[2024-01-24 10:57:26,783] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:57:26,790] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:57:26,790] [INFO] DQC Reference Directory: /var/lib/cwl/stg53a4bb23-247f-4a92-9390-723a8571aa63/dqc_reference
[2024-01-24 10:57:28,202] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:57:28,203] [INFO] Task started: Prodigal
[2024-01-24 10:57:28,203] [INFO] Running command: gunzip -c /var/lib/cwl/stgbd361d5a-7b71-4705-8449-793e3bcc969d/GCF_017873765.1_ASM1787376v1_genomic.fna.gz | prodigal -d GCF_017873765.1_ASM1787376v1_genomic.fna/cds.fna -a GCF_017873765.1_ASM1787376v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:57:36,608] [INFO] Task succeeded: Prodigal
[2024-01-24 10:57:36,608] [INFO] Task started: HMMsearch
[2024-01-24 10:57:36,608] [INFO] Running command: hmmsearch --tblout GCF_017873765.1_ASM1787376v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg53a4bb23-247f-4a92-9390-723a8571aa63/dqc_reference/reference_markers.hmm GCF_017873765.1_ASM1787376v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:57:36,956] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:57:36,957] [INFO] Found 6/6 markers.
[2024-01-24 10:57:36,991] [INFO] Query marker FASTA was written to GCF_017873765.1_ASM1787376v1_genomic.fna/markers.fasta
[2024-01-24 10:57:36,992] [INFO] Task started: Blastn
[2024-01-24 10:57:36,992] [INFO] Running command: blastn -query GCF_017873765.1_ASM1787376v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg53a4bb23-247f-4a92-9390-723a8571aa63/dqc_reference/reference_markers.fasta -out GCF_017873765.1_ASM1787376v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:57:37,582] [INFO] Task succeeded: Blastn
[2024-01-24 10:57:37,588] [INFO] Selected 27 target genomes.
[2024-01-24 10:57:37,588] [INFO] Target genome list was writen to GCF_017873765.1_ASM1787376v1_genomic.fna/target_genomes.txt
[2024-01-24 10:57:37,712] [INFO] Task started: fastANI
[2024-01-24 10:57:37,712] [INFO] Running command: fastANI --query /var/lib/cwl/stgbd361d5a-7b71-4705-8449-793e3bcc969d/GCF_017873765.1_ASM1787376v1_genomic.fna.gz --refList GCF_017873765.1_ASM1787376v1_genomic.fna/target_genomes.txt --output GCF_017873765.1_ASM1787376v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:58:04,229] [INFO] Task succeeded: fastANI
[2024-01-24 10:58:04,230] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg53a4bb23-247f-4a92-9390-723a8571aa63/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:58:04,230] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg53a4bb23-247f-4a92-9390-723a8571aa63/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:58:04,251] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 10:58:04,251] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:58:04,251] [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 sediminis	strain=DSM 23491	GCA_017873765.1	664909	664909	type	True	100.0	1190	1190	95	conclusive
Paenibacillus tuaregi	strain=Marseille-P2472	GCA_900086655.1	1816681	1816681	type	True	77.7182	104	1190	95	below_threshold
Fontibacillus panacisegetis	strain=DSM 28129	GCA_900102215.1	670482	670482	type	True	77.7115	123	1190	95	below_threshold
Paenibacillus turicensis	strain=DSM 14349	GCA_017873435.1	160487	160487	type	True	77.6869	90	1190	95	below_threshold
Paenibacillus zeisoli	strain=3-5-3	GCA_003994465.1	2496267	2496267	type	True	77.6178	117	1190	95	below_threshold
Paenibacillus dakarensis	strain=FF9	GCA_001373415.1	1527293	1527293	type	True	77.5964	132	1190	95	below_threshold
