[2024-01-24 11:58:57,306] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:58:57,309] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:58:57,309] [INFO] DQC Reference Directory: /var/lib/cwl/stg8abf883d-aa53-4431-b8a7-0e49a7b8cbb5/dqc_reference
[2024-01-24 11:58:58,630] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:58:58,631] [INFO] Task started: Prodigal
[2024-01-24 11:58:58,631] [INFO] Running command: gunzip -c /var/lib/cwl/stgb10fc511-7f4e-4f01-830d-8eae5e7322d5/GCF_019704135.1_ASM1970413v1_genomic.fna.gz | prodigal -d GCF_019704135.1_ASM1970413v1_genomic.fna/cds.fna -a GCF_019704135.1_ASM1970413v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:59:12,059] [INFO] Task succeeded: Prodigal
[2024-01-24 11:59:12,059] [INFO] Task started: HMMsearch
[2024-01-24 11:59:12,059] [INFO] Running command: hmmsearch --tblout GCF_019704135.1_ASM1970413v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8abf883d-aa53-4431-b8a7-0e49a7b8cbb5/dqc_reference/reference_markers.hmm GCF_019704135.1_ASM1970413v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:59:12,390] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:59:12,392] [INFO] Found 6/6 markers.
[2024-01-24 11:59:12,432] [INFO] Query marker FASTA was written to GCF_019704135.1_ASM1970413v1_genomic.fna/markers.fasta
[2024-01-24 11:59:12,433] [INFO] Task started: Blastn
[2024-01-24 11:59:12,433] [INFO] Running command: blastn -query GCF_019704135.1_ASM1970413v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8abf883d-aa53-4431-b8a7-0e49a7b8cbb5/dqc_reference/reference_markers.fasta -out GCF_019704135.1_ASM1970413v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:59:13,269] [INFO] Task succeeded: Blastn
[2024-01-24 11:59:13,272] [INFO] Selected 15 target genomes.
[2024-01-24 11:59:13,273] [INFO] Target genome list was writen to GCF_019704135.1_ASM1970413v1_genomic.fna/target_genomes.txt
[2024-01-24 11:59:13,279] [INFO] Task started: fastANI
[2024-01-24 11:59:13,279] [INFO] Running command: fastANI --query /var/lib/cwl/stgb10fc511-7f4e-4f01-830d-8eae5e7322d5/GCF_019704135.1_ASM1970413v1_genomic.fna.gz --refList GCF_019704135.1_ASM1970413v1_genomic.fna/target_genomes.txt --output GCF_019704135.1_ASM1970413v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:59:26,941] [INFO] Task succeeded: fastANI
[2024-01-24 11:59:26,942] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8abf883d-aa53-4431-b8a7-0e49a7b8cbb5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:59:26,942] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8abf883d-aa53-4431-b8a7-0e49a7b8cbb5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:59:26,954] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:59:26,954] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:59:26,954] [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
Desulfuromonas versatilis	strain=NIT-T3	GCA_019704135.1	2802975	2802975	type	True	100.0	1549	1552	95	conclusive
Desulfuromonas soudanensis	strain=WTL	GCA_001278055.1	1603606	1603606	type	True	79.4704	487	1552	95	below_threshold
Desulfuromonas acetexigens		GCA_900111775.1	38815	38815	type	True	78.9419	405	1552	95	below_threshold
Desulfuromonas acetexigens	strain=2873	GCA_007051125.1	38815	38815	type	True	78.9266	406	1552	95	below_threshold
Geothermobacter ehrlichii	strain=SS015	GCA_008124615.1	213224	213224	type	True	78.9037	388	1552	95	below_threshold
Geoalkalibacter halelectricus	strain=SAP-1	GCA_025263685.1	2847045	2847045	type	True	78.319	399	1552	95	below_threshold
Geothermobacter hydrogeniphilus	strain=EPR-M	GCA_002093115.1	1969733	1969733	type	True	78.2233	329	1552	95	below_threshold
Geobacter metallireducens	strain=GS-15	GCA_000012925.1	28232	28232	type	True	77.5673	180	1552	95	below_threshold
Geoalkalibacter ferrihydriticus	strain=DSM 17813	GCA_000820505.1	392333	392333	type	True	77.5641	275	1552	95	below_threshold
Geobacter grbiciae	strain=DSM 13689	GCA_018531165.1	155042	155042	type	True	77.4871	179	1552	95	below_threshold
Oceanibaculum pacificum	strain=MCCC 1A02656	GCA_001618175.1	580166	580166	type	True	75.6018	83	1552	95	below_threshold
Reyranella soli	strain=NBRC 108950	GCA_007992495.1	1230389	1230389	type	True	75.3294	115	1552	95	below_threshold
Burkholderia puraquae	strain=CAMPA 1040	GCA_002099195.1	1904757	1904757	type	True	75.1521	71	1552	95	below_threshold
Burkholderia puraquae	strain=LMG 29660	GCA_902859845.1	1904757	1904757	type	True	75.0185	73	1552	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:59:26,956] [INFO] DFAST Taxonomy check result was written to GCF_019704135.1_ASM1970413v1_genomic.fna/tc_result.tsv
[2024-01-24 11:59:26,956] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:59:26,957] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:59:26,957] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8abf883d-aa53-4431-b8a7-0e49a7b8cbb5/dqc_reference/checkm_data
[2024-01-24 11:59:26,958] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:59:27,002] [INFO] Task started: CheckM
[2024-01-24 11:59:27,003] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019704135.1_ASM1970413v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019704135.1_ASM1970413v1_genomic.fna/checkm_input GCF_019704135.1_ASM1970413v1_genomic.fna/checkm_result
[2024-01-24 12:00:06,215] [INFO] Task succeeded: CheckM
[2024-01-24 12:00:06,216] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:00:06,237] [INFO] ===== Completeness check finished =====
[2024-01-24 12:00:06,238] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:00:06,238] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019704135.1_ASM1970413v1_genomic.fna/markers.fasta)
[2024-01-24 12:00:06,238] [INFO] Task started: Blastn
[2024-01-24 12:00:06,238] [INFO] Running command: blastn -query GCF_019704135.1_ASM1970413v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8abf883d-aa53-4431-b8a7-0e49a7b8cbb5/dqc_reference/reference_markers_gtdb.fasta -out GCF_019704135.1_ASM1970413v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:00:07,519] [INFO] Task succeeded: Blastn
[2024-01-24 12:00:07,522] [INFO] Selected 22 target genomes.
