[2023-06-08 13:03:21,809] [INFO] DFAST_QC pipeline started.
[2023-06-08 13:03:21,826] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 13:03:21,827] [INFO] DQC Reference Directory: /var/lib/cwl/stgc3f6fedd-67b5-4a01-9dce-9c3681e1f679/dqc_reference
[2023-06-08 13:03:23,565] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 13:03:23,566] [INFO] Task started: Prodigal
[2023-06-08 13:03:23,566] [INFO] Running command: gunzip -c /var/lib/cwl/stgfd0fd162-6ef5-4634-8e39-634702b959c3/GCA_945787285.1_FO.M.Desulfobacterota.26_genomic.fna.gz | prodigal -d GCA_945787285.1_FO.M.Desulfobacterota.26_genomic.fna/cds.fna -a GCA_945787285.1_FO.M.Desulfobacterota.26_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 13:03:32,873] [INFO] Task succeeded: Prodigal
[2023-06-08 13:03:32,873] [INFO] Task started: HMMsearch
[2023-06-08 13:03:32,873] [INFO] Running command: hmmsearch --tblout GCA_945787285.1_FO.M.Desulfobacterota.26_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc3f6fedd-67b5-4a01-9dce-9c3681e1f679/dqc_reference/reference_markers.hmm GCA_945787285.1_FO.M.Desulfobacterota.26_genomic.fna/protein.faa > /dev/null
[2023-06-08 13:03:33,183] [INFO] Task succeeded: HMMsearch
[2023-06-08 13:03:33,184] [INFO] Found 6/6 markers.
[2023-06-08 13:03:33,231] [INFO] Query marker FASTA was written to GCA_945787285.1_FO.M.Desulfobacterota.26_genomic.fna/markers.fasta
[2023-06-08 13:03:33,232] [INFO] Task started: Blastn
[2023-06-08 13:03:33,232] [INFO] Running command: blastn -query GCA_945787285.1_FO.M.Desulfobacterota.26_genomic.fna/markers.fasta -db /var/lib/cwl/stgc3f6fedd-67b5-4a01-9dce-9c3681e1f679/dqc_reference/reference_markers.fasta -out GCA_945787285.1_FO.M.Desulfobacterota.26_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 13:03:33,904] [INFO] Task succeeded: Blastn
[2023-06-08 13:03:33,908] [INFO] Selected 15 target genomes.
[2023-06-08 13:03:33,909] [INFO] Target genome list was writen to GCA_945787285.1_FO.M.Desulfobacterota.26_genomic.fna/target_genomes.txt
[2023-06-08 13:03:33,913] [INFO] Task started: fastANI
[2023-06-08 13:03:33,914] [INFO] Running command: fastANI --query /var/lib/cwl/stgfd0fd162-6ef5-4634-8e39-634702b959c3/GCA_945787285.1_FO.M.Desulfobacterota.26_genomic.fna.gz --refList GCA_945787285.1_FO.M.Desulfobacterota.26_genomic.fna/target_genomes.txt --output GCA_945787285.1_FO.M.Desulfobacterota.26_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 13:03:44,227] [INFO] Task succeeded: fastANI
[2023-06-08 13:03:44,228] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc3f6fedd-67b5-4a01-9dce-9c3681e1f679/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 13:03:44,228] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc3f6fedd-67b5-4a01-9dce-9c3681e1f679/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 13:03:44,239] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 13:03:44,239] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-08 13:03:44,239] [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	79.1604	373	1070	95	below_threshold
Desulfuromonas soudanensis	strain=WTL	GCA_001278055.1	1603606	1603606	type	True	78.5636	277	1070	95	below_threshold
Desulfuromonas acetexigens		GCA_900111775.1	38815	38815	type	True	78.2387	277	1070	95	below_threshold
Desulfuromonas acetexigens	strain=2873	GCA_007051125.1	38815	38815	type	True	78.2248	278	1070	95	below_threshold
Geothermobacter ehrlichii	strain=SS015	GCA_008124615.1	213224	213224	type	True	77.72	213	1070	95	below_threshold
Geoalkalibacter halelectricus	strain=SAP-1	GCA_025263685.1	2847045	2847045	type	True	77.2549	193	1070	95	below_threshold
Syntrophotalea carbinolica	strain=DSM 2380	GCA_000012885.1	19	19	type	True	76.8174	93	1070	95	below_threshold
Geobacter grbiciae	strain=DSM 13689	GCA_018531165.1	155042	155042	type	True	76.81	78	1070	95	below_threshold
Geobacter sulfurreducens	strain=PCA	GCA_000007985.2	35554	35554	type	True	76.555	78	1070	95	below_threshold
Geobacter hydrogenophilus	strain=DSM 13691	GCA_018501225.1	40983	40983	type	True	76.3446	83	1070	95	below_threshold
Pelobacter propionicus	strain=DSM 2379	GCA_000015045.1	29543	29543	type	True	76.1376	76	1070	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 13:03:44,242] [INFO] DFAST Taxonomy check result was written to GCA_945787285.1_FO.M.Desulfobacterota.26_genomic.fna/tc_result.tsv
[2023-06-08 13:03:44,242] [INFO] ===== Taxonomy check completed =====
[2023-06-08 13:03:44,242] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 13:03:44,243] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc3f6fedd-67b5-4a01-9dce-9c3681e1f679/dqc_reference/checkm_data
[2023-06-08 13:03:44,244] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 13:03:44,290] [INFO] Task started: CheckM
[2023-06-08 13:03:44,291] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_945787285.1_FO.M.Desulfobacterota.26_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_945787285.1_FO.M.Desulfobacterota.26_genomic.fna/checkm_input GCA_945787285.1_FO.M.Desulfobacterota.26_genomic.fna/checkm_result
[2023-06-08 13:04:16,111] [INFO] Task succeeded: CheckM
[2023-06-08 13:04:16,112] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 78.79%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 13:04:16,134] [INFO] ===== Completeness check finished =====
[2023-06-08 13:04:16,134] [INFO] ===== Start GTDB Search =====
[2023-06-08 13:04:16,135] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_945787285.1_FO.M.Desulfobacterota.26_genomic.fna/markers.fasta)
[2023-06-08 13:04:16,135] [INFO] Task started: Blastn
[2023-06-08 13:04:16,135] [INFO] Running command: blastn -query GCA_945787285.1_FO.M.Desulfobacterota.26_genomic.fna/markers.fasta -db /var/lib/cwl/stgc3f6fedd-67b5-4a01-9dce-9c3681e1f679/dqc_reference/reference_markers_gtdb.fasta -out GCA_945787285.1_FO.M.Desulfobacterota.26_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 13:04:17,025] [INFO] Task succeeded: Blastn
[2023-06-08 13:04:17,030] [INFO] Selected 29 target genomes.
