[2024-01-24 15:18:50,837] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:18:50,852] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:18:50,853] [INFO] DQC Reference Directory: /var/lib/cwl/stg831819fd-ee67-4434-bfff-bb55ea002c37/dqc_reference
[2024-01-24 15:18:52,198] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:18:52,199] [INFO] Task started: Prodigal
[2024-01-24 15:18:52,199] [INFO] Running command: gunzip -c /var/lib/cwl/stg424afcf4-c570-4d60-a7bb-d6d9c2c26d7a/GCF_014193515.1_ASM1419351v1_genomic.fna.gz | prodigal -d GCF_014193515.1_ASM1419351v1_genomic.fna/cds.fna -a GCF_014193515.1_ASM1419351v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:19:07,444] [INFO] Task succeeded: Prodigal
[2024-01-24 15:19:07,444] [INFO] Task started: HMMsearch
[2024-01-24 15:19:07,444] [INFO] Running command: hmmsearch --tblout GCF_014193515.1_ASM1419351v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg831819fd-ee67-4434-bfff-bb55ea002c37/dqc_reference/reference_markers.hmm GCF_014193515.1_ASM1419351v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:19:07,784] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:19:07,785] [INFO] Found 6/6 markers.
[2024-01-24 15:19:07,835] [INFO] Query marker FASTA was written to GCF_014193515.1_ASM1419351v1_genomic.fna/markers.fasta
[2024-01-24 15:19:07,835] [INFO] Task started: Blastn
[2024-01-24 15:19:07,835] [INFO] Running command: blastn -query GCF_014193515.1_ASM1419351v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg831819fd-ee67-4434-bfff-bb55ea002c37/dqc_reference/reference_markers.fasta -out GCF_014193515.1_ASM1419351v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:19:08,613] [INFO] Task succeeded: Blastn
[2024-01-24 15:19:08,616] [INFO] Selected 12 target genomes.
[2024-01-24 15:19:08,617] [INFO] Target genome list was writen to GCF_014193515.1_ASM1419351v1_genomic.fna/target_genomes.txt
[2024-01-24 15:19:08,622] [INFO] Task started: fastANI
[2024-01-24 15:19:08,622] [INFO] Running command: fastANI --query /var/lib/cwl/stg424afcf4-c570-4d60-a7bb-d6d9c2c26d7a/GCF_014193515.1_ASM1419351v1_genomic.fna.gz --refList GCF_014193515.1_ASM1419351v1_genomic.fna/target_genomes.txt --output GCF_014193515.1_ASM1419351v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:19:22,254] [INFO] Task succeeded: fastANI
[2024-01-24 15:19:22,255] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg831819fd-ee67-4434-bfff-bb55ea002c37/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:19:22,256] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg831819fd-ee67-4434-bfff-bb55ea002c37/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:19:22,275] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:19:22,275] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:19:22,276] [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
Geomonas silvestris	strain=Red330	GCA_014193515.1	2740184	2740184	type	True	100.0	1685	1686	95	conclusive
Geomonas limicola	strain=Red745	GCA_014193675.1	2740186	2740186	type	True	88.7117	1409	1686	95	below_threshold
Geomonas azotofigens	strain=Red51	GCA_018919395.1	2843196	2843196	type	True	81.5727	799	1686	95	below_threshold
Geomonas paludis	strain=Red736	GCA_014193585.1	2740185	2740185	type	True	81.3803	814	1686	95	below_threshold
Geomonas anaerohicana	strain=Red421	GCA_016458305.1	2798583	2798583	type	True	81.2509	791	1686	95	below_threshold
Geomonas propionica	strain=Red259	GCA_016458235.1	2798582	2798582	type	True	81.1361	766	1686	95	below_threshold
Geomonas oryzae	strain=S43	GCA_004117875.1	2364273	2364273	type	True	81.1255	775	1686	95	below_threshold
Geomonas ferrireducens	strain=S62	GCA_004917065.1	2570227	2570227	type	True	81.0029	749	1686	95	below_threshold
Geomonas terrae	strain=Red111	GCA_004791675.1	2562681	2562681	type	True	80.897	737	1686	95	below_threshold
Geomonas edaphica	strain=Red53	GCA_004917075.1	2570226	2570226	type	True	80.7635	739	1686	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:19:22,279] [INFO] DFAST Taxonomy check result was written to GCF_014193515.1_ASM1419351v1_genomic.fna/tc_result.tsv
[2024-01-24 15:19:22,279] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:19:22,279] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:19:22,280] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg831819fd-ee67-4434-bfff-bb55ea002c37/dqc_reference/checkm_data
[2024-01-24 15:19:22,281] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:19:22,331] [INFO] Task started: CheckM
[2024-01-24 15:19:22,331] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014193515.1_ASM1419351v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014193515.1_ASM1419351v1_genomic.fna/checkm_input GCF_014193515.1_ASM1419351v1_genomic.fna/checkm_result
[2024-01-24 15:20:04,435] [INFO] Task succeeded: CheckM
[2024-01-24 15:20:04,437] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:20:04,454] [INFO] ===== Completeness check finished =====
[2024-01-24 15:20:04,454] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:20:04,455] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014193515.1_ASM1419351v1_genomic.fna/markers.fasta)
[2024-01-24 15:20:04,455] [INFO] Task started: Blastn
[2024-01-24 15:20:04,455] [INFO] Running command: blastn -query GCF_014193515.1_ASM1419351v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg831819fd-ee67-4434-bfff-bb55ea002c37/dqc_reference/reference_markers_gtdb.fasta -out GCF_014193515.1_ASM1419351v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:20:05,594] [INFO] Task succeeded: Blastn
[2024-01-24 15:20:05,598] [INFO] Selected 19 target genomes.
