[2024-01-24 13:22:11,378] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:22:11,384] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:22:11,384] [INFO] DQC Reference Directory: /var/lib/cwl/stg30837dd1-8a66-43ab-831e-5386aa54ca3d/dqc_reference
[2024-01-24 13:22:13,355] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:22:13,356] [INFO] Task started: Prodigal
[2024-01-24 13:22:13,356] [INFO] Running command: gunzip -c /var/lib/cwl/stg44bde52b-cb21-47bc-be8b-4cdbb915655b/GCF_011043685.1_ASM1104368v1_genomic.fna.gz | prodigal -d GCF_011043685.1_ASM1104368v1_genomic.fna/cds.fna -a GCF_011043685.1_ASM1104368v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:22:26,088] [INFO] Task succeeded: Prodigal
[2024-01-24 13:22:26,088] [INFO] Task started: HMMsearch
[2024-01-24 13:22:26,088] [INFO] Running command: hmmsearch --tblout GCF_011043685.1_ASM1104368v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg30837dd1-8a66-43ab-831e-5386aa54ca3d/dqc_reference/reference_markers.hmm GCF_011043685.1_ASM1104368v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:22:26,446] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:22:26,447] [INFO] Found 6/6 markers.
[2024-01-24 13:22:26,524] [INFO] Query marker FASTA was written to GCF_011043685.1_ASM1104368v1_genomic.fna/markers.fasta
[2024-01-24 13:22:26,525] [INFO] Task started: Blastn
[2024-01-24 13:22:26,525] [INFO] Running command: blastn -query GCF_011043685.1_ASM1104368v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg30837dd1-8a66-43ab-831e-5386aa54ca3d/dqc_reference/reference_markers.fasta -out GCF_011043685.1_ASM1104368v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:22:27,105] [INFO] Task succeeded: Blastn
[2024-01-24 13:22:27,107] [INFO] Selected 10 target genomes.
[2024-01-24 13:22:27,107] [INFO] Target genome list was writen to GCF_011043685.1_ASM1104368v1_genomic.fna/target_genomes.txt
[2024-01-24 13:22:27,110] [INFO] Task started: fastANI
[2024-01-24 13:22:27,110] [INFO] Running command: fastANI --query /var/lib/cwl/stg44bde52b-cb21-47bc-be8b-4cdbb915655b/GCF_011043685.1_ASM1104368v1_genomic.fna.gz --refList GCF_011043685.1_ASM1104368v1_genomic.fna/target_genomes.txt --output GCF_011043685.1_ASM1104368v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:22:39,480] [INFO] Task succeeded: fastANI
[2024-01-24 13:22:39,480] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg30837dd1-8a66-43ab-831e-5386aa54ca3d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:22:39,480] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg30837dd1-8a66-43ab-831e-5386aa54ca3d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:22:39,488] [INFO] Found 10 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:22:39,488] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 13:22:39,488] [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 apii	strain=7124	GCA_011043685.1	1850370	1850370	type	True	100.0	1781	1784	95	inconclusive
Paenibacillus sabinae	strain=T27	GCA_000612505.1	365617	365617	type	True	95.6757	1560	1784	95	inconclusive
Paenibacillus rhizophilus	strain=7197	GCA_003854965.1	1850366	1850366	type	True	88.77	1427	1784	95	below_threshold
Paenibacillus sophorae	strain=DSM 23020	GCA_018966525.1	1333845	1333845	type	True	85.1912	1309	1784	95	below_threshold
Paenibacillus sophorae	strain=CGMCC 1.10238	GCA_900110315.1	1333845	1333845	type	True	85.1845	1299	1784	95	below_threshold
Paenibacillus forsythiae	strain=T98	GCA_000520735.1	365616	365616	type	True	84.2604	922	1784	95	below_threshold
Paenibacillus sonchi	strain=LMG 24727	GCA_016772475.1	373687	373687	type	True	78.3965	491	1784	95	below_threshold
Paenibacillus piscarius	strain=P121	GCA_022234545.1	1089681	1089681	type	True	78.1354	469	1784	95	below_threshold
Paenibacillus macerans	strain=ATCC 8244	GCA_000746875.1	44252	44252	type	True	77.1724	234	1784	95	below_threshold
Paenibacillus timonensis	strain=DSM 16943	GCA_022427145.1	225915	225915	type	True	77.0335	209	1784	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:22:39,489] [INFO] DFAST Taxonomy check result was written to GCF_011043685.1_ASM1104368v1_genomic.fna/tc_result.tsv
[2024-01-24 13:22:39,490] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:22:39,490] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:22:39,490] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg30837dd1-8a66-43ab-831e-5386aa54ca3d/dqc_reference/checkm_data
[2024-01-24 13:22:39,491] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:22:39,542] [INFO] Task started: CheckM
[2024-01-24 13:22:39,542] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_011043685.1_ASM1104368v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_011043685.1_ASM1104368v1_genomic.fna/checkm_input GCF_011043685.1_ASM1104368v1_genomic.fna/checkm_result
[2024-01-24 13:23:17,136] [INFO] Task succeeded: CheckM
[2024-01-24 13:23:17,137] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.38%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:23:17,154] [INFO] ===== Completeness check finished =====
[2024-01-24 13:23:17,154] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:23:17,155] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_011043685.1_ASM1104368v1_genomic.fna/markers.fasta)
[2024-01-24 13:23:17,155] [INFO] Task started: Blastn
[2024-01-24 13:23:17,155] [INFO] Running command: blastn -query GCF_011043685.1_ASM1104368v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg30837dd1-8a66-43ab-831e-5386aa54ca3d/dqc_reference/reference_markers_gtdb.fasta -out GCF_011043685.1_ASM1104368v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:23:17,958] [INFO] Task succeeded: Blastn
[2024-01-24 13:23:17,961] [INFO] Selected 7 target genomes.
[2024-01-24 13:23:17,961] [INFO] Target genome list was writen to GCF_011043685.1_ASM1104368v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:23:17,965] [INFO] Task started: fastANI
[2024-01-24 13:23:17,965] [INFO] Running command: fastANI --query /var/lib/cwl/stg44bde52b-cb21-47bc-be8b-4cdbb915655b/GCF_011043685.1_ASM1104368v1_genomic.fna.gz --refList GCF_011043685.1_ASM1104368v1_genomic.fna/target_genomes_gtdb.txt --output GCF_011043685.1_ASM1104368v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:23:27,111] [INFO] Task succeeded: fastANI
[2024-01-24 13:23:27,116] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:23:27,117] [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_000612505.1	s__Paenibacillus sabinae	95.6757	1560	1784	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	95.70	95.69	0.89	0.89	3	conclusive
GCF_003854965.1	s__Paenibacillus sp003854965	88.7759	1426	1784	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	95.02	95.02	0.86	0.86	2	-
GCF_000993825.1	s__Paenibacillus durus_B	85.3246	1245	1784	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	85.2354	1296	1784	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018966525.1	s__Paenibacillus sophorae	85.188	1310	1784	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	84.8679	957	1784	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000520735.1	s__Paenibacillus forsythiae	84.2599	922	1784	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 13:23:27,118] [INFO] GTDB search result was written to GCF_011043685.1_ASM1104368v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:23:27,118] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:23:27,121] [INFO] DFAST_QC result json was written to GCF_011043685.1_ASM1104368v1_genomic.fna/dqc_result.json
[2024-01-24 13:23:27,121] [INFO] DFAST_QC completed!
[2024-01-24 13:23:27,121] [INFO] Total running time: 0h1m16s