[2023-06-08 13:04:17,030] [INFO] Target genome list was writen to GCA_945787285.1_FO.M.Desulfobacterota.26_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 13:04:17,046] [INFO] Task started: fastANI
[2023-06-08 13:04:17,047] [INFO] Running command: fastANI --query /var/lib/cwl/stgfd0fd162-6ef5-4634-8e39-634702b959c3/GCA_945787285.1_FO.M.Desulfobacterota.26_genomic.fna.gz --refList GCA_945787285.1_FO.M.Desulfobacterota.26_genomic.fna/target_genomes_gtdb.txt --output GCA_945787285.1_FO.M.Desulfobacterota.26_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 13:04:34,056] [INFO] Task succeeded: fastANI
[2023-06-08 13:04:34,079] [INFO] Found 20 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-08 13:04:34,079] [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_001278055.1	s__Deferrimonas soudanensis	78.5627	277	1070	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Desulfuromonadales;f__WTL;g__Deferrimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001825565.1	s__Trichloromonas sp001825565	78.2387	259	1070	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Desulfuromonadales;f__Trichloromonadaceae;g__Trichloromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900111775.1	s__Trichloromonas acetexigens	78.2233	277	1070	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Desulfuromonadales;f__Trichloromonadaceae;g__Trichloromonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001611275.1	s__DDH964 sp001611275	78.0492	242	1070	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Desulfuromonadales;f__DDH964;g__DDH964	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005774545.1	s__VAUL01 sp005774545	77.918	177	1070	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Desulfuromonadales;f__BM103;g__VAUL01	95.0	99.97	99.97	0.96	0.96	2	-
GCA_014860175.1	s__JACZKF01 sp014860175	77.8444	163	1070	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Desulfuromonadales;f__JACZKF01;g__JACZKF01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008124615.1	s__Geothermobacter ehrlichii	77.7313	211	1070	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Desulfuromonadales;f__Geothermobacteraceae;g__Geothermobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000472285.1	s__ATBO01 sp000472285	77.7258	227	1070	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Desulfuromonadales;f__ATBO01;g__ATBO01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002423365.1	s__Trichloromonas sp002423365	77.5852	201	1070	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Desulfuromonadales;f__Trichloromonadaceae;g__Trichloromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001799485.1	s__UBA12091 sp001799485	77.49	139	1070	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Desulfuromonadales;f__UBA2197;g__UBA12091	95.0	99.59	99.42	0.82	0.81	4	-
GCA_012026975.1	s__VAUL01 sp012026975	77.3283	158	1070	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Desulfuromonadales;f__BM103;g__VAUL01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000827125.1	s__Geoalkalibacter_A subterraneus	77.2523	128	1070	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	77.0078	95	1070	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Desulfuromonadales;f__Geopsychrobacteraceae;g__BM522	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003695205.1	s__Geothermobacter sp003695205	76.9563	103	1070	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Desulfuromonadales;f__Geothermobacteraceae;g__Geothermobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016926265.1	s__JAAYDE01 sp016926265	76.717	60	1070	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Desulfuromonadales;f__JAAYDE01;g__JAAYDE01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014859605.1	s__UBA2197 sp014859605	76.6152	91	1070	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Desulfuromonadales;f__UBA2197;g__UBA2197	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000016745.1	s__Geotalea uraniireducens	76.494	70	1070	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Geobacteraceae;g__Geotalea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002841765.1	s__UBA2197 sp002841765	76.3733	102	1070	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	76.2321	74	1070	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Desulfuromonadales;f__Syntrophotaleaceae;g__Syntrophotalea_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002869615.1	s__BM707 sp002869615	76.1761	76	1070	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Desulfuromonadales;f__UBA2294;g__BM707	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-08 13:04:34,082] [INFO] GTDB search result was written to GCA_945787285.1_FO.M.Desulfobacterota.26_genomic.fna/result_gtdb.tsv
[2023-06-08 13:04:34,082] [INFO] ===== GTDB Search completed =====
[2023-06-08 13:04:34,086] [INFO] DFAST_QC result json was written to GCA_945787285.1_FO.M.Desulfobacterota.26_genomic.fna/dqc_result.json
[2023-06-08 13:04:34,086] [INFO] DFAST_QC completed!
[2023-06-08 13:04:34,086] [INFO] Total running time: 0h1m12s