[2024-01-24 13:10:16,687] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:10:16,688] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:10:16,688] [INFO] DQC Reference Directory: /var/lib/cwl/stg380ed9a2-4fd9-40f2-8c2d-1d0265831605/dqc_reference
[2024-01-24 13:10:18,171] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:10:18,172] [INFO] Task started: Prodigal
[2024-01-24 13:10:18,172] [INFO] Running command: gunzip -c /var/lib/cwl/stg4c14bc0e-d64b-4c07-a3ee-e5bab364ded5/GCF_031954385.1_ASM3195438v1_genomic.fna.gz | prodigal -d GCF_031954385.1_ASM3195438v1_genomic.fna/cds.fna -a GCF_031954385.1_ASM3195438v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:10:32,133] [INFO] Task succeeded: Prodigal
[2024-01-24 13:10:32,133] [INFO] Task started: HMMsearch
[2024-01-24 13:10:32,134] [INFO] Running command: hmmsearch --tblout GCF_031954385.1_ASM3195438v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg380ed9a2-4fd9-40f2-8c2d-1d0265831605/dqc_reference/reference_markers.hmm GCF_031954385.1_ASM3195438v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:10:32,490] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:10:32,492] [INFO] Found 6/6 markers.
[2024-01-24 13:10:32,534] [INFO] Query marker FASTA was written to GCF_031954385.1_ASM3195438v1_genomic.fna/markers.fasta
[2024-01-24 13:10:32,536] [INFO] Task started: Blastn
[2024-01-24 13:10:32,536] [INFO] Running command: blastn -query GCF_031954385.1_ASM3195438v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg380ed9a2-4fd9-40f2-8c2d-1d0265831605/dqc_reference/reference_markers.fasta -out GCF_031954385.1_ASM3195438v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:10:33,212] [INFO] Task succeeded: Blastn
[2024-01-24 13:10:33,216] [INFO] Selected 13 target genomes.
[2024-01-24 13:10:33,216] [INFO] Target genome list was writen to GCF_031954385.1_ASM3195438v1_genomic.fna/target_genomes.txt
[2024-01-24 13:10:33,233] [INFO] Task started: fastANI
[2024-01-24 13:10:33,234] [INFO] Running command: fastANI --query /var/lib/cwl/stg4c14bc0e-d64b-4c07-a3ee-e5bab364ded5/GCF_031954385.1_ASM3195438v1_genomic.fna.gz --refList GCF_031954385.1_ASM3195438v1_genomic.fna/target_genomes.txt --output GCF_031954385.1_ASM3195438v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:10:49,633] [INFO] Task succeeded: fastANI
[2024-01-24 13:10:49,633] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg380ed9a2-4fd9-40f2-8c2d-1d0265831605/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:10:49,634] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg380ed9a2-4fd9-40f2-8c2d-1d0265831605/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:10:49,646] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:10:49,646] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:10:49,646] [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 forsythiae	strain=T98	GCA_000520735.1	365616	365616	type	True	99.6925	1289	1698	95	conclusive
Paenibacillus sophorae	strain=DSM 23020	GCA_018966525.1	1333845	1333845	type	True	87.8386	1351	1698	95	below_threshold
Paenibacillus sophorae	strain=CGMCC 1.10238	GCA_900110315.1	1333845	1333845	type	True	87.7954	1342	1698	95	below_threshold
Paenibacillus zanthoxyli	strain=JH29	GCA_000520715.1	369399	369399	type	True	87.097	1009	1698	95	below_threshold
Paenibacillus rhizophilus	strain=7197	GCA_003854965.1	1850366	1850366	type	True	84.7612	1187	1698	95	below_threshold
Paenibacillus apii	strain=7124	GCA_011043685.1	1850370	1850370	type	True	84.3533	1206	1698	95	below_threshold
Paenibacillus sabinae	strain=T27	GCA_000612505.1	365617	365617	type	True	84.2036	1201	1698	95	below_threshold
Paenibacillus stellifer	strain=DSM 14472	GCA_000758685.1	169760	169760	type	True	80.2839	702	1698	95	below_threshold
Paenibacillus sinensis	strain=HN-1	GCA_019904155.1	2834413	2834413	type	True	80.0438	708	1698	95	below_threshold
Paenibacillus piscarius	strain=P121	GCA_022234545.1	1089681	1089681	type	True	78.3545	450	1698	95	below_threshold
Paenibacillus tianjinensis	strain=TB2019	GCA_017086365.1	2810347	2810347	type	True	78.3434	425	1698	95	below_threshold
Paenibacillus macerans	strain=ATCC 8244	GCA_000746875.1	44252	44252	type	True	77.053	228	1698	95	below_threshold
