[2024-01-24 14:19:46,639] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:19:46,641] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:19:46,641] [INFO] DQC Reference Directory: /var/lib/cwl/stgd3b4d316-98ce-499b-aaa5-b53871c90716/dqc_reference
[2024-01-24 14:19:47,947] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:19:47,948] [INFO] Task started: Prodigal
[2024-01-24 14:19:47,948] [INFO] Running command: gunzip -c /var/lib/cwl/stgbf99f8cf-e1fe-43ea-b4cf-5035e74a4967/GCF_900155685.1_Paenibacillus_bouchesdurhonensis_genomic.fna.gz | prodigal -d GCF_900155685.1_Paenibacillus_bouchesdurhonensis_genomic.fna/cds.fna -a GCF_900155685.1_Paenibacillus_bouchesdurhonensis_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:20:02,761] [INFO] Task succeeded: Prodigal
[2024-01-24 14:20:02,762] [INFO] Task started: HMMsearch
[2024-01-24 14:20:02,762] [INFO] Running command: hmmsearch --tblout GCF_900155685.1_Paenibacillus_bouchesdurhonensis_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd3b4d316-98ce-499b-aaa5-b53871c90716/dqc_reference/reference_markers.hmm GCF_900155685.1_Paenibacillus_bouchesdurhonensis_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:20:03,086] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:20:03,090] [INFO] Found 6/6 markers.
[2024-01-24 14:20:03,137] [INFO] Query marker FASTA was written to GCF_900155685.1_Paenibacillus_bouchesdurhonensis_genomic.fna/markers.fasta
[2024-01-24 14:20:03,138] [INFO] Task started: Blastn
[2024-01-24 14:20:03,138] [INFO] Running command: blastn -query GCF_900155685.1_Paenibacillus_bouchesdurhonensis_genomic.fna/markers.fasta -db /var/lib/cwl/stgd3b4d316-98ce-499b-aaa5-b53871c90716/dqc_reference/reference_markers.fasta -out GCF_900155685.1_Paenibacillus_bouchesdurhonensis_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:20:03,796] [INFO] Task succeeded: Blastn
[2024-01-24 14:20:03,800] [INFO] Selected 18 target genomes.
[2024-01-24 14:20:03,801] [INFO] Target genome list was writen to GCF_900155685.1_Paenibacillus_bouchesdurhonensis_genomic.fna/target_genomes.txt
[2024-01-24 14:20:03,820] [INFO] Task started: fastANI
[2024-01-24 14:20:03,820] [INFO] Running command: fastANI --query /var/lib/cwl/stgbf99f8cf-e1fe-43ea-b4cf-5035e74a4967/GCF_900155685.1_Paenibacillus_bouchesdurhonensis_genomic.fna.gz --refList GCF_900155685.1_Paenibacillus_bouchesdurhonensis_genomic.fna/target_genomes.txt --output GCF_900155685.1_Paenibacillus_bouchesdurhonensis_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:20:23,515] [INFO] Task succeeded: fastANI
[2024-01-24 14:20:23,515] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd3b4d316-98ce-499b-aaa5-b53871c90716/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:20:23,516] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd3b4d316-98ce-499b-aaa5-b53871c90716/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:20:23,527] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:20:23,527] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:20:23,527] [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 bouchesdurhonensis	strain=Marseille-P3071	GCA_900155685.1	1870990	1870990	type	True	100.0	1938	1938	95	conclusive
Paenibacillus lentus	strain=DSM 25539	GCA_003931855.1	1338368	1338368	type	True	86.9112	1319	1938	95	below_threshold
Paenibacillus ihumii	strain=AT5	GCA_001403875.1	687436	687436	type	True	83.3418	1209	1938	95	below_threshold
Paenibacillus fonticola	strain=DSM 21315	GCA_000381905.1	379896	379896	type	True	82.39	1070	1938	95	below_threshold
Paenibacillus lutimineralis	strain=MBLB1234	GCA_003991425.1	2707005	2707005	type	True	78.3255	286	1938	95	below_threshold
Paenibacillus aceti	strain=CGMCC 1.15420	GCA_014642755.1	1820010	1820010	type	True	78.1014	276	1938	95	below_threshold
Paenibacillus macerans	strain=ATCC 8244	GCA_000746875.1	44252	44252	type	True	78.048	344	1938	95	below_threshold
Fontibacillus panacisegetis	strain=DSM 28129	GCA_900102215.1	670482	670482	type	True	78.0164	276	1938	95	below_threshold
Paenibacillus timonensis	strain=DSM 16943	GCA_022427145.1	225915	225915	type	True	77.9065	289	1938	95	below_threshold
