[2024-01-25 18:51:35,742] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:51:35,743] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:51:35,743] [INFO] DQC Reference Directory: /var/lib/cwl/stg5f18f8e8-4198-4f60-ae4b-f9cba0b007fc/dqc_reference
[2024-01-25 18:51:36,860] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:51:36,860] [INFO] Task started: Prodigal
[2024-01-25 18:51:36,860] [INFO] Running command: gunzip -c /var/lib/cwl/stg39d64720-00d7-4c63-8eec-95751d9b48c1/GCF_009846885.1_ASM984688v1_genomic.fna.gz | prodigal -d GCF_009846885.1_ASM984688v1_genomic.fna/cds.fna -a GCF_009846885.1_ASM984688v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:51:55,496] [INFO] Task succeeded: Prodigal
[2024-01-25 18:51:55,496] [INFO] Task started: HMMsearch
[2024-01-25 18:51:55,496] [INFO] Running command: hmmsearch --tblout GCF_009846885.1_ASM984688v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5f18f8e8-4198-4f60-ae4b-f9cba0b007fc/dqc_reference/reference_markers.hmm GCF_009846885.1_ASM984688v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:51:55,846] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:51:55,847] [INFO] Found 6/6 markers.
[2024-01-25 18:51:55,900] [INFO] Query marker FASTA was written to GCF_009846885.1_ASM984688v1_genomic.fna/markers.fasta
[2024-01-25 18:51:55,901] [INFO] Task started: Blastn
[2024-01-25 18:51:55,901] [INFO] Running command: blastn -query GCF_009846885.1_ASM984688v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5f18f8e8-4198-4f60-ae4b-f9cba0b007fc/dqc_reference/reference_markers.fasta -out GCF_009846885.1_ASM984688v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:51:56,472] [INFO] Task succeeded: Blastn
[2024-01-25 18:51:56,475] [INFO] Selected 20 target genomes.
[2024-01-25 18:51:56,475] [INFO] Target genome list was writen to GCF_009846885.1_ASM984688v1_genomic.fna/target_genomes.txt
[2024-01-25 18:51:56,487] [INFO] Task started: fastANI
[2024-01-25 18:51:56,487] [INFO] Running command: fastANI --query /var/lib/cwl/stg39d64720-00d7-4c63-8eec-95751d9b48c1/GCF_009846885.1_ASM984688v1_genomic.fna.gz --refList GCF_009846885.1_ASM984688v1_genomic.fna/target_genomes.txt --output GCF_009846885.1_ASM984688v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:52:17,314] [INFO] Task succeeded: fastANI
[2024-01-25 18:52:17,315] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5f18f8e8-4198-4f60-ae4b-f9cba0b007fc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:52:17,316] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5f18f8e8-4198-4f60-ae4b-f9cba0b007fc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:52:17,327] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:52:17,328] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:52:17,328] [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 puerhi	strain=SJY2	GCA_009846885.1	2692622	2692622	type	True	100.0	2186	2191	95	conclusive
Paenibacillus validus	strain=NBRC 15382	GCA_004000985.1	44253	44253	type	True	78.8555	437	2191	95	below_threshold
Paenibacillus tianmuensis	strain=CGMCC 1.8946	GCA_900100345.1	624147	624147	type	True	78.2143	349	2191	95	below_threshold
Paenibacillus tyrfis	strain=MSt1	GCA_000722545.1	1501230	1501230	type	True	78.171	375	2191	95	below_threshold
Paenibacillus elgii	strain=NBRC 100335	GCA_004000865.1	189691	189691	type	True	78.1168	375	2191	95	below_threshold
Paenibacillus ehimensis	strain=NBRC 15659	GCA_004000785.1	79264	79264	type	True	77.9541	392	2191	95	below_threshold
Paenibacillus doosanensis	strain=CAU 1055	GCA_025060755.1	1229154	1229154	type	True	77.3833	311	2191	95	below_threshold
Paenibacillus ginsengihumi	strain=DSM 21568	GCA_000380965.1	431596	431596	type	True	77.1715	284	2191	95	below_threshold
Paenibacillus beijingensis	strain=DSM 24997	GCA_000961095.1	1126833	1126833	type	True	76.9242	135	2191	95	below_threshold
Paenibacillus lycopersici	strain=12200R-189	GCA_010119935.1	2704462	2704462	type	True	76.8997	175	2191	95	below_threshold
Paenibacillus albicereus	strain=UniB2	GCA_012676905.1	2726185	2726185	type	True	76.8778	156	2191	95	below_threshold
Paenibacillus antri	strain=SYSU K30003	GCA_005765165.1	2582848	2582848	type	True	76.7466	151	2191	95	below_threshold
Paenibacillus nanensis	strain=DSM 22867	GCA_003583765.1	393251	393251	type	True	76.7372	152	2191	95	below_threshold
Paenibacillus oceani	strain=IB182363	GCA_014705615.1	2772510	2772510	type	True	76.7203	196	2191	95	below_threshold
Paenibacillus rhizophilus	strain=7197	GCA_003854965.1	1850366	1850366	type	True	76.6354	98	2191	95	below_threshold
Paenibacillus flagellatus	strain=DXL2	GCA_003217775.1	2211139	2211139	type	True	76.5855	194	2191	95	below_threshold
Paenibacillus algicola	strain=HB172198	GCA_005577435.1	2565926	2565926	type	True	76.4923	83	2191	95	below_threshold
