[2024-01-24 13:01:38,475] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:01:38,481] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:01:38,482] [INFO] DQC Reference Directory: /var/lib/cwl/stg5394885e-bd6a-41e9-8b12-cdb494f59b4c/dqc_reference
[2024-01-24 13:01:40,901] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:01:40,902] [INFO] Task started: Prodigal
[2024-01-24 13:01:40,902] [INFO] Running command: gunzip -c /var/lib/cwl/stg58e68a89-92d5-4bda-b6ff-4e21bd845738/GCF_000285515.1_ASM28551v1_genomic.fna.gz | prodigal -d GCF_000285515.1_ASM28551v1_genomic.fna/cds.fna -a GCF_000285515.1_ASM28551v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:01:55,171] [INFO] Task succeeded: Prodigal
[2024-01-24 13:01:55,171] [INFO] Task started: HMMsearch
[2024-01-24 13:01:55,171] [INFO] Running command: hmmsearch --tblout GCF_000285515.1_ASM28551v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5394885e-bd6a-41e9-8b12-cdb494f59b4c/dqc_reference/reference_markers.hmm GCF_000285515.1_ASM28551v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:01:55,573] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:01:55,575] [INFO] Found 6/6 markers.
[2024-01-24 13:01:55,647] [INFO] Query marker FASTA was written to GCF_000285515.1_ASM28551v1_genomic.fna/markers.fasta
[2024-01-24 13:01:55,647] [INFO] Task started: Blastn
[2024-01-24 13:01:55,651] [INFO] Running command: blastn -query GCF_000285515.1_ASM28551v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5394885e-bd6a-41e9-8b12-cdb494f59b4c/dqc_reference/reference_markers.fasta -out GCF_000285515.1_ASM28551v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:01:56,422] [INFO] Task succeeded: Blastn
[2024-01-24 13:01:56,426] [INFO] Selected 27 target genomes.
[2024-01-24 13:01:56,427] [INFO] Target genome list was writen to GCF_000285515.1_ASM28551v1_genomic.fna/target_genomes.txt
[2024-01-24 13:01:56,441] [INFO] Task started: fastANI
[2024-01-24 13:01:56,441] [INFO] Running command: fastANI --query /var/lib/cwl/stg58e68a89-92d5-4bda-b6ff-4e21bd845738/GCF_000285515.1_ASM28551v1_genomic.fna.gz --refList GCF_000285515.1_ASM28551v1_genomic.fna/target_genomes.txt --output GCF_000285515.1_ASM28551v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:02:22,934] [INFO] Task succeeded: fastANI
[2024-01-24 13:02:22,935] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5394885e-bd6a-41e9-8b12-cdb494f59b4c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:02:22,935] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5394885e-bd6a-41e9-8b12-cdb494f59b4c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:02:22,950] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:02:22,950] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:02:22,950] [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 senegalensis	strain=type strain: JC66	GCA_000285515.1	1465766	1465766	type	True	99.9998	1834	1847	95	conclusive
Paenibacillus ihumii	strain=AT5	GCA_001403875.1	687436	687436	type	True	79.0364	81	1847	95	below_threshold
Paenibacillus macerans	strain=NCTC6355	GCA_900454495.1	44252	44252	type	True	78.9191	73	1847	95	below_threshold
Paenibacillus macerans	strain=NBRC 15307	GCA_004000965.1	44252	44252	type	True	78.9078	72	1847	95	below_threshold
Paenibacillus macerans	strain=ATCC 8244	GCA_000746875.1	44252	44252	type	True	78.7692	76	1847	95	below_threshold
Paenibacillus oenotherae	strain=DT7-4	GCA_019443105.1	1435645	1435645	type	True	76.303	60	1847	95	below_threshold
Paenibacillus naphthalenovorans	strain=PR-N1	GCA_900099895.1	162209	162209	type	True	75.9494	64	1847	95	below_threshold
Paenibacillus antibioticophila	strain=GD11	GCA_000455265.1	1274374	1274374	type	True	75.9429	65	1847	95	below_threshold
Paenibacillus caui	strain=81-11	GCA_019904135.1	2873927	2873927	type	True	75.9063	62	1847	95	below_threshold
Paenibacillus brevis	strain=MSJ-6	GCA_018919145.1	2841508	2841508	type	True	75.8633	60	1847	95	below_threshold
Paenibacillus aceti	strain=L14	GCA_003614185.1	1820010	1820010	type	True	75.8525	56	1847	95	below_threshold
Paenibacillus faecalis	strain=Marseille-P3787	GCA_900289175.1	2079532	2079532	type	True	75.8408	62	1847	95	below_threshold
Paenibacillus algicola	strain=HB172198	GCA_005577435.1	2565926	2565926	type	True	75.7923	66	1847	95	below_threshold
Paenibacillus aceti	strain=CGMCC 1.15420	GCA_014642755.1	1820010	1820010	type	True	75.7277	52	1847	95	below_threshold
Paenibacillus foliorum	strain=LMG 31456	GCA_013141765.1	2654974	2654974	type	True	75.6636	75	1847	95	below_threshold
Paenibacillus elgii	strain=NBRC 100335	GCA_004000865.1	189691	189691	type	True	75.6033	92	1847	95	below_threshold
Paenibacillus plantarum	strain=LMG 31461	GCA_013141695.1	2654975	2654975	type	True	75.6019	63	1847	95	below_threshold
Paenibacillus tianmuensis	strain=CGMCC 1.8946	GCA_900100345.1	624147	624147	type	True	75.5617	81	1847	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:02:22,952] [INFO] DFAST Taxonomy check result was written to GCF_000285515.1_ASM28551v1_genomic.fna/tc_result.tsv
[2024-01-24 13:02:22,953] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:02:22,953] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:02:22,953] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5394885e-bd6a-41e9-8b12-cdb494f59b4c/dqc_reference/checkm_data
[2024-01-24 13:02:22,954] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:02:23,010] [INFO] Task started: CheckM