[2024-01-24 15:20:05,598] [INFO] Target genome list was writen to GCF_014193515.1_ASM1419351v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:20:05,625] [INFO] Task started: fastANI
[2024-01-24 15:20:05,625] [INFO] Running command: fastANI --query /var/lib/cwl/stg424afcf4-c570-4d60-a7bb-d6d9c2c26d7a/GCF_014193515.1_ASM1419351v1_genomic.fna.gz --refList GCF_014193515.1_ASM1419351v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014193515.1_ASM1419351v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:20:24,921] [INFO] Task succeeded: fastANI
[2024-01-24 15:20:24,938] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:20:24,938] [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_014193515.1	s__Geomonas silvestris	100.0	1685	1686	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Geobacteraceae;g__Geomonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014193675.1	s__Geomonas limicola	88.7033	1410	1686	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Geobacteraceae;g__Geomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018919395.1	s__Geomonas sp018919395	81.5837	798	1686	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Geobacteraceae;g__Geomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018986935.1	s__Geomonas sp018986935	81.4361	781	1686	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Geobacteraceae;g__Geomonas	95.0	99.24	99.10	0.94	0.94	3	-
GCF_014193585.1	s__Geomonas paludis	81.4214	810	1686	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Geobacteraceae;g__Geomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000175115.2	s__Geomonas sp000175115	81.3817	775	1686	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Geobacteraceae;g__Geomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018986915.1	s__Geomonas sp018986915	81.2501	779	1686	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Geobacteraceae;g__Geomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016458305.1	s__Geomonas anaerohicana	81.2426	792	1686	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Geobacteraceae;g__Geomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004117875.1	s__Geomonas oryzae	81.1601	771	1686	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Geobacteraceae;g__Geomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002117975.1	s__Geomonas pelophila	80.9796	727	1686	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Geobacteraceae;g__Geomonas	95.0	97.46	97.46	0.92	0.92	2	-
GCF_004917065.1	s__Geomonas ferrireducens	80.971	753	1686	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Geobacteraceae;g__Geomonas	95.0	96.45	96.45	0.86	0.86	2	-
GCA_003490025.1	s__Geomonas sp003490025	80.8504	661	1686	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Geobacteraceae;g__Geomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000023645.1	s__Geomonas sp000023645	80.8119	734	1686	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Geobacteraceae;g__Geomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004917075.1	s__Geomonas edaphica	80.7727	739	1686	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Geobacteraceae;g__Geomonas	95.0	96.10	96.10	0.87	0.87	2	-
GCF_000426865.1	s__Geomonas bremensis	80.7539	730	1686	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Geobacteraceae;g__Geomonas	95.6689	N/A	N/A	N/A	N/A	1	-
GCA_903925075.1	s__Geomonas sp903925075	80.4039	683	1686	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Geobacteraceae;g__Geomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:20:24,940] [INFO] GTDB search result was written to GCF_014193515.1_ASM1419351v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:20:24,941] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:20:24,944] [INFO] DFAST_QC result json was written to GCF_014193515.1_ASM1419351v1_genomic.fna/dqc_result.json
[2024-01-24 15:20:24,944] [INFO] DFAST_QC completed!
[2024-01-24 15:20:24,944] [INFO] Total running time: 0h1m34s