[2024-01-24 13:22:17,678] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:22:17,680] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:22:17,680] [INFO] DQC Reference Directory: /var/lib/cwl/stg34a35d8e-1207-4c87-9b9c-b076387471e8/dqc_reference
[2024-01-24 13:22:19,033] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:22:19,034] [INFO] Task started: Prodigal
[2024-01-24 13:22:19,034] [INFO] Running command: gunzip -c /var/lib/cwl/stgc3d8fc94-71b7-4602-82dc-b780cbfdb686/GCF_014836635.1_ASM1483663v1_genomic.fna.gz | prodigal -d GCF_014836635.1_ASM1483663v1_genomic.fna/cds.fna -a GCF_014836635.1_ASM1483663v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:22:31,302] [INFO] Task succeeded: Prodigal
[2024-01-24 13:22:31,303] [INFO] Task started: HMMsearch
[2024-01-24 13:22:31,303] [INFO] Running command: hmmsearch --tblout GCF_014836635.1_ASM1483663v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg34a35d8e-1207-4c87-9b9c-b076387471e8/dqc_reference/reference_markers.hmm GCF_014836635.1_ASM1483663v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:22:31,751] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:22:31,753] [INFO] Found 6/6 markers.
[2024-01-24 13:22:31,812] [INFO] Query marker FASTA was written to GCF_014836635.1_ASM1483663v1_genomic.fna/markers.fasta
[2024-01-24 13:22:31,813] [INFO] Task started: Blastn
[2024-01-24 13:22:31,813] [INFO] Running command: blastn -query GCF_014836635.1_ASM1483663v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg34a35d8e-1207-4c87-9b9c-b076387471e8/dqc_reference/reference_markers.fasta -out GCF_014836635.1_ASM1483663v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:22:32,428] [INFO] Task succeeded: Blastn
[2024-01-24 13:22:32,432] [INFO] Selected 25 target genomes.
[2024-01-24 13:22:32,432] [INFO] Target genome list was writen to GCF_014836635.1_ASM1483663v1_genomic.fna/target_genomes.txt
[2024-01-24 13:22:32,460] [INFO] Task started: fastANI
[2024-01-24 13:22:32,461] [INFO] Running command: fastANI --query /var/lib/cwl/stgc3d8fc94-71b7-4602-82dc-b780cbfdb686/GCF_014836635.1_ASM1483663v1_genomic.fna.gz --refList GCF_014836635.1_ASM1483663v1_genomic.fna/target_genomes.txt --output GCF_014836635.1_ASM1483663v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:22:58,076] [INFO] Task succeeded: fastANI
[2024-01-24 13:22:58,077] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg34a35d8e-1207-4c87-9b9c-b076387471e8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:22:58,077] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg34a35d8e-1207-4c87-9b9c-b076387471e8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:22:58,092] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:22:58,093] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:22:58,093] [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
Paenibacillus gallinarum	strain=Sa2BVA9	GCA_014836635.1	2762232	2762232	type	True	100.0	1774	1776	95	conclusive
Paenibacillus polymyxa	strain=ATCC 842	GCA_000217775.1	1406	1406	type	True	78.0293	121	1776	95	below_threshold
Paenibacillus solani	strain=FJAT-22460	GCA_001277345.1	1705565	1705565	type	True	77.9967	124	1776	95	below_threshold
Paenibacillus taichungensis	strain=DSM 19942	GCA_013359905.1	484184	484184	type	True	77.9493	215	1776	95	below_threshold
Paenibacillus amylolyticus	strain=NBRC 15957	GCA_004001025.1	1451	1451	suspected-type	True	77.8732	202	1776	95	below_threshold
Paenibacillus xylanilyticus	strain=LMG 21957	GCA_013359935.1	248903	248903	type	True	77.8603	215	1776	95	below_threshold
Paenibacillus illinoisensis	strain=NBRC 15959	GCA_004000925.1	59845	59845	type	True	77.7635	188	1776	95	below_threshold
Paenibacillus polysaccharolyticus	strain=BL9	GCA_900102085.1	582692	582692	type	True	77.6269	189	1776	95	below_threshold
Paenibacillus dakarensis	strain=FF9	GCA_001373415.1	1527293	1527293	type	True	77.5812	135	1776	95	below_threshold
Paenibacillus pini	strain=JCM 16418	GCA_001315125.1	669461	669461	type	True	77.4578	139	1776	95	below_threshold
Paenibacillus pini	strain=JCM 16418	GCA_000576305.1	669461	669461	type	True	77.4426	139	1776	95	below_threshold
Paenibacillus tengchongensis	strain=SYSU G01003	GCA_008973665.1	2608684	2608684	type	True	77.4353	67	1776	95	below_threshold
Paenibacillus turicensis	strain=DSM 14349	GCA_017873435.1	160487	160487	type	True	77.3131	91	1776	95	below_threshold
Paenibacillus caui	strain=81-11	GCA_019904135.1	2873927	2873927	type	True	77.23	66	1776	95	below_threshold
