[2024-01-24 13:32:25,294] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:32:25,296] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:32:25,296] [INFO] DQC Reference Directory: /var/lib/cwl/stg10a01079-9e61-4392-ad43-a29da3efe3f7/dqc_reference
[2024-01-24 13:32:26,619] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:32:26,619] [INFO] Task started: Prodigal
[2024-01-24 13:32:26,620] [INFO] Running command: gunzip -c /var/lib/cwl/stg432e9198-91e9-46c1-9d37-a9e148ec70a7/GCF_002220865.2_ASM222086v2_genomic.fna.gz | prodigal -d GCF_002220865.2_ASM222086v2_genomic.fna/cds.fna -a GCF_002220865.2_ASM222086v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:32:40,354] [INFO] Task succeeded: Prodigal
[2024-01-24 13:32:40,354] [INFO] Task started: HMMsearch
[2024-01-24 13:32:40,354] [INFO] Running command: hmmsearch --tblout GCF_002220865.2_ASM222086v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg10a01079-9e61-4392-ad43-a29da3efe3f7/dqc_reference/reference_markers.hmm GCF_002220865.2_ASM222086v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:32:40,671] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:32:40,673] [INFO] Found 6/6 markers.
[2024-01-24 13:32:40,719] [INFO] Query marker FASTA was written to GCF_002220865.2_ASM222086v2_genomic.fna/markers.fasta
[2024-01-24 13:32:40,719] [INFO] Task started: Blastn
[2024-01-24 13:32:40,719] [INFO] Running command: blastn -query GCF_002220865.2_ASM222086v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg10a01079-9e61-4392-ad43-a29da3efe3f7/dqc_reference/reference_markers.fasta -out GCF_002220865.2_ASM222086v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:41,362] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:41,365] [INFO] Selected 21 target genomes.
[2024-01-24 13:32:41,365] [INFO] Target genome list was writen to GCF_002220865.2_ASM222086v2_genomic.fna/target_genomes.txt
[2024-01-24 13:32:41,393] [INFO] Task started: fastANI
[2024-01-24 13:32:41,393] [INFO] Running command: fastANI --query /var/lib/cwl/stg432e9198-91e9-46c1-9d37-a9e148ec70a7/GCF_002220865.2_ASM222086v2_genomic.fna.gz --refList GCF_002220865.2_ASM222086v2_genomic.fna/target_genomes.txt --output GCF_002220865.2_ASM222086v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:33:05,060] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:05,061] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg10a01079-9e61-4392-ad43-a29da3efe3f7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:33:05,061] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg10a01079-9e61-4392-ad43-a29da3efe3f7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:33:05,079] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:33:05,079] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:33:05,079] [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 xerothermodurans	strain=ATCC 27380	GCA_002220865.2	1977292	1977292	type	True	100.0	1436	1438	95	conclusive
Paenibacillus foliorum	strain=LMG 31456	GCA_013141765.1	2654974	2654974	type	True	78.0676	211	1438	95	below_threshold
Paenibacillus rigui	strain=JCM 16352	GCA_002234615.1	554312	554312	type	True	77.925	210	1438	95	below_threshold
Paenibacillus piri	strain=MS74	GCA_004354045.1	2547395	2547395	type	True	77.9165	275	1438	95	below_threshold
Paenibacillus doosanensis	strain=CAU 1055	GCA_025060755.1	1229154	1229154	type	True	77.6447	241	1438	95	below_threshold
Paenibacillus germinis	strain=LMG 31460	GCA_013141785.1	2654979	2654979	type	True	77.4023	66	1438	95	below_threshold
Paenibacillus phytorum	strain=LMG 31458	GCA_013141715.1	2654977	2654977	type	True	77.3252	65	1438	95	below_threshold
Paenibacillus ehimensis	strain=NBRC 15659	GCA_004000785.1	79264	79264	type	True	77.2418	144	1438	95	below_threshold
Paenibacillus allorhizosphaerae	strain=CIP 111802	GCA_910594985.1	2849866	2849866	type	True	77.1866	163	1438	95	below_threshold
Paenibacillus tyrfis	strain=MSt1	GCA_000722545.1	1501230	1501230	type	True	77.1472	166	1438	95	below_threshold
Paenibacillus naphthalenovorans	strain=PR-N1	GCA_900099895.1	162209	162209	type	True	77.1089	134	1438	95	below_threshold
Paenibacillus elgii	strain=NBRC 100335	GCA_004000865.1	189691	189691	type	True	77.0055	167	1438	95	below_threshold
Paenibacillus macerans	strain=ATCC 8244	GCA_000746875.1	44252	44252	type	True	76.6485	62	1438	95	below_threshold
Paenibacillus timonensis	strain=DSM 16943	GCA_022427145.1	225915	225915	type	True	76.3314	54	1438	95	below_threshold
Paenibacillus oceani	strain=IB182363	GCA_014705615.1	2772510	2772510	type	True	76.2829	66	1438	95	below_threshold
Paenibacillus darwinianus	strain=Br	GCA_000598065.1	1380763	1380763	type	True	76.1494	50	1438	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:33:05,081] [INFO] DFAST Taxonomy check result was written to GCF_002220865.2_ASM222086v2_genomic.fna/tc_result.tsv
