[2024-01-24 13:12:54,982] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:12:54,984] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:12:54,984] [INFO] DQC Reference Directory: /var/lib/cwl/stg0e4ec290-0384-4722-818b-87e557c93c09/dqc_reference
[2024-01-24 13:12:56,451] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:12:56,452] [INFO] Task started: Prodigal
[2024-01-24 13:12:56,452] [INFO] Running command: gunzip -c /var/lib/cwl/stg44f12bda-7134-409f-b2d9-160add4c54ca/GCF_000971985.1_ASM97198v1_genomic.fna.gz | prodigal -d GCF_000971985.1_ASM97198v1_genomic.fna/cds.fna -a GCF_000971985.1_ASM97198v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:13:10,722] [INFO] Task succeeded: Prodigal
[2024-01-24 13:13:10,722] [INFO] Task started: HMMsearch
[2024-01-24 13:13:10,722] [INFO] Running command: hmmsearch --tblout GCF_000971985.1_ASM97198v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0e4ec290-0384-4722-818b-87e557c93c09/dqc_reference/reference_markers.hmm GCF_000971985.1_ASM97198v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:13:11,038] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:13:11,039] [INFO] Found 6/6 markers.
[2024-01-24 13:13:11,083] [INFO] Query marker FASTA was written to GCF_000971985.1_ASM97198v1_genomic.fna/markers.fasta
[2024-01-24 13:13:11,084] [INFO] Task started: Blastn
[2024-01-24 13:13:11,084] [INFO] Running command: blastn -query GCF_000971985.1_ASM97198v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0e4ec290-0384-4722-818b-87e557c93c09/dqc_reference/reference_markers.fasta -out GCF_000971985.1_ASM97198v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:13:11,713] [INFO] Task succeeded: Blastn
[2024-01-24 13:13:11,717] [INFO] Selected 14 target genomes.
[2024-01-24 13:13:11,718] [INFO] Target genome list was writen to GCF_000971985.1_ASM97198v1_genomic.fna/target_genomes.txt
[2024-01-24 13:13:11,727] [INFO] Task started: fastANI
[2024-01-24 13:13:11,728] [INFO] Running command: fastANI --query /var/lib/cwl/stg44f12bda-7134-409f-b2d9-160add4c54ca/GCF_000971985.1_ASM97198v1_genomic.fna.gz --refList GCF_000971985.1_ASM97198v1_genomic.fna/target_genomes.txt --output GCF_000971985.1_ASM97198v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:13:26,620] [INFO] Task succeeded: fastANI
[2024-01-24 13:13:26,620] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0e4ec290-0384-4722-818b-87e557c93c09/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:13:26,621] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0e4ec290-0384-4722-818b-87e557c93c09/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:13:26,631] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:13:26,631] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:13:26,631] [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 dauci	strain=H9	GCA_000971985.1	1567106	1567106	type	True	100.0	1787	1808	95	conclusive
Paenibacillus bovis	strain=BD3526	GCA_001421015.2	1616788	1616788	type	True	89.3709	1584	1808	95	below_threshold
Paenibacillus wulumuqiensis	strain=Y24	GCA_000971965.1	1567107	1567107	type	True	85.0883	1431	1808	95	below_threshold
Paenibacillus hunanensis	strain=CGMCC 1.8907	GCA_014645615.1	539262	539262	type	True	79.2401	643	1808	95	below_threshold
Paenibacillus nuruki	strain=TI45-13ar	GCA_001721045.1	1886670	1886670	type	True	78.2756	379	1808	95	below_threshold
Paenibacillus kribbensis	strain=AM49	GCA_002240415.1	172713	172713	type	True	77.7738	132	1808	95	below_threshold
Paenibacillus faecalis	strain=Marseille-P3787	GCA_900289175.1	2079532	2079532	type	True	77.3201	93	1808	95	below_threshold
Paenibacillus illinoisensis	strain=NBRC 15959	GCA_004000925.1	59845	59845	type	True	77.0778	159	1808	95	below_threshold
Paenibacillus gallinarum	strain=Sa2BVA9	GCA_014836635.1	2762232	2762232	type	True	77.0322	91	1808	95	below_threshold
Paenibacillus albidus	strain=CGMCC 1.16134	GCA_014644435.1	2041023	2041023	type	True	76.8308	125	1808	95	below_threshold
Paenibacillus periandrae	strain=PM10	GCA_022458865.1	1761741	1761741	type	True	76.2422	59	1808	95	below_threshold