[2024-01-24 13:02:23,010] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000285515.1_ASM28551v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000285515.1_ASM28551v1_genomic.fna/checkm_input GCF_000285515.1_ASM28551v1_genomic.fna/checkm_result
[2024-01-24 13:03:08,272] [INFO] Task succeeded: CheckM
[2024-01-24 13:03:08,274] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:03:08,301] [INFO] ===== Completeness check finished =====
[2024-01-24 13:03:08,302] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:03:08,302] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000285515.1_ASM28551v1_genomic.fna/markers.fasta)
[2024-01-24 13:03:08,303] [INFO] Task started: Blastn
[2024-01-24 13:03:08,303] [INFO] Running command: blastn -query GCF_000285515.1_ASM28551v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5394885e-bd6a-41e9-8b12-cdb494f59b4c/dqc_reference/reference_markers_gtdb.fasta -out GCF_000285515.1_ASM28551v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:03:09,132] [INFO] Task succeeded: Blastn
[2024-01-24 13:03:09,137] [INFO] Selected 29 target genomes.
[2024-01-24 13:03:09,137] [INFO] Target genome list was writen to GCF_000285515.1_ASM28551v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:03:09,157] [INFO] Task started: fastANI
[2024-01-24 13:03:09,158] [INFO] Running command: fastANI --query /var/lib/cwl/stg58e68a89-92d5-4bda-b6ff-4e21bd845738/GCF_000285515.1_ASM28551v1_genomic.fna.gz --refList GCF_000285515.1_ASM28551v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000285515.1_ASM28551v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:03:35,765] [INFO] Task succeeded: fastANI
[2024-01-24 13:03:35,797] [INFO] Found 23 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:03:35,797] [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_000285515.1	s__Paenibacillus_L senegalensis	99.9998	1834	1847	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_L	95.0	100.00	100.00	0.99	0.99	2	conclusive
GCF_018918005.1	s__MSJ-34 sp018918005	79.9826	93	1847	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__MSJ-34	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001403875.1	s__Paenibacillus_A ihumii	79.0364	81	1847	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_A	95.0	100.00	100.00	1.00	1.00	2	-
GCF_007679495.1	s__Paenibacillus_L sp007679495	77.9453	175	1847	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_L	95.0	99.12	99.12	0.91	0.91	2	-
GCF_018403245.1	s__Paenibacillus_L sp018403245	77.0059	174	1847	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_L	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018403265.1	s__J31TS4 sp018403265	76.2399	87	1847	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__J31TS4	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900104695.1	s__Paenibacillus_AI sp900104695	76.1632	60	1847	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_AI	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017833255.1	s__Paenibacillus_G sp017833255	76.1293	60	1847	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_018403065.1	s__Paenibacillus_B dendritiformis_B	75.9539	56	1847	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_900099895.1	s__Paenibacillus_G naphthalenovorans	75.9483	63	1847	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_004135365.1	s__Paenibacillus_C protaetiae	75.943	57	1847	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_910593845.1	s__Paenibacillus_G solanacearum	75.9034	86	1847	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_003614185.1	s__Paenibacillus_A aceti	75.8935	56	1847	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_A	95.0	99.99	99.99	1.00	1.00	2	-
GCF_011440305.1	s__Paenibacillus_S sp011440305	75.877	76	1847	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_005577435.1	s__Paenibacillus sp005577435	75.8094	67	1847	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	98.84	98.84	0.91	0.91	2	-
GCF_000513275.1	s__Paenibacillus_C gorillae	75.6384	60	1847	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_000411255.1	s__Paenibacillus_F sp000411255	75.6298	71	1847	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_F	95.0	99.59	98.79	0.98	0.94	4	-
GCF_013141765.1	s__Paenibacillus_S foliorum	75.6244	74	1847	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_900100345.1	s__Paenibacillus_G tianmuensis	75.5924	79	1847	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_001429545.1	s__Paenibacillus_E sp001429545	75.5701	60	1847	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_000799595.1	s__Paenibacillus_E chondroitinus_A	75.5505	58	1847	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_900107975.1	s__Paenibacillus_F sp900107975	75.5165	83	1847	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_F	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001956295.1	s__Paenibacillus_C sp001956295	75.2853	55	1847	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_C	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:03:35,799] [INFO] GTDB search result was written to GCF_000285515.1_ASM28551v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:03:35,800] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:03:35,805] [INFO] DFAST_QC result json was written to GCF_000285515.1_ASM28551v1_genomic.fna/dqc_result.json
[2024-01-24 13:03:35,805] [INFO] DFAST_QC completed!
[2024-01-24 13:03:35,805] [INFO] Total running time: 0h1m57s