[2023-06-29 02:46:05,695] [INFO] DFAST_QC pipeline started.
[2023-06-29 02:46:05,699] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 02:46:05,699] [INFO] DQC Reference Directory: /var/lib/cwl/stg876d70ee-4dfb-45bc-bab6-17e239679e8d/dqc_reference
[2023-06-29 02:46:07,059] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 02:46:07,060] [INFO] Task started: Prodigal
[2023-06-29 02:46:07,061] [INFO] Running command: gunzip -c /var/lib/cwl/stg9c039ece-dd2b-4c27-b1a0-8ab9ab3e7d34/GCA_005884335.1_ASM588433v1_genomic.fna.gz | prodigal -d GCA_005884335.1_ASM588433v1_genomic.fna/cds.fna -a GCA_005884335.1_ASM588433v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 02:46:14,930] [INFO] Task succeeded: Prodigal
[2023-06-29 02:46:14,930] [INFO] Task started: HMMsearch
[2023-06-29 02:46:14,930] [INFO] Running command: hmmsearch --tblout GCA_005884335.1_ASM588433v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg876d70ee-4dfb-45bc-bab6-17e239679e8d/dqc_reference/reference_markers.hmm GCA_005884335.1_ASM588433v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 02:46:15,202] [INFO] Task succeeded: HMMsearch
[2023-06-29 02:46:15,203] [INFO] Found 6/6 markers.
[2023-06-29 02:46:15,234] [INFO] Query marker FASTA was written to GCA_005884335.1_ASM588433v1_genomic.fna/markers.fasta
[2023-06-29 02:46:15,234] [INFO] Task started: Blastn
[2023-06-29 02:46:15,235] [INFO] Running command: blastn -query GCA_005884335.1_ASM588433v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg876d70ee-4dfb-45bc-bab6-17e239679e8d/dqc_reference/reference_markers.fasta -out GCA_005884335.1_ASM588433v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 02:46:16,068] [INFO] Task succeeded: Blastn
[2023-06-29 02:46:16,073] [INFO] Selected 36 target genomes.
[2023-06-29 02:46:16,073] [INFO] Target genome list was writen to GCA_005884335.1_ASM588433v1_genomic.fna/target_genomes.txt
[2023-06-29 02:46:16,082] [INFO] Task started: fastANI
[2023-06-29 02:46:16,083] [INFO] Running command: fastANI --query /var/lib/cwl/stg9c039ece-dd2b-4c27-b1a0-8ab9ab3e7d34/GCA_005884335.1_ASM588433v1_genomic.fna.gz --refList GCA_005884335.1_ASM588433v1_genomic.fna/target_genomes.txt --output GCA_005884335.1_ASM588433v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 02:46:39,600] [INFO] Task succeeded: fastANI
[2023-06-29 02:46:39,601] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg876d70ee-4dfb-45bc-bab6-17e239679e8d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 02:46:39,601] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg876d70ee-4dfb-45bc-bab6-17e239679e8d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 02:46:39,621] [INFO] Found 26 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 02:46:39,621] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 02:46:39,621] [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
Sulfurisoma sediminicola	strain=DSM 26916	GCA_003663955.1	1381557	1381557	type	True	76.9276	113	858	95	below_threshold
Sulfurisoma sediminicola	strain=BSN1	GCA_003865015.1	1381557	1381557	type	True	76.8741	115	858	95	below_threshold
Usitatibacter palustris	strain=Swamp67	GCA_013003985.1	2732487	2732487	type	True	76.8257	128	858	95	below_threshold
Methyloversatilis universalis	strain=FAM5	GCA_000214035.3	378211	378211	type	True	76.5747	87	858	95	below_threshold
Thauera chlorobenzoica	strain=3CB1	GCA_001922305.1	96773	96773	type	True	76.5415	120	858	95	below_threshold
Sulfuritortus calidifontis	strain=DSM 103923	GCA_004346085.1	1914471	1914471	type	True	76.5408	89	858	95	below_threshold
Thauera chlorobenzoica	strain=3CB-1	GCA_900108255.1	96773	96773	type	True	76.5126	117	858	95	below_threshold
Sulfuritortus calidifontis	strain=J1A	GCA_003967275.1	1914471	1914471	type	True	76.4643	89	858	95	below_threshold
Crenobacter luteus	strain=DSM 27258	GCA_004345725.1	1452487	1452487	type	True	76.4483	94	858	95	below_threshold
Methyloversatilis discipulorum	strain=FAM1	GCA_000527135.1	1119528	1119528	type	True	76.4005	101	858	95	below_threshold
Thauera aromatica	strain=K172	GCA_003030465.1	59405	59405	type	True	76.342	117	858	95	below_threshold
Sphaerotilus natans	strain=ATCC 13338	GCA_900156335.1	34103	34103	type	True	76.3187	117	858	95	below_threshold
Sphaerotilus natans subsp. natans	strain=DSM 6575	GCA_000689195.1	882627	34103	type	True	76.308	115	858	95	below_threshold
Sulfurimicrobium lacus	strain=skT11	GCA_011764585.1	2715678	2715678	type	True	76.2704	54	858	95	below_threshold
Crenobacter sedimenti	strain=HX-7-9	GCA_010435965.1	2705474	2705474	type	True	76.2221	88	858	95	below_threshold
Ramlibacter alkalitolerans	strain=KACC 19305	GCA_016722765.1	2039631	2039631	type	True	76.0711	140	858	95	below_threshold
Dokdonella koreensis	strain=DS-123	GCA_001632775.1	323415	323415	type	True	76.0164	75	858	95	below_threshold
Vulcaniibacterium gelatinicum	strain=R-5-52-3	GCA_008033445.1	2598725	2598725	type	True	75.9068	76	858	95	below_threshold
Pseudomonas aeruginosa	strain=CCUG 551	GCA_008801675.1	287	287	type	True	75.7566	53	858	95	below_threshold
