[2024-01-24 13:40:42,751] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:42,758] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:42,758] [INFO] DQC Reference Directory: /var/lib/cwl/stg7166ca41-5c84-4347-ab9b-0fa1cc5b7778/dqc_reference
[2024-01-24 13:40:44,096] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:44,097] [INFO] Task started: Prodigal
[2024-01-24 13:40:44,097] [INFO] Running command: gunzip -c /var/lib/cwl/stg47f70649-ee97-4212-a2d4-d55f17d14895/GCF_007844305.1_ASM784430v1_genomic.fna.gz | prodigal -d GCF_007844305.1_ASM784430v1_genomic.fna/cds.fna -a GCF_007844305.1_ASM784430v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:40:57,871] [INFO] Task succeeded: Prodigal
[2024-01-24 13:40:57,872] [INFO] Task started: HMMsearch
[2024-01-24 13:40:57,872] [INFO] Running command: hmmsearch --tblout GCF_007844305.1_ASM784430v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7166ca41-5c84-4347-ab9b-0fa1cc5b7778/dqc_reference/reference_markers.hmm GCF_007844305.1_ASM784430v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:40:58,176] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:40:58,178] [INFO] Found 6/6 markers.
[2024-01-24 13:40:58,229] [INFO] Query marker FASTA was written to GCF_007844305.1_ASM784430v1_genomic.fna/markers.fasta
[2024-01-24 13:40:58,230] [INFO] Task started: Blastn
[2024-01-24 13:40:58,230] [INFO] Running command: blastn -query GCF_007844305.1_ASM784430v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7166ca41-5c84-4347-ab9b-0fa1cc5b7778/dqc_reference/reference_markers.fasta -out GCF_007844305.1_ASM784430v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:40:59,065] [INFO] Task succeeded: Blastn
[2024-01-24 13:40:59,068] [INFO] Selected 17 target genomes.
[2024-01-24 13:40:59,068] [INFO] Target genome list was writen to GCF_007844305.1_ASM784430v1_genomic.fna/target_genomes.txt
[2024-01-24 13:40:59,072] [INFO] Task started: fastANI
[2024-01-24 13:40:59,073] [INFO] Running command: fastANI --query /var/lib/cwl/stg47f70649-ee97-4212-a2d4-d55f17d14895/GCF_007844305.1_ASM784430v1_genomic.fna.gz --refList GCF_007844305.1_ASM784430v1_genomic.fna/target_genomes.txt --output GCF_007844305.1_ASM784430v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:11,911] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:11,912] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7166ca41-5c84-4347-ab9b-0fa1cc5b7778/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:11,912] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7166ca41-5c84-4347-ab9b-0fa1cc5b7778/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:11,925] [INFO] Found 17 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:41:11,925] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:41:11,926] [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
Denitratisoma oestradiolicum	strain=DSM 16959	GCA_007844305.1	311182	311182	type	True	100.0	1344	1350	95	conclusive
Denitratisoma oestradiolicum	strain=DSM 16959	GCA_902813185.1	311182	311182	type	True	99.9937	1339	1350	95	conclusive
Azospira oryzae	strain=DSM 21223	GCA_004217225.1	146939	146939	type	True	79.0032	393	1350	95	below_threshold
Sulfurisoma sediminicola	strain=BSN1	GCA_003865015.1	1381557	1381557	type	True	78.8246	323	1350	95	below_threshold
Sulfurisoma sediminicola	strain=DSM 26916	GCA_003663955.1	1381557	1381557	type	True	78.7568	327	1350	95	below_threshold
Azoarcus rhizosphaerae	strain=CC-YHH848	GCA_004801305.1	2565932	2565932	type	True	78.2911	340	1350	95	below_threshold
Georgfuchsia toluolica	strain=G5G6	GCA_907163265.1	424218	424218	type	True	78.1171	253	1350	95	below_threshold
Nitrogeniibacter mangrovi	strain=M9-3-2	GCA_010983895.1	2016596	2016596	type	True	78.0256	245	1350	95	below_threshold
Zoogloea ramigera	strain=NBRC 15342	GCA_006539865.1	350	350	type	True	78.0204	291	1350	95	below_threshold
Azoarcus indigens	strain=VB32	GCA_012910835.1	29545	29545	type	True	77.9417	281	1350	95	below_threshold
Thauera butanivorans	strain=NBRC 103042	GCA_001591165.1	86174	86174	type	True	77.6289	267	1350	95	below_threshold
Nitrogeniibacter aestuarii	strain=H1-1-2A	GCA_017309585.1	2815343	2815343	type	True	77.5117	174	1350	95	below_threshold
Aromatoleum toluolicum	strain=T	GCA_012911005.2	90060	90060	type	True	77.465	231	1350	95	below_threshold
Sterolibacterium denitrificans	strain=DSM 13999	GCA_001586935.1	157592	157592	type	True	77.3773	102	1350	95	below_threshold
Methyloversatilis universalis	strain=FAM5	GCA_000214035.3	378211	378211	type	True	77.3431	245	1350	95	below_threshold
Aromatoleum buckelii	strain=U120	GCA_012910785.2	200254	200254	type	True	77.2714	157	1350	95	below_threshold
Aromatoleum anaerobium	strain=LuFRes1	GCA_012910705.2	182180	182180	type	True	76.8848	172	1350	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:11,927] [INFO] DFAST Taxonomy check result was written to GCF_007844305.1_ASM784430v1_genomic.fna/tc_result.tsv
[2024-01-24 13:41:11,928] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:11,928] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:11,928] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7166ca41-5c84-4347-ab9b-0fa1cc5b7778/dqc_reference/checkm_data
