaerotilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008329925.1	s__Sphaerotilus sulfidivorans	81.4425	784	1744	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Sphaerotilus	95.0	99.98	99.98	1.00	1.00	2	-
GCF_004011805.1	s__Piscinibacter defluvii	81.4232	927	1744	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Piscinibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000430725.1	s__Azohydromonas australica	81.1863	933	1744	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Azohydromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012932665.1	s__Rhizobacter sp012932665	81.1333	880	1744	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhizobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902826655.1	s__Methylibium sp902826655	81.1046	705	1744	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Methylibium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012927045.1	s__Azohydromonas caseinilytica	81.0817	933	1744	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Azohydromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142965.1	s__Rhizobacter sp900142965	80.908	849	1744	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhizobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002930615.1	s__Zhizhongheella caldifontis	80.8053	637	1744	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Zhizhongheella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016219375.1	s__Aquabacterium sp016219375	80.7825	644	1744	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquabacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001017435.1	s__Polyangium_A brachysporum	80.6419	770	1744	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polyangium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001571085.1	s__Azohydromonas lata	80.2574	825	1744	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Azohydromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002761755.1	s__Mitsuaria sp002761755	80.0982	688	1744	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Mitsuaria	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019232985.1	s__JAFAMW01 sp019232985	79.957	532	1744	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__JAFAMW01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009909205.1	s__Aquabacterium fontiphilum	79.2621	464	1744	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquabacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:43:17,169] [INFO] GTDB search result was written to GCF_003569765.1_ASM356976v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:43:17,170] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:43:17,179] [INFO] DFAST_QC result json was written to GCF_003569765.1_ASM356976v1_genomic.fna/dqc_result.json
[2024-01-24 13:43:17,179] [INFO] DFAST_QC completed!
[2024-01-24 13:43:17,179] [INFO] Total running time: 0h2m22s