[2023-06-19 12:40:30,686] [INFO] DFAST_QC pipeline started.
[2023-06-19 12:40:30,689] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 12:40:30,689] [INFO] DQC Reference Directory: /var/lib/cwl/stgb0cb33e2-9cb4-4fa4-b79b-111de3ccb83c/dqc_reference
[2023-06-19 12:40:33,016] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 12:40:33,017] [INFO] Task started: Prodigal
[2023-06-19 12:40:33,018] [INFO] Running command: gunzip -c /var/lib/cwl/stg97bfb504-7530-4e9e-aa18-d87f44f6b633/GCA_013694695.1_ASM1369469v1_genomic.fna.gz | prodigal -d GCA_013694695.1_ASM1369469v1_genomic.fna/cds.fna -a GCA_013694695.1_ASM1369469v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 12:40:41,430] [INFO] Task succeeded: Prodigal
[2023-06-19 12:40:41,431] [INFO] Task started: HMMsearch
[2023-06-19 12:40:41,431] [INFO] Running command: hmmsearch --tblout GCA_013694695.1_ASM1369469v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb0cb33e2-9cb4-4fa4-b79b-111de3ccb83c/dqc_reference/reference_markers.hmm GCA_013694695.1_ASM1369469v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 12:40:41,674] [INFO] Task succeeded: HMMsearch
[2023-06-19 12:40:41,676] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg97bfb504-7530-4e9e-aa18-d87f44f6b633/GCA_013694695.1_ASM1369469v1_genomic.fna.gz]
[2023-06-19 12:40:41,721] [INFO] Query marker FASTA was written to GCA_013694695.1_ASM1369469v1_genomic.fna/markers.fasta
[2023-06-19 12:40:41,722] [INFO] Task started: Blastn
[2023-06-19 12:40:41,722] [INFO] Running command: blastn -query GCA_013694695.1_ASM1369469v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb0cb33e2-9cb4-4fa4-b79b-111de3ccb83c/dqc_reference/reference_markers.fasta -out GCA_013694695.1_ASM1369469v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 12:40:42,329] [INFO] Task succeeded: Blastn
[2023-06-19 12:40:42,334] [INFO] Selected 18 target genomes.
[2023-06-19 12:40:42,334] [INFO] Target genome list was writen to GCA_013694695.1_ASM1369469v1_genomic.fna/target_genomes.txt
[2023-06-19 12:40:42,338] [INFO] Task started: fastANI
[2023-06-19 12:40:42,338] [INFO] Running command: fastANI --query /var/lib/cwl/stg97bfb504-7530-4e9e-aa18-d87f44f6b633/GCA_013694695.1_ASM1369469v1_genomic.fna.gz --refList GCA_013694695.1_ASM1369469v1_genomic.fna/target_genomes.txt --output GCA_013694695.1_ASM1369469v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 12:40:55,936] [INFO] Task succeeded: fastANI
[2023-06-19 12:40:55,937] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb0cb33e2-9cb4-4fa4-b79b-111de3ccb83c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 12:40:55,938] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb0cb33e2-9cb4-4fa4-b79b-111de3ccb83c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 12:40:55,951] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 12:40:55,951] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-19 12:40:55,951] [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
Gemmatirosa kalamazoonensis	strain=KBS708	GCA_000522985.1	861299	861299	type	True	75.7871	131	831	95	below_threshold
Gemmatimonas groenlandica	strain=TET16	GCA_013004105.1	2732249	2732249	type	True	75.6119	55	831	95	below_threshold
Longimicrobium terrae	strain=CB-286315	GCA_013000925.1	1639882	1639882	type	True	75.4099	60	831	95	below_threshold
Patulibacter medicamentivorans	strain=I11	GCA_000240225.2	1097667	1097667	type	True	74.9715	52	831	95	below_threshold
Nannocystis exedens	strain=DSM 71	GCA_002343915.1	54	54	type	True	74.904	101	831	95	below_threshold
Nocardioides perillae	strain=DSM 24552	GCA_013409425.1	1119534	1119534	type	True	74.8986	52	831	95	below_threshold
Nannocystis exedens	strain=ATCC 25963	GCA_900112715.1	54	54	type	True	74.865	101	831	95	below_threshold
Nocardioides marinisabuli	strain=DSM 18965	GCA_013466785.1	419476	419476	type	True	74.7322	53	831	95	below_threshold
Nocardioides marinisabuli	strain=DSM 18965	GCA_013409965.1	419476	419476	type	True	74.7205	55	831	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-19 12:40:55,953] [INFO] DFAST Taxonomy check result was written to GCA_013694695.1_ASM1369469v1_genomic.fna/tc_result.tsv
