[2024-01-24 13:01:24,598] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:01:24,609] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:01:24,609] [INFO] DQC Reference Directory: /var/lib/cwl/stgccbd06ac-a976-4b79-863a-1a4b1dfb7c03/dqc_reference
[2024-01-24 13:01:25,932] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:01:25,933] [INFO] Task started: Prodigal
[2024-01-24 13:01:25,934] [INFO] Running command: gunzip -c /var/lib/cwl/stg1d7b6f03-a0d2-489e-b9d8-1702075a093c/GCF_009363075.1_ASM936307v1_genomic.fna.gz | prodigal -d GCF_009363075.1_ASM936307v1_genomic.fna/cds.fna -a GCF_009363075.1_ASM936307v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:01:44,872] [INFO] Task succeeded: Prodigal
[2024-01-24 13:01:44,873] [INFO] Task started: HMMsearch
[2024-01-24 13:01:44,873] [INFO] Running command: hmmsearch --tblout GCF_009363075.1_ASM936307v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgccbd06ac-a976-4b79-863a-1a4b1dfb7c03/dqc_reference/reference_markers.hmm GCF_009363075.1_ASM936307v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:01:45,206] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:01:45,207] [INFO] Found 6/6 markers.
[2024-01-24 13:01:45,270] [INFO] Query marker FASTA was written to GCF_009363075.1_ASM936307v1_genomic.fna/markers.fasta
[2024-01-24 13:01:45,271] [INFO] Task started: Blastn
[2024-01-24 13:01:45,271] [INFO] Running command: blastn -query GCF_009363075.1_ASM936307v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgccbd06ac-a976-4b79-863a-1a4b1dfb7c03/dqc_reference/reference_markers.fasta -out GCF_009363075.1_ASM936307v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:01:45,888] [INFO] Task succeeded: Blastn
[2024-01-24 13:01:45,892] [INFO] Selected 21 target genomes.
[2024-01-24 13:01:45,892] [INFO] Target genome list was writen to GCF_009363075.1_ASM936307v1_genomic.fna/target_genomes.txt
[2024-01-24 13:01:45,901] [INFO] Task started: fastANI
[2024-01-24 13:01:45,902] [INFO] Running command: fastANI --query /var/lib/cwl/stg1d7b6f03-a0d2-489e-b9d8-1702075a093c/GCF_009363075.1_ASM936307v1_genomic.fna.gz --refList GCF_009363075.1_ASM936307v1_genomic.fna/target_genomes.txt --output GCF_009363075.1_ASM936307v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:02:07,548] [INFO] Task succeeded: fastANI
[2024-01-24 13:02:07,549] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgccbd06ac-a976-4b79-863a-1a4b1dfb7c03/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:02:07,550] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgccbd06ac-a976-4b79-863a-1a4b1dfb7c03/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:02:07,569] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:02:07,570] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:02:07,570] [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 guangzhouensis	strain=KCTC 33171	GCA_009363075.1	1473112	1473112	type	True	100.0	2315	2315	95	conclusive
Paenibacillus terrigena	strain=DSM 21567	GCA_000374845.1	369333	369333	type	True	85.394	1552	2315	95	below_threshold
Paenibacillus selenitireducens	strain=ES3-24	GCA_002021565.1	1324314	1324314	type	True	80.8327	758	2315	95	below_threshold
Paenibacillus alvei	strain=DSM 29	GCA_000293805.1	44250	44250	type	True	78.6803	179	2315	95	below_threshold
Paenibacillus faecalis	strain=Marseille-P3787	GCA_900289175.1	2079532	2079532	type	True	78.615	104	2315	95	below_threshold
Paenibacillus albus	strain=18JY67-1	GCA_003952225.1	2495582	2495582	type	True	78.3121	141	2315	95	below_threshold
Paenibacillus allorhizosphaerae	strain=CIP 111802	GCA_910594985.1	2849866	2849866	type	True	78.1644	106	2315	95	below_threshold
Paenibacillus agri	strain=JW14	GCA_013359945.1	2744309	2744309	type	True	77.9817	126	2315	95	below_threshold
Paenibacillus pabuli	strain=NBRC 13638	GCA_001514495.1	1472	1472	suspected-type	True	77.9699	118	2315	95	below_threshold
Paenibacillus caui	strain=81-11	GCA_019904135.1	2873927	2873927	type	True	77.6572	99	2315	95	below_threshold
Paenibacillus rhizosphaerae	strain=CECT 5831	GCA_014192015.1	297318	297318	type	True	77.652	154	2315	95	below_threshold
Paenibacillus xylanexedens	strain=DSM 21292	GCA_017874615.1	528191	528191	suspected-type	True	77.3874	126	2315	95	below_threshold
Paenibacillus zeisoli	strain=3-5-3	GCA_003994465.1	2496267	2496267	type	True	77.1723	103	2315	95	below_threshold
Paenibacillus chibensis	strain=NBRC 15958	GCA_004001045.1	59846	59846	type	True	76.8059	141	2315	95	below_threshold
Paenibacillus brevis	strain=MSJ-6	GCA_018919145.1	2841508	2841508	type	True	76.805	105	2315	95	below_threshold
Paenibacillus pinihumi	strain=DSM 23905	GCA_000422505.1	669462	669462	type	True	76.7615	119	2315	95	below_threshold
Paenibacillus timonensis	strain=DSM 16943	GCA_022427145.1	225915	225915	type	True	76.5665	107	2315	95	below_threshold
Cohnella lubricantis	strain=DSM 103658	GCA_014212015.1	2163172	2163172	type	True	76.035	64	2315	95	below_threshold
Cohnella lubricantis	strain=DSM 103658	GCA_017874835.1	2163172	2163172	type	True	75.9304	65	2315	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:02:07,571] [INFO] DFAST Taxonomy check result was written to GCF_009363075.1_ASM936307v1_genomic.fna/tc_result.tsv
