[2024-01-24 11:51:11,379] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:51:11,382] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:51:11,382] [INFO] DQC Reference Directory: /var/lib/cwl/stg0d0bc8b9-280b-4670-8de9-dd0fea254372/dqc_reference
[2024-01-24 11:51:12,647] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:51:12,648] [INFO] Task started: Prodigal
[2024-01-24 11:51:12,648] [INFO] Running command: gunzip -c /var/lib/cwl/stg84d2ba8f-0214-4584-bba4-4fbf0bdd5e5b/GCF_007786455.1_ASM778645v1_genomic.fna.gz | prodigal -d GCF_007786455.1_ASM778645v1_genomic.fna/cds.fna -a GCF_007786455.1_ASM778645v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:51:29,543] [INFO] Task succeeded: Prodigal
[2024-01-24 11:51:29,544] [INFO] Task started: HMMsearch
[2024-01-24 11:51:29,544] [INFO] Running command: hmmsearch --tblout GCF_007786455.1_ASM778645v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0d0bc8b9-280b-4670-8de9-dd0fea254372/dqc_reference/reference_markers.hmm GCF_007786455.1_ASM778645v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:51:29,913] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:51:29,914] [INFO] Found 6/6 markers.
[2024-01-24 11:51:29,994] [INFO] Query marker FASTA was written to GCF_007786455.1_ASM778645v1_genomic.fna/markers.fasta
[2024-01-24 11:51:29,994] [INFO] Task started: Blastn
[2024-01-24 11:51:29,995] [INFO] Running command: blastn -query GCF_007786455.1_ASM778645v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0d0bc8b9-280b-4670-8de9-dd0fea254372/dqc_reference/reference_markers.fasta -out GCF_007786455.1_ASM778645v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:51:30,648] [INFO] Task succeeded: Blastn
[2024-01-24 11:51:30,651] [INFO] Selected 25 target genomes.
[2024-01-24 11:51:30,652] [INFO] Target genome list was writen to GCF_007786455.1_ASM778645v1_genomic.fna/target_genomes.txt
[2024-01-24 11:51:30,663] [INFO] Task started: fastANI
[2024-01-24 11:51:30,663] [INFO] Running command: fastANI --query /var/lib/cwl/stg84d2ba8f-0214-4584-bba4-4fbf0bdd5e5b/GCF_007786455.1_ASM778645v1_genomic.fna.gz --refList GCF_007786455.1_ASM778645v1_genomic.fna/target_genomes.txt --output GCF_007786455.1_ASM778645v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:51:55,817] [INFO] Task succeeded: fastANI
[2024-01-24 11:51:55,817] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0d0bc8b9-280b-4670-8de9-dd0fea254372/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:51:55,818] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0d0bc8b9-280b-4670-8de9-dd0fea254372/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:51:55,831] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:51:55,831] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:51:55,831] [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 arenosi	strain=CAU 1523	GCA_014841135.1	2774142	2774142	type	True	88.6319	1475	1928	95	below_threshold
Paenibacillus assamensis	strain=DSM 18201	GCA_000422445.1	311244	311244	type	True	88.2977	1461	1928	95	below_threshold
Paenibacillus alvei	strain=DSM 29	GCA_000293805.1	44250	44250	type	True	79.0551	208	1928	95	below_threshold
Paenibacillus aquistagni	strain=11	GCA_900177815.1	1852522	1852522	type	True	78.7316	184	1928	95	below_threshold
Paenibacillus thiaminolyticus	strain=NRRL B-4156	GCA_007066085.1	49283	49283	type	True	78.6868	148	1928	95	below_threshold
Paenibacillus taiwanensis	strain=DSM 18679	GCA_000425125.1	401638	401638	type	True	78.444	220	1928	95	below_threshold
Paenibacillus thiaminolyticus	strain=NRRL B-4156	GCA_002161855.1	49283	49283	type	True	78.3638	145	1928	95	below_threshold
Paenibacillus phyllosphaerae	strain=CECT 5862	GCA_014192105.1	274593	274593	type	True	77.5735	53	1928	95	below_threshold
Paenibacillus algicola	strain=HB172198	GCA_005577435.1	2565926	2565926	type	True	77.4764	50	1928	95	below_threshold
Paenibacillus plantarum	strain=LMG 31461	GCA_013141695.1	2654975	2654975	type	True	77.3599	73	1928	95	below_threshold
Paenibacillus dokdonensis	strain=YH-JAE5	GCA_004916975.1	2567944	2567944	type	True	77.3249	61	1928	95	below_threshold
Paenibacillus terrigena	strain=DSM 21567	GCA_000374845.1	369333	369333	type	True	77.2755	112	1928	95	below_threshold
Paenibacillus montanisoli	strain=RA17	GCA_003268025.1	2081970	2081970	type	True	77.1123	55	1928	95	below_threshold
Paenibacillus catalpae	strain=CGMCC 1.10784	GCA_900112695.1	1045775	1045775	type	True	76.8725	61	1928	95	below_threshold
Paenibacillus taihuensis	strain=CGMCC 1.10966	GCA_003386535.1	1156355	1156355	type	True	76.6235	64	1928	95	below_threshold
Paenibacillus dauci	strain=H9	GCA_000971985.1	1567106	1567106	type	True	76.5994	68	1928	95	below_threshold
Paenibacillus oenotherae	strain=DT7-4	GCA_019443105.1	1435645	1435645	type	True	76.5358	66	1928	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:51:55,833] [INFO] DFAST Taxonomy check result was written to GCF_007786455.1_ASM778645v1_genomic.fna/tc_result.tsv