Paenibacillus xylanilyticus	strain=LMG 21957	GCA_013359935.1	248903	248903	type	True	77.3461	124	1190	95	below_threshold
Paenibacillus chibensis	strain=NBRC 15958	GCA_004001045.1	59846	59846	type	True	77.3273	126	1190	95	below_threshold
Paenibacillus glucanolyticus	strain=NBRC 15330	GCA_004000885.1	59843	59843	type	True	77.3135	111	1190	95	below_threshold
Paenibacillus amylolyticus	strain=NBRC 15957	GCA_004001025.1	1451	1451	suspected-type	True	77.2861	101	1190	95	below_threshold
Paenibacillus fonticola	strain=DSM 21315	GCA_000381905.1	379896	379896	type	True	77.2399	119	1190	95	below_threshold
Paenibacillus borealis	strain=DSM 13188	GCA_000758665.1	160799	160799	type	True	77.1928	89	1190	95	below_threshold
Paenibacillus pini	strain=JCM 16418	GCA_000576305.1	669461	669461	type	True	77.1647	147	1190	95	below_threshold
Paenibacillus terrigena	strain=DSM 21567	GCA_000374845.1	369333	369333	type	True	77.1454	111	1190	95	below_threshold
Paenibacillus lactis	strain=DSM 15596	GCA_017873605.1	228574	228574	type	True	77.1432	118	1190	95	below_threshold
Paenibacillus antarcticus	strain=CECT 5836	GCA_001637225.1	253703	253703	type	True	77.1229	117	1190	95	below_threshold
Paenibacillus polysaccharolyticus	strain=BL9	GCA_900102085.1	582692	582692	type	True	77.106	109	1190	95	below_threshold
Paenibacillus taichungensis	strain=DSM 19942	GCA_013359905.1	484184	484184	type	True	77.0799	112	1190	95	below_threshold
Paenibacillus donghaensis	strain=KCTC 13049	GCA_002192415.1	414771	414771	type	True	77.0695	74	1190	95	below_threshold
Paenibacillus glycanilyticus subsp. hiroshimensis	strain=CCI5	GCA_015473105.1	2805378	126569	type	True	76.9555	63	1190	95	below_threshold
Paenibacillus phytohabitans	strain=LMG 31459	GCA_013141775.1	2654978	2654978	type	True	76.6297	86	1190	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:58:04,256] [INFO] DFAST Taxonomy check result was written to GCF_017873765.1_ASM1787376v1_genomic.fna/tc_result.tsv
[2024-01-24 10:58:04,257] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:58:04,257] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:58:04,258] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg53a4bb23-247f-4a92-9390-723a8571aa63/dqc_reference/checkm_data
[2024-01-24 10:58:04,259] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:58:04,314] [INFO] Task started: CheckM
[2024-01-24 10:58:04,314] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017873765.1_ASM1787376v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017873765.1_ASM1787376v1_genomic.fna/checkm_input GCF_017873765.1_ASM1787376v1_genomic.fna/checkm_result
[2024-01-24 10:58:34,916] [INFO] Task succeeded: CheckM
[2024-01-24 10:58:34,917] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:58:34,932] [INFO] ===== Completeness check finished =====
[2024-01-24 10:58:34,933] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:58:34,933] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017873765.1_ASM1787376v1_genomic.fna/markers.fasta)
[2024-01-24 10:58:34,933] [INFO] Task started: Blastn
[2024-01-24 10:58:34,934] [INFO] Running command: blastn -query GCF_017873765.1_ASM1787376v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg53a4bb23-247f-4a92-9390-723a8571aa63/dqc_reference/reference_markers_gtdb.fasta -out GCF_017873765.1_ASM1787376v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:58:35,726] [INFO] Task succeeded: Blastn
[2024-01-24 10:58:35,731] [INFO] Selected 28 target genomes.