[2024-01-24 13:02:07,572] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:02:07,572] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:02:07,572] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgccbd06ac-a976-4b79-863a-1a4b1dfb7c03/dqc_reference/checkm_data
[2024-01-24 13:02:07,574] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:02:07,639] [INFO] Task started: CheckM
[2024-01-24 13:02:07,640] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009363075.1_ASM936307v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009363075.1_ASM936307v1_genomic.fna/checkm_input GCF_009363075.1_ASM936307v1_genomic.fna/checkm_result
[2024-01-24 13:03:03,509] [INFO] Task succeeded: CheckM
[2024-01-24 13:03:03,510] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.38%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:03:03,541] [INFO] ===== Completeness check finished =====
[2024-01-24 13:03:03,541] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:03:03,542] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009363075.1_ASM936307v1_genomic.fna/markers.fasta)
[2024-01-24 13:03:03,542] [INFO] Task started: Blastn
[2024-01-24 13:03:03,542] [INFO] Running command: blastn -query GCF_009363075.1_ASM936307v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgccbd06ac-a976-4b79-863a-1a4b1dfb7c03/dqc_reference/reference_markers_gtdb.fasta -out GCF_009363075.1_ASM936307v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:03:04,414] [INFO] Task succeeded: Blastn
[2024-01-24 13:03:04,418] [INFO] Selected 17 target genomes.
[2024-01-24 13:03:04,419] [INFO] Target genome list was writen to GCF_009363075.1_ASM936307v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:03:04,434] [INFO] Task started: fastANI
[2024-01-24 13:03:04,434] [INFO] Running command: fastANI --query /var/lib/cwl/stg1d7b6f03-a0d2-489e-b9d8-1702075a093c/GCF_009363075.1_ASM936307v1_genomic.fna.gz --refList GCF_009363075.1_ASM936307v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009363075.1_ASM936307v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:03:23,909] [INFO] Task succeeded: fastANI
[2024-01-24 13:03:23,924] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:03:23,925] [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_009363075.1	s__Paenibacillus_K guangzhouensis	100.0	2315	2315	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_K	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000374845.1	s__Paenibacillus_K terrigena	85.3983	1551	2315	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_K	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002021565.1	s__Paenibacillus_K selenitireducens	80.8246	759	2315	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_K	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009363095.1	s__Paenibacillus cellulositrophicus_A	78.9951	187	2315	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	96.73	96.59	0.92	0.91	14	-
GCF_000293805.1	s__Paenibacillus_B alvei	78.8401	181	2315	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_B	95.0	97.68	97.62	0.90	0.89	5	-
GCF_910594985.1	s__Paenibacillus_G sp910594985	78.1825	105	2315	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_013359945.1	s__Paenibacillus sp013359945	77.981	126	2315	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001682855.1	s__Paenibacillus sp001682855	77.7994	119	2315	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014192015.1	s__Paenibacillus rhizosphaerae	77.652	154	2315	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003614185.1	s__Paenibacillus_A aceti	77.592	168	2315	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_015845845.1	s__Paenibacillus_B dendritiformis_C	77.5132	111	2315	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_001955855.1	s__Paenibacillus sp001955855	77.3939	110	2315	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.7262	N/A	N/A	N/A	N/A	1	-
GCF_003955665.1	s__Paenibacillus_E whitsoniae	77.3554	114	2315	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_018918005.1	s__MSJ-34 sp018918005	77.2544	164	2315	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_003994465.1	s__Paenibacillus_A zeisoli	77.1723	103	2315	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001426865.1	s__Paenibacillus sp001426865	77.1589	116	2315	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	96.30	96.30	0.92	0.92	2	-
GCF_013266915.1	s__Paenibacillus_B sp900539405	76.9528	139	2315	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_B	95.0	99.54	99.32	0.96	0.95	4	-
--------------------------------------------------------------------------------
[2024-01-24 13:03:23,927] [INFO] GTDB search result was written to GCF_009363075.1_ASM936307v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:03:23,927] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:03:23,932] [INFO] DFAST_QC result json was written to GCF_009363075.1_ASM936307v1_genomic.fna/dqc_result.json
[2024-01-24 13:03:23,932] [INFO] DFAST_QC completed!
[2024-01-24 13:03:23,932] [INFO] Total running time: 0h1m59s