[2024-01-24 13:41:11,929] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:11,970] [INFO] Task started: CheckM
[2024-01-24 13:41:11,970] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007844305.1_ASM784430v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007844305.1_ASM784430v1_genomic.fna/checkm_input GCF_007844305.1_ASM784430v1_genomic.fna/checkm_result
[2024-01-24 13:41:55,118] [INFO] Task succeeded: CheckM
[2024-01-24 13:41:55,119] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:41:55,139] [INFO] ===== Completeness check finished =====
[2024-01-24 13:41:55,139] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:41:55,140] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007844305.1_ASM784430v1_genomic.fna/markers.fasta)
[2024-01-24 13:41:55,140] [INFO] Task started: Blastn
[2024-01-24 13:41:55,140] [INFO] Running command: blastn -query GCF_007844305.1_ASM784430v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7166ca41-5c84-4347-ab9b-0fa1cc5b7778/dqc_reference/reference_markers_gtdb.fasta -out GCF_007844305.1_ASM784430v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:56,789] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:56,794] [INFO] Selected 17 target genomes.
[2024-01-24 13:41:56,794] [INFO] Target genome list was writen to GCF_007844305.1_ASM784430v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:41:56,823] [INFO] Task started: fastANI
[2024-01-24 13:41:56,824] [INFO] Running command: fastANI --query /var/lib/cwl/stg47f70649-ee97-4212-a2d4-d55f17d14895/GCF_007844305.1_ASM784430v1_genomic.fna.gz --refList GCF_007844305.1_ASM784430v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007844305.1_ASM784430v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:42:10,065] [INFO] Task succeeded: fastANI
[2024-01-24 13:42:10,079] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:42:10,079] [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_902813185.1	s__Denitratisoma oestradiolicum	99.9937	1340	1350	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Denitratisoma	95.0	99.99	99.99	0.99	0.99	2	conclusive
GCF_007833355.1	s__Denitratisoma sp007833355	84.1767	779	1350	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Denitratisoma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003963315.1	s__AWTP1-18 sp003963315	79.4889	403	1350	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__AWTP1-18	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018241695.1	s__SZAS-72 sp018241695	78.8459	335	1350	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__SZAS-72	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003865015.1	s__Sulfurisoma sediminicola	78.7862	326	1350	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Sulfurisoma	95.0	99.99	99.99	0.99	0.99	2	-
GCA_016708585.1	s__Sulfuritalea sp016708585	78.7204	331	1350	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Sulfuritalea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903908065.1	s__Sulfuritalea sp903908065	78.3556	299	1350	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Sulfuritalea	95.0	99.89	99.84	0.95	0.93	5	-
GCA_017302275.1	s__Sulfuritalea sp017302275	78.3551	322	1350	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Sulfuritalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004801305.1	s__Thauera_A rhizosphaerae	78.2795	341	1350	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016791145.1	s__JAEUNJ01 sp016791145	78.2076	346	1350	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__JAEUNJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016235765.1	s__Fen-999 sp016235765	78.144	278	1350	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Fen-999	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016716965.1	s__Sulfuritalea sp016716965	78.1009	340	1350	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Sulfuritalea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019136545.1	s__Fen-999 sp019136545	77.9717	283	1350	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Fen-999	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002347285.1	s__UBA2250 sp002347285	77.9117	255	1350	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__UBA2250	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016235805.1	s__Sulfuritalea sp016235805	77.9064	242	1350	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Sulfuritalea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018819515.1	s__Fen-999 sp018819515	77.8434	233	1350	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Fen-999	95.0	100.00	100.00	1.00	1.00	2	-
GCA_016214175.1	s__JACRPB01 sp016214175	77.318	276	1350	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__JACRPB01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:42:10,081] [INFO] GTDB search result was written to GCF_007844305.1_ASM784430v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:42:10,082] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:42:10,086] [INFO] DFAST_QC result json was written to GCF_007844305.1_ASM784430v1_genomic.fna/dqc_result.json
[2024-01-24 13:42:10,086] [INFO] DFAST_QC completed!
[2024-01-24 13:42:10,086] [INFO] Total running time: 0h1m27s