[2024-01-25 19:10:50,679] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:10:50,681] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:10:50,681] [INFO] DQC Reference Directory: /var/lib/cwl/stg0f7f1f61-2487-4c3f-9b62-42ab26f04650/dqc_reference
[2024-01-25 19:10:51,847] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:10:51,847] [INFO] Task started: Prodigal
[2024-01-25 19:10:51,848] [INFO] Running command: gunzip -c /var/lib/cwl/stg3da3730d-501d-4f44-b7a6-ca799421eebb/GCF_030517755.1_ASM3051775v1_genomic.fna.gz | prodigal -d GCF_030517755.1_ASM3051775v1_genomic.fna/cds.fna -a GCF_030517755.1_ASM3051775v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:11:03,669] [INFO] Task succeeded: Prodigal
[2024-01-25 19:11:03,669] [INFO] Task started: HMMsearch
[2024-01-25 19:11:03,669] [INFO] Running command: hmmsearch --tblout GCF_030517755.1_ASM3051775v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0f7f1f61-2487-4c3f-9b62-42ab26f04650/dqc_reference/reference_markers.hmm GCF_030517755.1_ASM3051775v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:11:04,020] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:11:04,021] [INFO] Found 6/6 markers.
[2024-01-25 19:11:04,059] [INFO] Query marker FASTA was written to GCF_030517755.1_ASM3051775v1_genomic.fna/markers.fasta
[2024-01-25 19:11:04,060] [INFO] Task started: Blastn
[2024-01-25 19:11:04,060] [INFO] Running command: blastn -query GCF_030517755.1_ASM3051775v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0f7f1f61-2487-4c3f-9b62-42ab26f04650/dqc_reference/reference_markers.fasta -out GCF_030517755.1_ASM3051775v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:11:04,746] [INFO] Task succeeded: Blastn
[2024-01-25 19:11:04,748] [INFO] Selected 16 target genomes.
[2024-01-25 19:11:04,749] [INFO] Target genome list was writen to GCF_030517755.1_ASM3051775v1_genomic.fna/target_genomes.txt
[2024-01-25 19:11:04,764] [INFO] Task started: fastANI
[2024-01-25 19:11:04,764] [INFO] Running command: fastANI --query /var/lib/cwl/stg3da3730d-501d-4f44-b7a6-ca799421eebb/GCF_030517755.1_ASM3051775v1_genomic.fna.gz --refList GCF_030517755.1_ASM3051775v1_genomic.fna/target_genomes.txt --output GCF_030517755.1_ASM3051775v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:11:17,157] [INFO] Task succeeded: fastANI
[2024-01-25 19:11:17,158] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0f7f1f61-2487-4c3f-9b62-42ab26f04650/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:11:17,158] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0f7f1f61-2487-4c3f-9b62-42ab26f04650/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:11:17,166] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:11:17,166] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:11:17,167] [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
Geoalkalibacter halelectricus	strain=SAP-1	GCA_025263685.1	2847045	2847045	type	True	99.7881	1348	1452	95	conclusive
Geoalkalibacter ferrihydriticus	strain=DSM 17813	GCA_000820505.1	392333	392333	type	True	81.3524	819	1452	95	below_threshold
Geoalkalibacter ferrihydriticus	strain=DSM 17813	GCA_900103065.1	392333	392333	type	True	81.3267	816	1452	95	below_threshold
Desulfuromonas versatilis	strain=NIT-T3	GCA_019704135.1	2802975	2802975	type	True	78.3966	393	1452	95	below_threshold
Geoalkalibacter subterraneus	strain=Red1	GCA_000827125.1	483547	483547	type	True	78.131	336	1452	95	below_threshold
Desulfuromonas acetexigens	strain=2873	GCA_007051125.1	38815	38815	type	True	77.9501	266	1452	95	below_threshold
Desulfuromonas acetexigens		GCA_900111775.1	38815	38815	type	True	77.8858	268	1452	95	below_threshold
Geothermobacter ehrlichii	strain=SS015	GCA_008124615.1	213224	213224	type	True	77.6591	232	1452	95	below_threshold
Geobacter soli	strain=GSS01	GCA_000816575.1	1510391	1510391	type	True	77.0461	109	1452	95	below_threshold
Geobacter sulfurreducens	strain=PCA	GCA_000007985.2	35554	35554	type	True	76.9204	107	1452	95	below_threshold
Geothermobacter hydrogeniphilus	strain=EPR-M	GCA_002093115.1	1969733	1969733	type	True	76.843	207	1452	95	below_threshold
Fundidesulfovibrio magnetotacticus	strain=FSS-1	GCA_013019105.1	2730080	2730080	type	True	75.6519	75	1452	95	below_threshold
Fundidesulfovibrio putealis	strain=DSM 16056	GCA_000429325.1	270496	270496	type	True	75.3498	58	1452	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:11:17,168] [INFO] DFAST Taxonomy check result was written to GCF_030517755.1_ASM3051775v1_genomic.fna/tc_result.tsv
[2024-01-25 19:11:17,169] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:11:17,169] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:11:17,169] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0f7f1f61-2487-4c3f-9b62-42ab26f04650/dqc_reference/checkm_data
[2024-01-25 19:11:17,170] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:11:17,211] [INFO] Task started: CheckM
[2024-01-25 19:11:17,211] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030517755.1_ASM3051775v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030517755.1_ASM3051775v1_genomic.fna/checkm_input GCF_030517755.1_ASM3051775v1_genomic.fna/checkm_result
[2024-01-25 19:11:53,405] [INFO] Task succeeded: CheckM
[2024-01-25 19:11:53,406] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:11:53,452] [INFO] ===== Completeness check finished =====
[2024-01-25 19:11:53,452] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:11:53,453] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030517755.1_ASM3051775v1_genomic.fna/markers.fasta)
[2024-01-25 19:11:53,453] [INFO] Task started: Blastn
[2024-01-25 19:11:53,453] [INFO] Running command: blastn -query GCF_030517755.1_ASM3051775v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0f7f1f61-2487-4c3f-9b62-42ab26f04650/dqc_reference/reference_markers_gtdb.fasta -out GCF_030517755.1_ASM3051775v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:11:54,569] [INFO] Task succeeded: Blastn
[2024-01-25 19:11:54,572] [INFO] Selected 25 target genomes.
