[2024-01-24 12:31:33,185] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:31:33,186] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:31:33,186] [INFO] DQC Reference Directory: /var/lib/cwl/stg1d4ee154-b13f-4e15-961b-80765a55495c/dqc_reference
[2024-01-24 12:31:34,347] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:31:34,347] [INFO] Task started: Prodigal
[2024-01-24 12:31:34,348] [INFO] Running command: gunzip -c /var/lib/cwl/stgab67fb41-2d1f-44ff-b7d3-1e399baae463/GCF_004307995.1_ASM430799v1_genomic.fna.gz | prodigal -d GCF_004307995.1_ASM430799v1_genomic.fna/cds.fna -a GCF_004307995.1_ASM430799v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:31:57,869] [INFO] Task succeeded: Prodigal
[2024-01-24 12:31:57,870] [INFO] Task started: HMMsearch
[2024-01-24 12:31:57,870] [INFO] Running command: hmmsearch --tblout GCF_004307995.1_ASM430799v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1d4ee154-b13f-4e15-961b-80765a55495c/dqc_reference/reference_markers.hmm GCF_004307995.1_ASM430799v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:31:58,195] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:31:58,198] [INFO] Found 6/6 markers.
[2024-01-24 12:31:58,263] [INFO] Query marker FASTA was written to GCF_004307995.1_ASM430799v1_genomic.fna/markers.fasta
[2024-01-24 12:31:58,264] [INFO] Task started: Blastn
[2024-01-24 12:31:58,264] [INFO] Running command: blastn -query GCF_004307995.1_ASM430799v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1d4ee154-b13f-4e15-961b-80765a55495c/dqc_reference/reference_markers.fasta -out GCF_004307995.1_ASM430799v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:31:58,819] [INFO] Task succeeded: Blastn
[2024-01-24 12:31:58,822] [INFO] Selected 23 target genomes.
[2024-01-24 12:31:58,822] [INFO] Target genome list was writen to GCF_004307995.1_ASM430799v1_genomic.fna/target_genomes.txt
[2024-01-24 12:31:58,828] [INFO] Task started: fastANI
[2024-01-24 12:31:58,828] [INFO] Running command: fastANI --query /var/lib/cwl/stgab67fb41-2d1f-44ff-b7d3-1e399baae463/GCF_004307995.1_ASM430799v1_genomic.fna.gz --refList GCF_004307995.1_ASM430799v1_genomic.fna/target_genomes.txt --output GCF_004307995.1_ASM430799v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:32:26,120] [INFO] Task succeeded: fastANI
[2024-01-24 12:32:26,121] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1d4ee154-b13f-4e15-961b-80765a55495c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:32:26,121] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1d4ee154-b13f-4e15-961b-80765a55495c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:32:26,133] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:32:26,133] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:32:26,133] [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 thalictri	strain=N2SHLJ1	GCA_004307995.1	2527873	2527873	type	True	100.0	3093	3098	95	conclusive
Paenibacillus piri	strain=MS74	GCA_004354045.1	2547395	2547395	type	True	77.7034	458	3098	95	below_threshold
Paenibacillus periandrae	strain=PM10	GCA_022458865.1	1761741	1761741	type	True	77.4804	232	3098	95	below_threshold
Paenibacillus doosanensis	strain=CAU 1055	GCA_025060755.1	1229154	1229154	type	True	77.422	432	3098	95	below_threshold
Paenibacillus allorhizosphaerae	strain=CIP 111802	GCA_910594985.1	2849866	2849866	type	True	77.3739	334	3098	95	below_threshold
Paenibacillus tyrfis	strain=MSt1	GCA_000722545.1	1501230	1501230	type	True	77.2892	287	3098	95	below_threshold
Paenibacillus beijingensis	strain=DSM 24997	GCA_000961095.1	1126833	1126833	type	True	77.1355	134	3098	95	below_threshold
Paenibacillus validus	strain=NBRC 15382	GCA_004000985.1	44253	44253	type	True	77.0811	238	3098	95	below_threshold
Paenibacillus elgii	strain=NBRC 100335	GCA_004000865.1	189691	189691	type	True	77.0401	290	3098	95	below_threshold
Paenibacillus ginsengarvi	strain=KCTC 13059	GCA_003626695.1	400777	400777	type	True	76.9489	244	3098	95	below_threshold
Paenibacillus athensensis	strain=MEC069	GCA_004514475.2	1967502	1967502	type	True	76.9282	233	3098	95	below_threshold
Paenibacillus protaetiae	strain=FW100M-2	GCA_004135365.1	2509456	2509456	type	True	76.8721	155	3098	95	below_threshold
Paenibacillus ehimensis	strain=NBRC 15659	GCA_004000785.1	79264	79264	type	True	76.7836	308	3098	95	below_threshold
Paenibacillus puerhi	strain=SJY2	GCA_009846885.1	2692622	2692622	type	True	76.6778	223	3098	95	below_threshold
Paenibacillus oceani	strain=IB182363	GCA_014705615.1	2772510	2772510	type	True	76.6308	206	3098	95	below_threshold
Paenibacillus albicereus	strain=UniB2	GCA_012676905.1	2726185	2726185	type	True	76.5375	105	3098	95	below_threshold
Paenibacillus lautus	strain=NBRC 15380	GCA_004000945.1	1401	1401	suspected-type	True	76.4932	118	3098	95	below_threshold
Paenibacillus cymbidii	strain=R196	GCA_004764705.1	1639034	1639034	type	True	76.453	274	3098	95	below_threshold
Paenibacillus caui	strain=81-11	GCA_019904135.1	2873927	2873927	type	True	76.4214	103	3098	95	below_threshold
Paenibacillus macerans	strain=ATCC 8244	GCA_000746875.1	44252	44252	type	True	76.1938	165	3098	95	below_threshold
Paenibacillus sinensis	strain=HN-1	GCA_019904155.1	2834413	2834413	type	True	76.0218	98	3098	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:32:26,134] [INFO] DFAST Taxonomy check result was written to GCF_004307995.1_ASM430799v1_genomic.fna/tc_result.tsv
[2024-01-24 12:32:26,135] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:32:26,135] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:32:26,135] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1d4ee154-b13f-4e15-961b-80765a55495c/dqc_reference/checkm_data
