[2024-01-25 17:42:20,451] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:42:20,452] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:42:20,452] [INFO] DQC Reference Directory: /var/lib/cwl/stg3f29ed6b-20c1-40cd-8410-df1181218e96/dqc_reference
[2024-01-25 17:42:21,529] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:42:21,530] [INFO] Task started: Prodigal
[2024-01-25 17:42:21,530] [INFO] Running command: gunzip -c /var/lib/cwl/stgee1b0d42-a391-4277-aab6-a10d22c46536/GCF_001421015.2_ASM142101v2_genomic.fna.gz | prodigal -d GCF_001421015.2_ASM142101v2_genomic.fna/cds.fna -a GCF_001421015.2_ASM142101v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:42:36,627] [INFO] Task succeeded: Prodigal
[2024-01-25 17:42:36,627] [INFO] Task started: HMMsearch
[2024-01-25 17:42:36,628] [INFO] Running command: hmmsearch --tblout GCF_001421015.2_ASM142101v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3f29ed6b-20c1-40cd-8410-df1181218e96/dqc_reference/reference_markers.hmm GCF_001421015.2_ASM142101v2_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:42:36,911] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:42:36,912] [INFO] Found 6/6 markers.
[2024-01-25 17:42:36,953] [INFO] Query marker FASTA was written to GCF_001421015.2_ASM142101v2_genomic.fna/markers.fasta
[2024-01-25 17:42:36,953] [INFO] Task started: Blastn
[2024-01-25 17:42:36,953] [INFO] Running command: blastn -query GCF_001421015.2_ASM142101v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg3f29ed6b-20c1-40cd-8410-df1181218e96/dqc_reference/reference_markers.fasta -out GCF_001421015.2_ASM142101v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:42:37,513] [INFO] Task succeeded: Blastn
[2024-01-25 17:42:37,517] [INFO] Selected 15 target genomes.
[2024-01-25 17:42:37,517] [INFO] Target genome list was writen to GCF_001421015.2_ASM142101v2_genomic.fna/target_genomes.txt
[2024-01-25 17:42:37,528] [INFO] Task started: fastANI
[2024-01-25 17:42:37,528] [INFO] Running command: fastANI --query /var/lib/cwl/stgee1b0d42-a391-4277-aab6-a10d22c46536/GCF_001421015.2_ASM142101v2_genomic.fna.gz --refList GCF_001421015.2_ASM142101v2_genomic.fna/target_genomes.txt --output GCF_001421015.2_ASM142101v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:42:52,961] [INFO] Task succeeded: fastANI
[2024-01-25 17:42:52,962] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3f29ed6b-20c1-40cd-8410-df1181218e96/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:42:52,962] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3f29ed6b-20c1-40cd-8410-df1181218e96/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:42:52,970] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:42:52,971] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:42:52,971] [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 bovis	strain=BD3526	GCA_001421015.2	1616788	1616788	type	True	100.0	1838	1838	95	conclusive
Paenibacillus dauci	strain=H9	GCA_000971985.1	1567106	1567106	type	True	89.3002	1592	1838	95	below_threshold
Paenibacillus wulumuqiensis	strain=Y24	GCA_000971965.1	1567107	1567107	type	True	85.3777	1449	1838	95	below_threshold
Paenibacillus hunanensis	strain=CGMCC 1.8907	GCA_014645615.1	539262	539262	type	True	79.1907	693	1838	95	below_threshold
Paenibacillus nuruki	strain=TI45-13ar	GCA_001721045.1	1886670	1886670	type	True	77.9702	388	1838	95	below_threshold
Paenibacillus silvae	strain=CGMCC 1.12770	GCA_014639235.1	1325358	1325358	type	True	77.3607	162	1838	95	below_threshold
Paenibacillus gallinarum	strain=Sa2BVA9	GCA_014836635.1	2762232	2762232	type	True	77.1655	90	1838	95	below_threshold
Paenibacillus typhae	strain=CGMCC 1.11012	GCA_900099765.1	1174501	1174501	type	True	76.9994	132	1838	95	below_threshold
Paenibacillus lemnae	strain=L7-75	GCA_012933385.1	1330551	1330551	type	True	76.9419	124	1838	95	below_threshold
Paenibacillus tengchongensis	strain=SYSU G01003	GCA_008973665.1	2608684	2608684	type	True	76.9133	122	1838	95	below_threshold
Paenibacillus maysiensis	strain=1-49	GCA_000520815.1	1155954	1155954	type	True	76.8656	132	1838	95	below_threshold