[2024-01-24 11:51:55,835] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:51:55,835] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:51:55,835] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0d0bc8b9-280b-4670-8de9-dd0fea254372/dqc_reference/checkm_data
[2024-01-24 11:51:55,836] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:51:55,894] [INFO] Task started: CheckM
[2024-01-24 11:51:55,894] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007786455.1_ASM778645v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007786455.1_ASM778645v1_genomic.fna/checkm_input GCF_007786455.1_ASM778645v1_genomic.fna/checkm_result
[2024-01-24 11:52:41,168] [INFO] Task succeeded: CheckM
[2024-01-24 11:52:41,170] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:52:41,189] [INFO] ===== Completeness check finished =====
[2024-01-24 11:52:41,189] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:52:41,189] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007786455.1_ASM778645v1_genomic.fna/markers.fasta)
[2024-01-24 11:52:41,190] [INFO] Task started: Blastn
[2024-01-24 11:52:41,190] [INFO] Running command: blastn -query GCF_007786455.1_ASM778645v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0d0bc8b9-280b-4670-8de9-dd0fea254372/dqc_reference/reference_markers_gtdb.fasta -out GCF_007786455.1_ASM778645v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:52:41,929] [INFO] Task succeeded: Blastn
[2024-01-24 11:52:41,932] [INFO] Selected 20 target genomes.
[2024-01-24 11:52:41,932] [INFO] Target genome list was writen to GCF_007786455.1_ASM778645v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:52:41,945] [INFO] Task started: fastANI
[2024-01-24 11:52:41,945] [INFO] Running command: fastANI --query /var/lib/cwl/stg84d2ba8f-0214-4584-bba4-4fbf0bdd5e5b/GCF_007786455.1_ASM778645v1_genomic.fna.gz --refList GCF_007786455.1_ASM778645v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007786455.1_ASM778645v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:53:02,313] [INFO] Task succeeded: fastANI
[2024-01-24 11:53:02,327] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:53:02,328] [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_007786455.1	s__Paenibacillus_B sp007786455	100.0	1928	1928	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_B	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014841135.1	s__Paenibacillus_B sp014841135	88.6241	1476	1928	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000422445.1	s__Paenibacillus_B assamensis	88.3072	1460	1928	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018403065.1	s__Paenibacillus_B dendritiformis_B	79.3877	117	1928	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000293805.1	s__Paenibacillus_B alvei	79.0688	206	1928	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_B	95.0	97.68	97.62	0.90	0.89	5	-
GCF_000425125.1	s__Paenibacillus_B taiwanensis	78.444	220	1928	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001894745.1	s__Paenibacillus_B sp001894745	77.9536	204	1928	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_B	95.0	96.43	95.29	0.89	0.85	9	-
GCF_015558675.1	s__Paenibacillus_B sp015558675	77.7838	191	1928	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014192105.1	s__Paenibacillus_Z phyllosphaerae	77.5487	53	1928	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_Z	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017052585.1	s__Paenibacillus_B apiarius	77.3842	168	1928	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_B	95.0	98.54	98.54	0.95	0.95	2	-
GCF_018310695.1	s__Paenibacillus sp018310695	77.3149	76	1928	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004916975.1	s__Paenibacillus dokdonensis	77.308	60	1928	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000374845.1	s__Paenibacillus_K terrigena	77.2659	111	1928	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_K	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000426545.1	s__Paenibacillus panacisoli	77.0653	63	1928	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	96.1083	98.22	98.22	0.93	0.93	2	-
GCF_003268025.1	s__Paenibacillus_Z montanisoli	77.0303	55	1928	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_Z	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001721045.1	s__Paenibacillus_J nuruki	76.9724	59	1928	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_J	95.0	98.40	98.40	0.93	0.93	2	-
GCF_900112695.1	s__Paenibacillus_C catalpae	76.8725	61	1928	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000971985.1	s__Paenibacillus_J dauci	76.7296	69	1928	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_J	95.0	97.87	97.87	0.93	0.93	2	-
--------------------------------------------------------------------------------
[2024-01-24 11:53:02,329] [INFO] GTDB search result was written to GCF_007786455.1_ASM778645v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:53:02,330] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:53:02,333] [INFO] DFAST_QC result json was written to GCF_007786455.1_ASM778645v1_genomic.fna/dqc_result.json
[2024-01-24 11:53:02,333] [INFO] DFAST_QC completed!
[2024-01-24 11:53:02,333] [INFO] Total running time: 0h1m51s