[2023-06-19 12:40:55,954] [INFO] ===== Taxonomy check completed =====
[2023-06-19 12:40:55,954] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 12:40:55,954] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb0cb33e2-9cb4-4fa4-b79b-111de3ccb83c/dqc_reference/checkm_data
[2023-06-19 12:40:55,955] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 12:40:55,989] [INFO] Task started: CheckM
[2023-06-19 12:40:55,989] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_013694695.1_ASM1369469v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_013694695.1_ASM1369469v1_genomic.fna/checkm_input GCA_013694695.1_ASM1369469v1_genomic.fna/checkm_result
[2023-06-19 12:41:32,294] [INFO] Task succeeded: CheckM
[2023-06-19 12:41:32,296] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 12:41:32,317] [INFO] ===== Completeness check finished =====
[2023-06-19 12:41:32,317] [INFO] ===== Start GTDB Search =====
[2023-06-19 12:41:32,318] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_013694695.1_ASM1369469v1_genomic.fna/markers.fasta)
[2023-06-19 12:41:32,318] [INFO] Task started: Blastn
[2023-06-19 12:41:32,318] [INFO] Running command: blastn -query GCA_013694695.1_ASM1369469v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb0cb33e2-9cb4-4fa4-b79b-111de3ccb83c/dqc_reference/reference_markers_gtdb.fasta -out GCA_013694695.1_ASM1369469v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 12:41:33,194] [INFO] Task succeeded: Blastn
[2023-06-19 12:41:33,198] [INFO] Selected 8 target genomes.
[2023-06-19 12:41:33,199] [INFO] Target genome list was writen to GCA_013694695.1_ASM1369469v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 12:41:33,229] [INFO] Task started: fastANI
[2023-06-19 12:41:33,230] [INFO] Running command: fastANI --query /var/lib/cwl/stg97bfb504-7530-4e9e-aa18-d87f44f6b633/GCA_013694695.1_ASM1369469v1_genomic.fna.gz --refList GCA_013694695.1_ASM1369469v1_genomic.fna/target_genomes_gtdb.txt --output GCA_013694695.1_ASM1369469v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 12:41:37,903] [INFO] Task succeeded: fastANI
[2023-06-19 12:41:37,918] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 12:41:37,918] [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
GCA_013694695.1	s__Palsa-1233 sp013694695	100.0	826	831	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__GWC2-71-9;g__Palsa-1233	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_016704275.1	s__Palsa-1233 sp016704275	78.2564	253	831	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__GWC2-71-9;g__Palsa-1233	95.0	97.87	97.54	0.90	0.86	5	-
GCA_016720805.1	s__Palsa-1233 sp016720805	78.136	255	831	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__GWC2-71-9;g__Palsa-1233	95.0	98.28	98.28	0.94	0.94	2	-
GCA_011390645.1	s__Palsa-1233 sp011390645	77.7034	183	831	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__GWC2-71-9;g__Palsa-1233	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003169895.1	s__Palsa-1233 sp003169895	77.4928	158	831	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__GWC2-71-9;g__Palsa-1233	95.0	99.93	99.86	0.99	0.98	6	-
GCA_016713785.1	s__JADJOM01 sp016713785	77.0941	167	831	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__GWC2-71-9;g__JADJOM01	95.0	99.05	98.46	0.95	0.91	10	-
GCA_011362545.1	s__DSTP01 sp011362545	76.9615	152	831	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__GWC2-71-9;g__DSTP01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013813675.1	s__JACDDX01 sp013813675	75.8973	102	831	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__GWC2-71-9;g__JACDDX01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-19 12:41:37,920] [INFO] GTDB search result was written to GCA_013694695.1_ASM1369469v1_genomic.fna/result_gtdb.tsv
[2023-06-19 12:41:37,920] [INFO] ===== GTDB Search completed =====
[2023-06-19 12:41:37,924] [INFO] DFAST_QC result json was written to GCA_013694695.1_ASM1369469v1_genomic.fna/dqc_result.json
[2023-06-19 12:41:37,924] [INFO] DFAST_QC completed!
[2023-06-19 12:41:37,924] [INFO] Total running time: 0h1m7s