Paenibacillus periandrae	strain=PM10	GCA_022458865.1	1761741	1761741	type	True	75.8173	68	1838	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:42:52,972] [INFO] DFAST Taxonomy check result was written to GCF_001421015.2_ASM142101v2_genomic.fna/tc_result.tsv
[2024-01-25 17:42:52,973] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:42:52,973] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:42:52,973] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3f29ed6b-20c1-40cd-8410-df1181218e96/dqc_reference/checkm_data
[2024-01-25 17:42:52,974] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:42:53,028] [INFO] Task started: CheckM
[2024-01-25 17:42:53,028] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001421015.2_ASM142101v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001421015.2_ASM142101v2_genomic.fna/checkm_input GCF_001421015.2_ASM142101v2_genomic.fna/checkm_result
[2024-01-25 17:43:38,793] [INFO] Task succeeded: CheckM
[2024-01-25 17:43:38,794] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:43:38,811] [INFO] ===== Completeness check finished =====
[2024-01-25 17:43:38,811] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:43:38,811] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001421015.2_ASM142101v2_genomic.fna/markers.fasta)
[2024-01-25 17:43:38,811] [INFO] Task started: Blastn
[2024-01-25 17:43:38,811] [INFO] Running command: blastn -query GCF_001421015.2_ASM142101v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg3f29ed6b-20c1-40cd-8410-df1181218e96/dqc_reference/reference_markers_gtdb.fasta -out GCF_001421015.2_ASM142101v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:43:39,582] [INFO] Task succeeded: Blastn
[2024-01-25 17:43:39,586] [INFO] Selected 10 target genomes.
[2024-01-25 17:43:39,586] [INFO] Target genome list was writen to GCF_001421015.2_ASM142101v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:43:39,595] [INFO] Task started: fastANI
[2024-01-25 17:43:39,595] [INFO] Running command: fastANI --query /var/lib/cwl/stgee1b0d42-a391-4277-aab6-a10d22c46536/GCF_001421015.2_ASM142101v2_genomic.fna.gz --refList GCF_001421015.2_ASM142101v2_genomic.fna/target_genomes_gtdb.txt --output GCF_001421015.2_ASM142101v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:43:50,798] [INFO] Task succeeded: fastANI
[2024-01-25 17:43:50,805] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:43:50,805] [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_001421015.2	s__Paenibacillus_J bovis	100.0	1838	1838	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_J	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000971985.1	s__Paenibacillus_J dauci	89.2957	1593	1838	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_J	95.0	97.87	97.87	0.93	0.93	2	-
GCF_000971965.1	s__Paenibacillus_J wulumuqiensis	85.3777	1449	1838	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_J	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014645615.1	s__Paenibacillus_J hunanensis	79.184	694	1838	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_J	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001721045.1	s__Paenibacillus_J nuruki	77.9702	388	1838	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_014639235.1	s__Paenibacillus silvae	77.3848	164	1838	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	96.52	95.24	0.88	0.86	5	-
GCF_900099765.1	s__Paenibacillus typhae	77.0222	133	1838	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	98.38	98.38	0.94	0.94	2	-
GCF_012933385.1	s__Paenibacillus lemnae	76.9865	124	1838	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008973665.1	s__Paenibacillus tengchongensis	76.9133	122	1838	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000520815.1	s__Paenibacillus maysiensis	76.852	134	1838	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	95.32	95.30	0.82	0.80	4	-
--------------------------------------------------------------------------------
[2024-01-25 17:43:50,806] [INFO] GTDB search result was written to GCF_001421015.2_ASM142101v2_genomic.fna/result_gtdb.tsv
[2024-01-25 17:43:50,807] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:43:50,809] [INFO] DFAST_QC result json was written to GCF_001421015.2_ASM142101v2_genomic.fna/dqc_result.json
[2024-01-25 17:43:50,810] [INFO] DFAST_QC completed!
[2024-01-25 17:43:50,810] [INFO] Total running time: 0h1m30s