Paenibacillus macerans	strain=NBRC 15307	GCA_004000965.1	44252	44252	type	True	77.8188	326	1938	95	below_threshold
Paenibacillus rhizophilus	strain=7197	GCA_003854965.1	1850366	1850366	type	True	76.8109	116	1938	95	below_threshold
Paenibacillus piscarius	strain=P121	GCA_022234545.1	1089681	1089681	type	True	76.3036	130	1938	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:20:23,529] [INFO] DFAST Taxonomy check result was written to GCF_900155685.1_Paenibacillus_bouchesdurhonensis_genomic.fna/tc_result.tsv
[2024-01-24 14:20:23,529] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:20:23,530] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:20:23,530] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd3b4d316-98ce-499b-aaa5-b53871c90716/dqc_reference/checkm_data
[2024-01-24 14:20:23,531] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:20:23,600] [INFO] Task started: CheckM
[2024-01-24 14:20:23,601] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900155685.1_Paenibacillus_bouchesdurhonensis_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900155685.1_Paenibacillus_bouchesdurhonensis_genomic.fna/checkm_input GCF_900155685.1_Paenibacillus_bouchesdurhonensis_genomic.fna/checkm_result
[2024-01-24 14:21:11,874] [INFO] Task succeeded: CheckM
[2024-01-24 14:21:11,875] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:21:11,893] [INFO] ===== Completeness check finished =====
[2024-01-24 14:21:11,893] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:21:11,894] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900155685.1_Paenibacillus_bouchesdurhonensis_genomic.fna/markers.fasta)
[2024-01-24 14:21:11,894] [INFO] Task started: Blastn
[2024-01-24 14:21:11,894] [INFO] Running command: blastn -query GCF_900155685.1_Paenibacillus_bouchesdurhonensis_genomic.fna/markers.fasta -db /var/lib/cwl/stgd3b4d316-98ce-499b-aaa5-b53871c90716/dqc_reference/reference_markers_gtdb.fasta -out GCF_900155685.1_Paenibacillus_bouchesdurhonensis_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:21:12,778] [INFO] Task succeeded: Blastn
[2024-01-24 14:21:12,782] [INFO] Selected 8 target genomes.
[2024-01-24 14:21:12,783] [INFO] Target genome list was writen to GCF_900155685.1_Paenibacillus_bouchesdurhonensis_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:21:12,794] [INFO] Task started: fastANI
[2024-01-24 14:21:12,794] [INFO] Running command: fastANI --query /var/lib/cwl/stgbf99f8cf-e1fe-43ea-b4cf-5035e74a4967/GCF_900155685.1_Paenibacillus_bouchesdurhonensis_genomic.fna.gz --refList GCF_900155685.1_Paenibacillus_bouchesdurhonensis_genomic.fna/target_genomes_gtdb.txt --output GCF_900155685.1_Paenibacillus_bouchesdurhonensis_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:21:21,995] [INFO] Task succeeded: fastANI
[2024-01-24 14:21:22,001] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:21:22,002] [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_900155685.1	s__Paenibacillus_A bouchesdurhonensis	100.0	1938	1938	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_A	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003931855.1	s__Paenibacillus_A lentus	86.9214	1323	1938	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001403875.1	s__Paenibacillus_A ihumii	83.3553	1208	1938	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_A	95.0	100.00	100.00	1.00	1.00	2	-
GCF_009725165.1	s__Paenibacillus_A woosongensis	83.1707	1213	1938	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_A	95.0	95.99	95.99	0.91	0.91	2	-
GCF_000381905.1	s__Paenibacillus_A fonticola	82.3955	1068	1938	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900766135.1	s__Paenibacillus_A sp900766135	77.5095	263	1938	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:21:22,003] [INFO] GTDB search result was written to GCF_900155685.1_Paenibacillus_bouchesdurhonensis_genomic.fna/result_gtdb.tsv
[2024-01-24 14:21:22,004] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:21:22,015] [INFO] DFAST_QC result json was written to GCF_900155685.1_Paenibacillus_bouchesdurhonensis_genomic.fna/dqc_result.json
[2024-01-24 14:21:22,015] [INFO] DFAST_QC completed!
[2024-01-24 14:21:22,015] [INFO] Total running time: 0h1m35s