Pandoraea morbifera	strain=LMG 31116	GCA_902459575.1	2508300	2508300	type	True	75.7478	72	858	95	below_threshold
Luteimonas marina	strain=FR1330	GCA_007859325.1	488485	488485	type	True	75.71	80	858	95	below_threshold
Pandoraea cepalis	strain=LMG 31106	GCA_902459665.1	2508294	2508294	type	True	75.6936	67	858	95	below_threshold
Luteimonas aquatica	strain=RIB1-20	GCA_022662575.1	450364	450364	type	True	75.5828	73	858	95	below_threshold
Thioalbus denitrificans	strain=DSM 26407	GCA_003337735.1	547122	547122	type	True	75.5553	55	858	95	below_threshold
Fulvimonas soli	strain=LMG 19981	GCA_006352285.1	155197	155197	type	True	75.4961	85	858	95	below_threshold
Dokdonella fugitiva	strain=A3	GCA_004342425.1	328517	328517	type	True	75.2514	90	858	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 02:46:39,623] [INFO] DFAST Taxonomy check result was written to GCA_005884335.1_ASM588433v1_genomic.fna/tc_result.tsv
[2023-06-29 02:46:39,624] [INFO] ===== Taxonomy check completed =====
[2023-06-29 02:46:39,624] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 02:46:39,624] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg876d70ee-4dfb-45bc-bab6-17e239679e8d/dqc_reference/checkm_data
[2023-06-29 02:46:39,625] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 02:46:39,663] [INFO] Task started: CheckM
[2023-06-29 02:46:39,663] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_005884335.1_ASM588433v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_005884335.1_ASM588433v1_genomic.fna/checkm_input GCA_005884335.1_ASM588433v1_genomic.fna/checkm_result
[2023-06-29 02:47:07,386] [INFO] Task succeeded: CheckM
[2023-06-29 02:47:07,388] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 82.20%
Contamintation: 4.63%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-29 02:47:07,412] [INFO] ===== Completeness check finished =====
[2023-06-29 02:47:07,412] [INFO] ===== Start GTDB Search =====
[2023-06-29 02:47:07,413] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_005884335.1_ASM588433v1_genomic.fna/markers.fasta)
[2023-06-29 02:47:07,413] [INFO] Task started: Blastn
[2023-06-29 02:47:07,413] [INFO] Running command: blastn -query GCA_005884335.1_ASM588433v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg876d70ee-4dfb-45bc-bab6-17e239679e8d/dqc_reference/reference_markers_gtdb.fasta -out GCA_005884335.1_ASM588433v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 02:47:08,831] [INFO] Task succeeded: Blastn
[2023-06-29 02:47:08,835] [INFO] Selected 8 target genomes.
[2023-06-29 02:47:08,835] [INFO] Target genome list was writen to GCA_005884335.1_ASM588433v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 02:47:08,838] [INFO] Task started: fastANI
[2023-06-29 02:47:08,838] [INFO] Running command: fastANI --query /var/lib/cwl/stg9c039ece-dd2b-4c27-b1a0-8ab9ab3e7d34/GCA_005884335.1_ASM588433v1_genomic.fna.gz --refList GCA_005884335.1_ASM588433v1_genomic.fna/target_genomes_gtdb.txt --output GCA_005884335.1_ASM588433v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 02:47:14,360] [INFO] Task succeeded: fastANI
[2023-06-29 02:47:14,374] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 02:47:14,374] [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_005884335.1	s__VBDM01 sp005884335	100.0	842	858	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__SG8-39;g__VBDM01	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_005883665.1	s__VBDM01 sp005883665	93.4118	483	858	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__SG8-39;g__VBDM01	95.0	95.45	95.45	0.64	0.64	2	-
GCA_005882235.1	s__VBDM01 sp005882235	89.4543	390	858	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__SG8-39;g__VBDM01	95.0	97.79	97.79	0.65	0.65	2	-
GCA_005884455.1	s__VBDM01 sp005884455	89.0462	655	858	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__SG8-39;g__VBDM01	95.0	99.10	99.10	0.85	0.85	2	-
GCA_005881575.1	s__VBDM01 sp005881575	88.9083	708	858	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__SG8-39;g__VBDM01	95.0	99.46	99.46	0.96	0.96	2	-
GCA_005881355.1	s__VBDM01 sp005881355	82.316	411	858	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__SG8-39;g__VBDM01	95.0	97.81	97.81	0.80	0.80	2	-
GCA_016234705.1	s__2-12-FULL-64-23 sp016234705	77.3812	172	858	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__SG8-39;g__2-12-FULL-64-23	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001770575.1	s__2-12-FULL-64-23 sp001770575	77.1349	139	858	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__SG8-39;g__2-12-FULL-64-23	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 02:47:14,376] [INFO] GTDB search result was written to GCA_005884335.1_ASM588433v1_genomic.fna/result_gtdb.tsv
[2023-06-29 02:47:14,377] [INFO] ===== GTDB Search completed =====
[2023-06-29 02:47:14,381] [INFO] DFAST_QC result json was written to GCA_005884335.1_ASM588433v1_genomic.fna/dqc_result.json
[2023-06-29 02:47:14,381] [INFO] DFAST_QC completed!
[2023-06-29 02:47:14,381] [INFO] Total running time: 0h1m9s