Paenibacillus daejeonensis	strain=DSM 15491	GCA_000378385.1	135193	135193	type	True	76.2341	78	1808	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:13:26,633] [INFO] DFAST Taxonomy check result was written to GCF_000971985.1_ASM97198v1_genomic.fna/tc_result.tsv
[2024-01-24 13:13:26,640] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:13:26,640] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:13:26,641] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0e4ec290-0384-4722-818b-87e557c93c09/dqc_reference/checkm_data
[2024-01-24 13:13:26,642] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:13:26,701] [INFO] Task started: CheckM
[2024-01-24 13:13:26,702] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000971985.1_ASM97198v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000971985.1_ASM97198v1_genomic.fna/checkm_input GCF_000971985.1_ASM97198v1_genomic.fna/checkm_result
[2024-01-24 13:14:13,113] [INFO] Task succeeded: CheckM
[2024-01-24 13:14:13,114] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:14:13,145] [INFO] ===== Completeness check finished =====
[2024-01-24 13:14:13,145] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:14:13,146] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000971985.1_ASM97198v1_genomic.fna/markers.fasta)
[2024-01-24 13:14:13,146] [INFO] Task started: Blastn
[2024-01-24 13:14:13,146] [INFO] Running command: blastn -query GCF_000971985.1_ASM97198v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0e4ec290-0384-4722-818b-87e557c93c09/dqc_reference/reference_markers_gtdb.fasta -out GCF_000971985.1_ASM97198v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:14:13,974] [INFO] Task succeeded: Blastn
[2024-01-24 13:14:13,978] [INFO] Selected 10 target genomes.
[2024-01-24 13:14:13,978] [INFO] Target genome list was writen to GCF_000971985.1_ASM97198v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:14:13,988] [INFO] Task started: fastANI
[2024-01-24 13:14:13,988] [INFO] Running command: fastANI --query /var/lib/cwl/stg44f12bda-7134-409f-b2d9-160add4c54ca/GCF_000971985.1_ASM97198v1_genomic.fna.gz --refList GCF_000971985.1_ASM97198v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000971985.1_ASM97198v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:14:25,880] [INFO] Task succeeded: fastANI
[2024-01-24 13:14:25,895] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:14:25,895] [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_000971985.1	s__Paenibacillus_J dauci	100.0	1787	1808	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_J	95.0	97.87	97.87	0.93	0.93	2	conclusive
GCF_001421015.2	s__Paenibacillus_J bovis	89.3709	1584	1808	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_000971965.1	s__Paenibacillus_J wulumuqiensis	85.0777	1433	1808	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	79.2401	643	1808	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	78.2767	380	1808	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_016908805.1	s__Paenibacillus_J nicotianae	78.0355	389	1808	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_014639235.1	s__Paenibacillus silvae	77.2602	167	1808	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	96.52	95.24	0.88	0.86	5	-
GCF_900116125.1	s__Paenibacillus_Z sp900116125	77.2163	60	1808	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_Z	95.0	95.31	95.31	0.87	0.87	2	-
GCF_004000925.1	s__Paenibacillus illinoisensis	77.0765	159	1808	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	95.55	95.10	0.89	0.77	9	-
GCF_014644435.1	s__Paenibacillus albidus	76.8226	125	1808	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	96.34	96.34	0.80	0.80	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:14:25,897] [INFO] GTDB search result was written to GCF_000971985.1_ASM97198v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:14:25,898] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:14:25,901] [INFO] DFAST_QC result json was written to GCF_000971985.1_ASM97198v1_genomic.fna/dqc_result.json
[2024-01-24 13:14:25,901] [INFO] DFAST_QC completed!
[2024-01-24 13:14:25,901] [INFO] Total running time: 0h1m31s