Paenibacillus hemerocallicola	strain=KCTC 33185	GCA_006265175.1	1172614	1172614	type	True	76.1842	121	1698	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:10:49,648] [INFO] DFAST Taxonomy check result was written to GCF_031954385.1_ASM3195438v1_genomic.fna/tc_result.tsv
[2024-01-24 13:10:49,649] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:10:49,650] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:10:49,650] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg380ed9a2-4fd9-40f2-8c2d-1d0265831605/dqc_reference/checkm_data
[2024-01-24 13:10:49,652] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:10:49,707] [INFO] Task started: CheckM
[2024-01-24 13:10:49,707] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_031954385.1_ASM3195438v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_031954385.1_ASM3195438v1_genomic.fna/checkm_input GCF_031954385.1_ASM3195438v1_genomic.fna/checkm_result
[2024-01-24 13:11:34,402] [INFO] Task succeeded: CheckM
[2024-01-24 13:11:34,403] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.38%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:11:34,423] [INFO] ===== Completeness check finished =====
[2024-01-24 13:11:34,424] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:11:34,424] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_031954385.1_ASM3195438v1_genomic.fna/markers.fasta)
[2024-01-24 13:11:34,425] [INFO] Task started: Blastn
[2024-01-24 13:11:34,425] [INFO] Running command: blastn -query GCF_031954385.1_ASM3195438v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg380ed9a2-4fd9-40f2-8c2d-1d0265831605/dqc_reference/reference_markers_gtdb.fasta -out GCF_031954385.1_ASM3195438v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:11:35,239] [INFO] Task succeeded: Blastn
[2024-01-24 13:11:35,243] [INFO] Selected 10 target genomes.
[2024-01-24 13:11:35,244] [INFO] Target genome list was writen to GCF_031954385.1_ASM3195438v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:11:35,363] [INFO] Task started: fastANI
[2024-01-24 13:11:35,363] [INFO] Running command: fastANI --query /var/lib/cwl/stg4c14bc0e-d64b-4c07-a3ee-e5bab364ded5/GCF_031954385.1_ASM3195438v1_genomic.fna.gz --refList GCF_031954385.1_ASM3195438v1_genomic.fna/target_genomes_gtdb.txt --output GCF_031954385.1_ASM3195438v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:11:47,479] [INFO] Task succeeded: fastANI
[2024-01-24 13:11:47,493] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:11:47,493] [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_000520735.1	s__Paenibacillus forsythiae	99.6925	1289	1698	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_018966525.1	s__Paenibacillus sophorae	87.8386	1351	1698	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000756615.1	s__Paenibacillus durus	87.6683	1348	1698	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000993825.1	s__Paenibacillus durus_B	87.536	1295	1698	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000520715.1	s__Paenibacillus zanthoxyli	87.1125	1007	1698	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003854965.1	s__Paenibacillus sp003854965	84.7507	1189	1698	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	95.02	95.02	0.86	0.86	2	-
GCF_000612505.1	s__Paenibacillus sabinae	84.2095	1200	1698	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	95.70	95.69	0.89	0.89	3	-
GCF_000758685.1	s__Paenibacillus stellifer	80.2963	699	1698	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008710135.1	s__Paenibacillus spiritus	78.7482	457	1698	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006265175.1	s__Paenibacillus_AB hemerocallicola	76.1842	121	1698	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_AB	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:11:47,495] [INFO] GTDB search result was written to GCF_031954385.1_ASM3195438v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:11:47,496] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:11:47,499] [INFO] DFAST_QC result json was written to GCF_031954385.1_ASM3195438v1_genomic.fna/dqc_result.json
[2024-01-24 13:11:47,500] [INFO] DFAST_QC completed!
[2024-01-24 13:11:47,500] [INFO] Total running time: 0h1m31s