[2024-01-24 10:58:35,731] [INFO] Target genome list was writen to GCF_017873765.1_ASM1787376v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:58:35,773] [INFO] Task started: fastANI
[2024-01-24 10:58:35,773] [INFO] Running command: fastANI --query /var/lib/cwl/stgbd361d5a-7b71-4705-8449-793e3bcc969d/GCF_017873765.1_ASM1787376v1_genomic.fna.gz --refList GCF_017873765.1_ASM1787376v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017873765.1_ASM1787376v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:59:03,464] [INFO] Task succeeded: fastANI
[2024-01-24 10:59:03,484] [INFO] Found 27 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:59:03,484] [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_017873765.1	s__Paenibacillus_AG sediminis	100.0	1190	1190	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_AG	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_018918005.1	s__MSJ-34 sp018918005	79.1267	96	1190	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_900086655.1	s__Paenibacillus_A tuaregi	77.7162	102	1190	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_A	95.0	98.53	97.06	0.96	0.92	3	-
GCF_900102215.1	s__Paenibacillus_A panacisegetis	77.7041	122	1190	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_A	95.0	97.17	97.17	0.85	0.85	2	-
GCF_017873435.1	s__Paenibacillus_A turicensis	77.6532	91	1190	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_003994465.1	s__Paenibacillus_A zeisoli	77.6178	117	1190	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_018403225.1	s__Paenibacillus sp018403225	77.4455	147	1190	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000758545.1	s__Paenibacillus sp000758545	77.3573	95	1190	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	97.87	97.65	0.91	0.90	4	-
GCF_004000885.1	s__Paenibacillus glucanolyticus	77.338	110	1190	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	99.37	98.87	0.95	0.92	9	-
GCF_004001045.1	s__Paenibacillus chibensis	77.3273	126	1190	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009807035.1	s__Paenibacillus sp009807035	77.3019	153	1190	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002573715.1	s__Paenibacillus sp002573715	77.2938	125	1190	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	96.52	95.81	0.89	0.84	4	-
GCF_018333315.1	s__Paenibacillus azoreducens	77.2472	137	1190	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	97.74	97.74	0.88	0.88	2	-
GCF_000381905.1	s__Paenibacillus_A fonticola	77.2399	119	1190	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_000520815.1	s__Paenibacillus maysiensis	77.2281	94	1190	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	95.32	95.30	0.82	0.80	4	-
GCF_000949425.1	s__Paenibacillus sp000949425	77.1694	129	1190	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017873605.1	s__Paenibacillus lactis	77.1432	118	1190	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	97.99	97.11	0.89	0.86	16	-
GCF_000758665.1	s__Paenibacillus borealis	77.136	90	1190	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001637225.1	s__Paenibacillus antarcticus	77.11	116	1190	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000374845.1	s__Paenibacillus_K terrigena	77.1019	113	1190	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_000023585.1	s__Paenibacillus_C sp000023585	77.1	68	1190	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_000758605.1	s__Paenibacillus sp000758605	77.0909	92	1190	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102085.1	s__Paenibacillus polysaccharolyticus	77.0568	109	1190	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	97.73	97.72	0.92	0.92	4	-
GCF_013359905.1	s__Paenibacillus taichungensis	77.0564	114	1190	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	96.85	95.16	0.90	0.85	6	-
GCF_003719335.1	s__Paenibacillus amylolyticus_D	77.0267	114	1190	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002192415.1	s__Paenibacillus donghaensis	77.0239	73	1190	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002264395.1	s__Paenibacillus sp002264395	76.8784	84	1190	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	98.86	98.86	0.89	0.89	2	-
--------------------------------------------------------------------------------
[2024-01-24 10:59:03,486] [INFO] GTDB search result was written to GCF_017873765.1_ASM1787376v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:59:03,487] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:59:03,491] [INFO] DFAST_QC result json was written to GCF_017873765.1_ASM1787376v1_genomic.fna/dqc_result.json
[2024-01-24 10:59:03,491] [INFO] DFAST_QC completed!
[2024-01-24 10:59:03,492] [INFO] Total running time: 0h1m37s