[2024-01-24 12:00:07,523] [INFO] Target genome list was writen to GCF_019704135.1_ASM1970413v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:00:07,553] [INFO] Task started: fastANI
[2024-01-24 12:00:07,553] [INFO] Running command: fastANI --query /var/lib/cwl/stgb10fc511-7f4e-4f01-830d-8eae5e7322d5/GCF_019704135.1_ASM1970413v1_genomic.fna.gz --refList GCF_019704135.1_ASM1970413v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019704135.1_ASM1970413v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:00:22,121] [INFO] Task succeeded: fastANI
[2024-01-24 12:00:22,137] [INFO] Found 21 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:00:22,138] [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_001611275.1	s__DDH964 sp001611275	79.5357	435	1552	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Desulfuromonadales;f__DDH964;g__DDH964	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001278055.1	s__Deferrimonas soudanensis	79.419	489	1552	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Desulfuromonadales;f__WTL;g__Deferrimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900111775.1	s__Trichloromonas acetexigens	78.9412	405	1552	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Desulfuromonadales;f__Trichloromonadaceae;g__Trichloromonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_008124615.1	s__Geothermobacter ehrlichii	78.915	387	1552	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	78.9069	285	1552	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Desulfuromonadales;f__BM103;g__VAUL01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000472285.1	s__ATBO01 sp000472285	78.827	415	1552	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Desulfuromonadales;f__ATBO01;g__ATBO01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014860175.1	s__JACZKF01 sp014860175	78.6893	334	1552	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Desulfuromonadales;f__JACZKF01;g__JACZKF01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009731355.2	s__SZUA-540 sp009731355	78.633	257	1552	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Desulfuromonadales;f__SZUA-540;g__SZUA-540	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002093115.1	s__PPFX01 sp002093115	78.2177	328	1552	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Desulfuromonadales;f__Geothermobacteraceae;g__PPFX01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003695205.1	s__Geothermobacter sp003695205	78.0813	186	1552	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Desulfuromonadales;f__Geothermobacteraceae;g__Geothermobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001799485.1	s__UBA12091 sp001799485	77.8692	254	1552	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Desulfuromonadales;f__UBA2197;g__UBA12091	95.0	99.59	99.42	0.82	0.81	4	-
GCF_000827125.1	s__Geoalkalibacter_A subterraneus	77.8533	244	1552	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Desulfuromonadales;f__Geoalkalibacteraceae;g__Geoalkalibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002869665.1	s__BM522 sp002869665	77.5613	171	1552	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Desulfuromonadales;f__Geopsychrobacteraceae;g__BM522	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003250235.1	s__SZUA-540 sp003250235	77.4789	209	1552	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Desulfuromonadales;f__SZUA-540;g__SZUA-540	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016458275.1	s__Geomesophilobacter sediminis	77.171	237	1552	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Geobacteraceae;g__Geomesophilobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014860225.1	s__M0040 sp014860225	77.1608	151	1552	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Desulfuromonadales;f__BM103;g__M0040	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013152145.1	s__Malonomonas sp013152145	76.767	129	1552	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Desulfuromonadales;f__Geopsychrobacteraceae;g__Malonomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007134025.1	s__SLLR01 sp007134025	76.6975	154	1552	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Desulfuromonadales;f__Syntrophotaleaceae;g__SLLR01	95.0	99.59	99.47	0.91	0.88	4	-
GCF_001618175.1	s__Oceanibaculum pacificum	75.6018	83	1552	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Oceanibaculales;f__Oceanibaculaceae;g__Oceanibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007992495.1	s__Reyranella soli	75.3374	114	1552	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016861185.1	s__DSNY01 sp016861185	75.296	75	1552	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__DSNY01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:00:22,139] [INFO] GTDB search result was written to GCF_019704135.1_ASM1970413v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:00:22,140] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:00:22,146] [INFO] DFAST_QC result json was written to GCF_019704135.1_ASM1970413v1_genomic.fna/dqc_result.json
[2024-01-24 12:00:22,146] [INFO] DFAST_QC completed!
[2024-01-24 12:00:22,147] [INFO] Total running time: 0h1m25s