[2023-06-08 17:27:44,999] [INFO] DFAST_QC pipeline started.
[2023-06-08 17:27:45,003] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 17:27:45,003] [INFO] DQC Reference Directory: /var/lib/cwl/stgc3d78d23-55f0-4c73-a003-3f5be29b528f/dqc_reference
[2023-06-08 17:27:46,293] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 17:27:46,294] [INFO] Task started: Prodigal
[2023-06-08 17:27:46,294] [INFO] Running command: gunzip -c /var/lib/cwl/stg061cd440-69ec-48ed-87b4-4f09c030771c/GCA_945861385.1_AH-24oct19-200_genomic.fna.gz | prodigal -d GCA_945861385.1_AH-24oct19-200_genomic.fna/cds.fna -a GCA_945861385.1_AH-24oct19-200_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 17:28:14,716] [INFO] Task succeeded: Prodigal
[2023-06-08 17:28:14,716] [INFO] Task started: HMMsearch
[2023-06-08 17:28:14,716] [INFO] Running command: hmmsearch --tblout GCA_945861385.1_AH-24oct19-200_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc3d78d23-55f0-4c73-a003-3f5be29b528f/dqc_reference/reference_markers.hmm GCA_945861385.1_AH-24oct19-200_genomic.fna/protein.faa > /dev/null
[2023-06-08 17:28:14,958] [INFO] Task succeeded: HMMsearch
[2023-06-08 17:28:14,963] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg061cd440-69ec-48ed-87b4-4f09c030771c/GCA_945861385.1_AH-24oct19-200_genomic.fna.gz]
[2023-06-08 17:28:15,010] [INFO] Query marker FASTA was written to GCA_945861385.1_AH-24oct19-200_genomic.fna/markers.fasta
[2023-06-08 17:28:15,011] [INFO] Task started: Blastn
[2023-06-08 17:28:15,011] [INFO] Running command: blastn -query GCA_945861385.1_AH-24oct19-200_genomic.fna/markers.fasta -db /var/lib/cwl/stgc3d78d23-55f0-4c73-a003-3f5be29b528f/dqc_reference/reference_markers.fasta -out GCA_945861385.1_AH-24oct19-200_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 17:28:15,511] [INFO] Task succeeded: Blastn
[2023-06-08 17:28:15,516] [INFO] Selected 12 target genomes.
[2023-06-08 17:28:15,516] [INFO] Target genome list was writen to GCA_945861385.1_AH-24oct19-200_genomic.fna/target_genomes.txt
[2023-06-08 17:28:15,522] [INFO] Task started: fastANI
[2023-06-08 17:28:15,522] [INFO] Running command: fastANI --query /var/lib/cwl/stg061cd440-69ec-48ed-87b4-4f09c030771c/GCA_945861385.1_AH-24oct19-200_genomic.fna.gz --refList GCA_945861385.1_AH-24oct19-200_genomic.fna/target_genomes.txt --output GCA_945861385.1_AH-24oct19-200_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 17:28:27,121] [INFO] Task succeeded: fastANI
[2023-06-08 17:28:27,122] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc3d78d23-55f0-4c73-a003-3f5be29b528f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 17:28:27,123] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc3d78d23-55f0-4c73-a003-3f5be29b528f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 17:28:27,137] [INFO] Found 7 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 17:28:27,137] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-08 17:28:27,138] [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
Chthoniobacter flavus	strain=Ellin428	GCA_000173075.1	191863	191863	type	True	76.1793	172	1341	95	below_threshold
Chthoniobacter flavus	strain=DSM 22515	GCA_004341915.1	191863	191863	type	True	76.1403	171	1341	95	below_threshold
Prosthecobacter vanneervenii	strain=DSM 12252	GCA_014203095.1	48466	48466	type	True	76.0423	60	1341	95	below_threshold
Terrimicrobium sacchariphilum	strain=NM-5	GCA_001613545.1	690879	690879	type	True	75.8369	59	1341	95	below_threshold
Brevifollis gellanilyticus	strain=NBRC 108608	GCA_007992435.1	748831	748831	type	True	75.3316	70	1341	95	below_threshold
Actinomadura algeriensis	strain=DSM 46744	GCA_014873935.1	1679523	1679523	type	True	74.7994	77	1341	95	below_threshold
Nonomuraea jiangxiensis	strain=CGMCC 4.6533	GCA_900099965.1	633440	633440	type	True	74.6993	68	1341	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 17:28:27,140] [INFO] DFAST Taxonomy check result was written to GCA_945861385.1_AH-24oct19-200_genomic.fna/tc_result.tsv
[2023-06-08 17:28:27,141] [INFO] ===== Taxonomy check completed =====
[2023-06-08 17:28:27,141] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 17:28:27,141] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc3d78d23-55f0-4c73-a003-3f5be29b528f/dqc_reference/checkm_data