[2024-01-25 19:11:54,572] [INFO] Target genome list was writen to GCF_030517755.1_ASM3051775v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:11:54,589] [INFO] Task started: fastANI
[2024-01-25 19:11:54,589] [INFO] Running command: fastANI --query /var/lib/cwl/stg3da3730d-501d-4f44-b7a6-ca799421eebb/GCF_030517755.1_ASM3051775v1_genomic.fna.gz --refList GCF_030517755.1_ASM3051775v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030517755.1_ASM3051775v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:12:10,256] [INFO] Task succeeded: fastANI
[2024-01-25 19:12:10,269] [INFO] Found 20 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 19:12:10,269] [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_000820505.1	s__Geoalkalibacter ferrihydriticus	81.332	823	1452	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Desulfuromonadales;f__Geoalkalibacteraceae;g__Geoalkalibacter	95.0	99.99	99.99	0.99	0.99	2	-
GCF_000827125.1	s__Geoalkalibacter_A subterraneus	78.1452	335	1452	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Desulfuromonadales;f__Geoalkalibacteraceae;g__Geoalkalibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900111775.1	s__Trichloromonas acetexigens	77.9166	270	1452	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Desulfuromonadales;f__Trichloromonadaceae;g__Trichloromonas	95.0	100.00	100.00	1.00	1.00	2	-
GCA_005774545.1	s__VAUL01 sp005774545	77.726	243	1452	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Desulfuromonadales;f__BM103;g__VAUL01	95.0	99.97	99.97	0.96	0.96	2	-
GCF_008124615.1	s__Geothermobacter ehrlichii	77.6732	231	1452	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Desulfuromonadales;f__Geothermobacteraceae;g__Geothermobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002868845.1	s__BM501 sp002868845	77.6184	248	1452	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Desulfuromonadales;f__BM501;g__BM501	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001611275.1	s__DDH964 sp001611275	77.444	249	1452	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Desulfuromonadales;f__DDH964;g__DDH964	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000817955.1	s__Geobacter pickeringii	77.3802	115	1452	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Geobacteraceae;g__Geobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014860175.1	s__JACZKF01 sp014860175	77.3531	202	1452	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Desulfuromonadales;f__JACZKF01;g__JACZKF01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001628815.1	s__Geobacter anodireducens	77.1461	105	1452	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Geobacteraceae;g__Geobacter	95.0	99.35	99.24	0.91	0.90	4	-
GCA_003695205.1	s__Geothermobacter sp003695205	77.0946	109	1452	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Desulfuromonadales;f__Geothermobacteraceae;g__Geothermobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012026975.1	s__VAUL01 sp012026975	77.0646	201	1452	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Desulfuromonadales;f__BM103;g__VAUL01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002423365.1	s__Trichloromonas sp002423365	77.0545	184	1452	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Desulfuromonadales;f__Trichloromonadaceae;g__Trichloromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000007985.2	s__Geobacter sulfurreducens	76.8683	103	1452	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Geobacteraceae;g__Geobacter	95.0	98.43	95.82	0.96	0.94	8	-
GCF_002093115.1	s__PPFX01 sp002093115	76.843	207	1452	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Desulfuromonadales;f__Geothermobacteraceae;g__PPFX01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009684525.1	s__Geoanaerobacter sp009684525	76.3984	89	1452	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Geobacteraceae;g__Geoanaerobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002869615.1	s__BM707 sp002869615	76.2967	66	1452	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Desulfuromonadales;f__UBA2294;g__BM707	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002435955.1	s__Syntrophotalea sp002435955	76.2711	126	1452	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Desulfuromonadales;f__Syntrophotaleaceae;g__Syntrophotalea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002841765.1	s__UBA2197 sp002841765	76.2268	90	1452	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Desulfuromonadales;f__UBA2197;g__UBA2197	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013619105.1	s__Syntrophotalea_A sp013619105	76.1862	90	1452	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Desulfuromonadales;f__Syntrophotaleaceae;g__Syntrophotalea_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:12:10,270] [INFO] GTDB search result was written to GCF_030517755.1_ASM3051775v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:12:10,272] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:12:10,275] [INFO] DFAST_QC result json was written to GCF_030517755.1_ASM3051775v1_genomic.fna/dqc_result.json
[2024-01-25 19:12:10,275] [INFO] DFAST_QC completed!
[2024-01-25 19:12:10,275] [INFO] Total running time: 0h1m20s