[2024-01-24 12:32:26,136] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:32:26,219] [INFO] Task started: CheckM
[2024-01-24 12:32:26,219] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004307995.1_ASM430799v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004307995.1_ASM430799v1_genomic.fna/checkm_input GCF_004307995.1_ASM430799v1_genomic.fna/checkm_result
[2024-01-24 12:33:29,959] [INFO] Task succeeded: CheckM
[2024-01-24 12:33:29,960] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:33:29,982] [INFO] ===== Completeness check finished =====
[2024-01-24 12:33:29,982] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:33:29,982] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004307995.1_ASM430799v1_genomic.fna/markers.fasta)
[2024-01-24 12:33:29,983] [INFO] Task started: Blastn
[2024-01-24 12:33:29,983] [INFO] Running command: blastn -query GCF_004307995.1_ASM430799v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1d4ee154-b13f-4e15-961b-80765a55495c/dqc_reference/reference_markers_gtdb.fasta -out GCF_004307995.1_ASM430799v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:33:30,717] [INFO] Task succeeded: Blastn
[2024-01-24 12:33:30,719] [INFO] Selected 22 target genomes.
[2024-01-24 12:33:30,719] [INFO] Target genome list was writen to GCF_004307995.1_ASM430799v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:33:30,730] [INFO] Task started: fastANI
[2024-01-24 12:33:30,730] [INFO] Running command: fastANI --query /var/lib/cwl/stgab67fb41-2d1f-44ff-b7d3-1e399baae463/GCF_004307995.1_ASM430799v1_genomic.fna.gz --refList GCF_004307995.1_ASM430799v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004307995.1_ASM430799v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:33:58,069] [INFO] Task succeeded: fastANI
[2024-01-24 12:33:58,081] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:33:58,082] [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_004307995.1	s__Paenibacillus_AF thalictri	100.0	3093	3098	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_AF	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_004354045.1	s__Paenibacillus_S piri	77.7217	456	3098	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_S	95.0	N/A	N/A	N/A	N/A	1	-
GCF_910593845.1	s__Paenibacillus_G solanacearum	77.4289	358	3098	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_G	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001399685.1	s__Paenibacillus_G sp001399685	77.3906	264	3098	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_G	95.0	N/A	N/A	N/A	N/A	1	-
GCF_910594985.1	s__Paenibacillus_G sp910594985	77.385	332	3098	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_G	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000722545.1	s__Paenibacillus_G tyrfis	77.2898	287	3098	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_G	95.0	98.07	98.07	0.93	0.93	2	-
GCF_900100345.1	s__Paenibacillus_G tianmuensis	77.2227	256	3098	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_G	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002042965.1	s__Paenibacillus_S sp002042965	77.1688	275	3098	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_S	95.0	97.63	97.63	0.93	0.93	2	-
GCF_900101595.1	s__Paenibacillus_G sp900101595	77.1107	265	3098	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_G	95.0	100.00	100.00	0.99	0.99	2	-
GCF_004000985.1	s__Paenibacillus_G validus	77.0688	240	3098	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_G	95.0	99.29	99.15	0.90	0.89	6	-
GCF_000961095.1	s__Paenibacillus_O beijingensis	77.054	135	3098	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_O	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004000865.1	s__Paenibacillus_G elgii	77.0415	290	3098	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_G	95.0	97.83	95.93	0.93	0.85	6	-
GCF_003626695.1	s__Paenibacillus_AB ginsengarvi	76.953	244	3098	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	-
GCF_004135365.1	s__Paenibacillus_C protaetiae	76.8718	155	3098	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_003285015.1	s__Paenibacillus_V contaminans	76.8668	253	3098	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_V	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004000785.1	s__Paenibacillus_G ehimensis	76.8051	305	3098	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_G	95.0	99.10	99.10	0.93	0.93	2	-
GCF_009846885.1	s__Paenibacillus_G puerhi	76.6902	221	3098	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_G	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014705615.1	s__Paenibacillus_AB sp014705615	76.6321	204	3098	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	-
GCF_004000945.1	s__Paenibacillus lautus	76.5439	115	3098	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	96.53	96.53	0.89	0.89	2	-
GCF_004764705.1	s__R196 sp004764705	76.4611	273	3098	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__R196	95.0	95.77	95.77	0.86	0.86	2	-
GCF_015326965.1	s__Paenibacillus sp001860525	76.4514	135	3098	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	96.48	95.93	0.88	0.85	4	-
GCF_900111565.1	s__Paenibacillus sp900111565	76.1983	133	3098	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 12:33:58,084] [INFO] GTDB search result was written to GCF_004307995.1_ASM430799v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:33:58,084] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:33:58,087] [INFO] DFAST_QC result json was written to GCF_004307995.1_ASM430799v1_genomic.fna/dqc_result.json
[2024-01-24 12:33:58,088] [INFO] DFAST_QC completed!
[2024-01-24 12:33:58,088] [INFO] Total running time: 0h2m25s