Paenibacillus massiliensis subsp. panacisoli	strain=DSM 21345	GCA_000426545.1	363858	225917	type	True	76.9509	111	1776	95	below_threshold
Paenibacillus nuruki	strain=TI45-13ar	GCA_001721045.1	1886670	1886670	type	True	76.9093	110	1776	95	below_threshold
Paenibacillus glycanilyticus	strain=NBRC 16618	GCA_004000805.1	126569	126569	type	True	76.8186	60	1776	95	below_threshold
Paenibacillus periandrae	strain=PM10	GCA_022458865.1	1761741	1761741	type	True	76.7583	53	1776	95	below_threshold
Paenibacillus glycanilyticus subsp. hiroshimensis	strain=CCI5	GCA_015473105.1	2805378	126569	type	True	76.6477	60	1776	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:22:58,095] [INFO] DFAST Taxonomy check result was written to GCF_014836635.1_ASM1483663v1_genomic.fna/tc_result.tsv
[2024-01-24 13:22:58,095] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:22:58,095] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:22:58,096] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg34a35d8e-1207-4c87-9b9c-b076387471e8/dqc_reference/checkm_data
[2024-01-24 13:22:58,097] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:22:58,153] [INFO] Task started: CheckM
[2024-01-24 13:22:58,153] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014836635.1_ASM1483663v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014836635.1_ASM1483663v1_genomic.fna/checkm_input GCF_014836635.1_ASM1483663v1_genomic.fna/checkm_result
[2024-01-24 13:23:40,193] [INFO] Task succeeded: CheckM
[2024-01-24 13:23:40,195] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:23:40,217] [INFO] ===== Completeness check finished =====
[2024-01-24 13:23:40,218] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:23:40,218] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014836635.1_ASM1483663v1_genomic.fna/markers.fasta)
[2024-01-24 13:23:40,219] [INFO] Task started: Blastn
[2024-01-24 13:23:40,219] [INFO] Running command: blastn -query GCF_014836635.1_ASM1483663v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg34a35d8e-1207-4c87-9b9c-b076387471e8/dqc_reference/reference_markers_gtdb.fasta -out GCF_014836635.1_ASM1483663v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:23:41,179] [INFO] Task succeeded: Blastn
[2024-01-24 13:23:41,187] [INFO] Selected 9 target genomes.
[2024-01-24 13:23:41,188] [INFO] Target genome list was writen to GCF_014836635.1_ASM1483663v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:23:41,204] [INFO] Task started: fastANI
[2024-01-24 13:23:41,205] [INFO] Running command: fastANI --query /var/lib/cwl/stgc3d8fc94-71b7-4602-82dc-b780cbfdb686/GCF_014836635.1_ASM1483663v1_genomic.fna.gz --refList GCF_014836635.1_ASM1483663v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014836635.1_ASM1483663v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:23:52,237] [INFO] Task succeeded: fastANI
[2024-01-24 13:23:52,253] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:23:52,253] [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_014836635.1	s__Paenibacillus sp014836635	100.0	1774	1776	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_018403285.1	s__Paenibacillus sp018403285	94.0337	1479	1776	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009870785.1	s__Paenibacillus sp009870785	91.7076	1328	1776	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018310695.1	s__Paenibacillus sp018310695	82.5123	1003	1776	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016908215.1	s__Paenibacillus urinalis	79.1726	378	1776	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	98.24	98.24	0.89	0.89	2	-
GCF_001955535.1	s__Paenibacillus sp001955535	79.0662	388	1776	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	98.62	98.62	0.85	0.85	2	-
GCF_900116105.1	s__Paenibacillus sp900116105	78.9341	398	1776	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013359905.1	s__Paenibacillus taichungensis	77.9285	216	1776	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	96.85	95.16	0.90	0.85	6	-
GCF_013359935.1	s__Paenibacillus xylanilyticus	77.8671	216	1776	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:23:52,255] [INFO] GTDB search result was written to GCF_014836635.1_ASM1483663v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:23:52,256] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:23:52,260] [INFO] DFAST_QC result json was written to GCF_014836635.1_ASM1483663v1_genomic.fna/dqc_result.json
[2024-01-24 13:23:52,260] [INFO] DFAST_QC completed!
[2024-01-24 13:23:52,261] [INFO] Total running time: 0h1m35s