[2023-06-08 17:28:27,143] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 17:28:27,190] [INFO] Task started: CheckM
[2023-06-08 17:28:27,190] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_945861385.1_AH-24oct19-200_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_945861385.1_AH-24oct19-200_genomic.fna/checkm_input GCA_945861385.1_AH-24oct19-200_genomic.fna/checkm_result
[2023-06-08 17:29:45,716] [INFO] Task succeeded: CheckM
[2023-06-08 17:29:45,718] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 17:29:45,741] [INFO] ===== Completeness check finished =====
[2023-06-08 17:29:45,741] [INFO] ===== Start GTDB Search =====
[2023-06-08 17:29:45,741] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_945861385.1_AH-24oct19-200_genomic.fna/markers.fasta)
[2023-06-08 17:29:45,742] [INFO] Task started: Blastn
[2023-06-08 17:29:45,742] [INFO] Running command: blastn -query GCA_945861385.1_AH-24oct19-200_genomic.fna/markers.fasta -db /var/lib/cwl/stgc3d78d23-55f0-4c73-a003-3f5be29b528f/dqc_reference/reference_markers_gtdb.fasta -out GCA_945861385.1_AH-24oct19-200_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 17:29:46,190] [INFO] Task succeeded: Blastn
[2023-06-08 17:29:46,195] [INFO] Selected 9 target genomes.
[2023-06-08 17:29:46,195] [INFO] Target genome list was writen to GCA_945861385.1_AH-24oct19-200_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 17:29:46,197] [INFO] Task started: fastANI
[2023-06-08 17:29:46,197] [INFO] Running command: fastANI --query /var/lib/cwl/stg061cd440-69ec-48ed-87b4-4f09c030771c/GCA_945861385.1_AH-24oct19-200_genomic.fna.gz --refList GCA_945861385.1_AH-24oct19-200_genomic.fna/target_genomes_gtdb.txt --output GCA_945861385.1_AH-24oct19-200_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 17:29:53,541] [INFO] Task succeeded: fastANI
[2023-06-08 17:29:53,552] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-08 17:29:53,552] [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_903874975.1	s__Chthoniobacter sp903874975	79.1585	296	1341	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Chthoniobacterales;f__Chthoniobacteraceae;g__Chthoniobacter	95.0	97.99	97.82	0.84	0.83	3	-
GCA_014189875.1	s__SXWH01 sp014189875	78.6697	342	1341	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Chthoniobacterales;f__Chthoniobacteraceae;g__SXWH01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903929475.1	s__SXWH01 sp903929475	78.6404	369	1341	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Chthoniobacterales;f__Chthoniobacteraceae;g__SXWH01	95.0	99.90	99.90	0.94	0.94	2	-
GCA_903882875.1	s__SXWH01 sp903882875	78.33	420	1341	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Chthoniobacterales;f__Chthoniobacteraceae;g__SXWH01	95.0	99.98	99.97	0.98	0.98	3	-
GCA_009885995.1	s__VFJQ01 sp009885995	77.3154	277	1341	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Chthoniobacterales;f__Chthoniobacteraceae;g__VFJQ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005791535.1	s__SXWH01 sp005791535	77.0351	197	1341	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Chthoniobacterales;f__Chthoniobacteraceae;g__SXWH01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000173075.1	s__Chthoniobacter flavus	76.1851	170	1341	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Chthoniobacterales;f__Chthoniobacteraceae;g__Chthoniobacter	95.0	99.97	99.97	0.99	0.99	2	-
GCA_007280915.1	s__QYQL01 sp007280915	76.084	53	1341	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Chthoniobacterales;f__Terrimicrobiaceae;g__QYQL01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017305195.1	s__Terrimicrobium sp001897195	75.9282	73	1341	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Chthoniobacterales;f__Terrimicrobiaceae;g__Terrimicrobium	95.0	99.90	99.90	0.94	0.94	2	-
--------------------------------------------------------------------------------
[2023-06-08 17:29:53,554] [INFO] GTDB search result was written to GCA_945861385.1_AH-24oct19-200_genomic.fna/result_gtdb.tsv
[2023-06-08 17:29:53,555] [INFO] ===== GTDB Search completed =====
[2023-06-08 17:29:53,558] [INFO] DFAST_QC result json was written to GCA_945861385.1_AH-24oct19-200_genomic.fna/dqc_result.json
[2023-06-08 17:29:53,558] [INFO] DFAST_QC completed!
[2023-06-08 17:29:53,558] [INFO] Total running time: 0h2m9s