[2024-01-24 13:33:05,081] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:33:05,081] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:33:05,081] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg10a01079-9e61-4392-ad43-a29da3efe3f7/dqc_reference/checkm_data
[2024-01-24 13:33:05,082] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:33:05,125] [INFO] Task started: CheckM
[2024-01-24 13:33:05,126] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002220865.2_ASM222086v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002220865.2_ASM222086v2_genomic.fna/checkm_input GCF_002220865.2_ASM222086v2_genomic.fna/checkm_result
[2024-01-24 13:33:51,228] [INFO] Task succeeded: CheckM
[2024-01-24 13:33:51,230] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:33:51,246] [INFO] ===== Completeness check finished =====
[2024-01-24 13:33:51,247] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:33:51,247] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002220865.2_ASM222086v2_genomic.fna/markers.fasta)
[2024-01-24 13:33:51,248] [INFO] Task started: Blastn
[2024-01-24 13:33:51,248] [INFO] Running command: blastn -query GCF_002220865.2_ASM222086v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg10a01079-9e61-4392-ad43-a29da3efe3f7/dqc_reference/reference_markers_gtdb.fasta -out GCF_002220865.2_ASM222086v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:33:52,021] [INFO] Task succeeded: Blastn
[2024-01-24 13:33:52,025] [INFO] Selected 21 target genomes.
[2024-01-24 13:33:52,026] [INFO] Target genome list was writen to GCF_002220865.2_ASM222086v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:33:52,043] [INFO] Task started: fastANI
[2024-01-24 13:33:52,044] [INFO] Running command: fastANI --query /var/lib/cwl/stg432e9198-91e9-46c1-9d37-a9e148ec70a7/GCF_002220865.2_ASM222086v2_genomic.fna.gz --refList GCF_002220865.2_ASM222086v2_genomic.fna/target_genomes_gtdb.txt --output GCF_002220865.2_ASM222086v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:34:18,933] [INFO] Task succeeded: fastANI
[2024-01-24 13:34:18,951] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:34:18,952] [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_002220865.2	s__Paenibacillus_S xerothermodurans	100.0	1436	1438	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	conclusive
GCF_013141765.1	s__Paenibacillus_S foliorum	78.0604	212	1438	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_004354045.1	s__Paenibacillus_S piri	77.9142	274	1438	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_002234615.1	s__Paenibacillus_S rigui	77.9022	212	1438	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_002042965.1	s__Paenibacillus_S sp002042965	77.7981	204	1438	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_017833255.1	s__Paenibacillus_G sp017833255	77.5088	126	1438	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_G	95.0	100.00	100.00	1.00	1.00	3	-
GCF_003955665.1	s__Paenibacillus_E whitsoniae	77.4519	77	1438	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_910593845.1	s__Paenibacillus_G solanacearum	77.3512	136	1438	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_900101595.1	s__Paenibacillus_G sp900101595	77.3431	125	1438	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_001399685.1	s__Paenibacillus_G sp001399685	77.2884	150	1438	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_004000985.1	s__Paenibacillus_G validus	77.2761	134	1438	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_004000785.1	s__Paenibacillus_G ehimensis	77.2418	144	1438	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_018998565.1	s__Paenibacillus_G sp018998565	77.2219	156	1438	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	77.2039	162	1438	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_900099895.1	s__Paenibacillus_G naphthalenovorans	77.0762	134	1438	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_G	95.0	99.27	98.99	0.91	0.86	5	-
GCF_004000865.1	s__Paenibacillus_G elgii	77.0055	167	1438	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_000380965.1	s__Paenibacillus_M ginsengihumi	76.6777	121	1438	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_000829455.1	s__VKM-B-2647 sp000829455	76.4888	76	1438	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__VKM-B-2647	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:34:18,954] [INFO] GTDB search result was written to GCF_002220865.2_ASM222086v2_genomic.fna/result_gtdb.tsv
[2024-01-24 13:34:18,954] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:34:18,959] [INFO] DFAST_QC result json was written to GCF_002220865.2_ASM222086v2_genomic.fna/dqc_result.json
[2024-01-24 13:34:18,959] [INFO] DFAST_QC completed!
[2024-01-24 13:34:18,959] [INFO] Total running time: 0h1m54s