Paenibacillus phocaensis	strain=mt24	GCA_900021165.1	1776378	1776378	type	True	76.4726	103	2191	95	below_threshold
Thermobacillus xylanilyticus	strain=XE	GCA_907165215.1	76633	76633	type	True	76.1757	121	2191	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:52:17,329] [INFO] DFAST Taxonomy check result was written to GCF_009846885.1_ASM984688v1_genomic.fna/tc_result.tsv
[2024-01-25 18:52:17,330] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:52:17,330] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:52:17,330] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5f18f8e8-4198-4f60-ae4b-f9cba0b007fc/dqc_reference/checkm_data
[2024-01-25 18:52:17,331] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:52:17,391] [INFO] Task started: CheckM
[2024-01-25 18:52:17,392] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009846885.1_ASM984688v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009846885.1_ASM984688v1_genomic.fna/checkm_input GCF_009846885.1_ASM984688v1_genomic.fna/checkm_result
[2024-01-25 18:53:10,740] [INFO] Task succeeded: CheckM
[2024-01-25 18:53:10,741] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:53:10,758] [INFO] ===== Completeness check finished =====
[2024-01-25 18:53:10,758] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:53:10,759] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009846885.1_ASM984688v1_genomic.fna/markers.fasta)
[2024-01-25 18:53:10,759] [INFO] Task started: Blastn
[2024-01-25 18:53:10,759] [INFO] Running command: blastn -query GCF_009846885.1_ASM984688v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5f18f8e8-4198-4f60-ae4b-f9cba0b007fc/dqc_reference/reference_markers_gtdb.fasta -out GCF_009846885.1_ASM984688v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:53:11,549] [INFO] Task succeeded: Blastn
[2024-01-25 18:53:11,554] [INFO] Selected 14 target genomes.
[2024-01-25 18:53:11,554] [INFO] Target genome list was writen to GCF_009846885.1_ASM984688v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:53:11,572] [INFO] Task started: fastANI
[2024-01-25 18:53:11,572] [INFO] Running command: fastANI --query /var/lib/cwl/stg39d64720-00d7-4c63-8eec-95751d9b48c1/GCF_009846885.1_ASM984688v1_genomic.fna.gz --refList GCF_009846885.1_ASM984688v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009846885.1_ASM984688v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:53:29,889] [INFO] Task succeeded: fastANI
[2024-01-25 18:53:29,899] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:53:29,900] [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_009846885.1	s__Paenibacillus_G puerhi	100.0	2186	2191	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	conclusive
GCF_900101595.1	s__Paenibacillus_G sp900101595	81.3318	1014	2191	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	78.8547	437	2191	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_001399685.1	s__Paenibacillus_G sp001399685	78.4843	364	2191	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	78.1762	375	2191	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_018998565.1	s__Paenibacillus_G sp018998565	78.0098	394	2191	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_004000785.1	s__Paenibacillus_G ehimensis	77.9624	391	2191	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_910593845.1	s__Paenibacillus_G solanacearum	77.7955	359	2191	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_004354045.1	s__Paenibacillus_S piri	77.718	297	2191	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_000250655.1	s__Paenibacillus_G mucilaginosus	77.6581	423	2191	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_G	95.0	98.86	98.79	0.96	0.95	3	-
GCF_000380965.1	s__Paenibacillus_M ginsengihumi	77.1442	287	2191	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_M	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010119935.1	s__Paenibacillus_Z lycopersici	76.8873	176	2191	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_015845845.1	s__Paenibacillus_B dendritiformis_C	76.5548	123	2191	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_900021165.1	s__Paenibacillus_A phocaensis	76.4726	103	2191	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_A	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-25 18:53:29,902] [INFO] GTDB search result was written to GCF_009846885.1_ASM984688v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:53:29,903] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:53:29,906] [INFO] DFAST_QC result json was written to GCF_009846885.1_ASM984688v1_genomic.fna/dqc_result.json
[2024-01-25 18:53:29,906] [INFO] DFAST_QC completed!
[2024-01-25 18:53:29,906] [INFO] Total running time: 0h1m54s