[2024-01-24 13:28:18,170] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:28:18,172] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:28:18,172] [INFO] DQC Reference Directory: /var/lib/cwl/stgc999696e-58ed-4bcd-92f4-3f6c2e8212c3/dqc_reference
[2024-01-24 13:28:19,638] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:28:19,639] [INFO] Task started: Prodigal
[2024-01-24 13:28:19,639] [INFO] Running command: gunzip -c /var/lib/cwl/stg1f417458-7a84-4c90-a57a-4439b9915bdd/GCF_927798095.1_CIP111893_genomic.fna.gz | prodigal -d GCF_927798095.1_CIP111893_genomic.fna/cds.fna -a GCF_927798095.1_CIP111893_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:28:36,831] [INFO] Task succeeded: Prodigal
[2024-01-24 13:28:36,831] [INFO] Task started: HMMsearch
[2024-01-24 13:28:36,832] [INFO] Running command: hmmsearch --tblout GCF_927798095.1_CIP111893_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc999696e-58ed-4bcd-92f4-3f6c2e8212c3/dqc_reference/reference_markers.hmm GCF_927798095.1_CIP111893_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:28:37,259] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:28:37,261] [INFO] Found 6/6 markers.
[2024-01-24 13:28:37,309] [INFO] Query marker FASTA was written to GCF_927798095.1_CIP111893_genomic.fna/markers.fasta
[2024-01-24 13:28:37,309] [INFO] Task started: Blastn
[2024-01-24 13:28:37,309] [INFO] Running command: blastn -query GCF_927798095.1_CIP111893_genomic.fna/markers.fasta -db /var/lib/cwl/stgc999696e-58ed-4bcd-92f4-3f6c2e8212c3/dqc_reference/reference_markers.fasta -out GCF_927798095.1_CIP111893_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:28:37,942] [INFO] Task succeeded: Blastn
[2024-01-24 13:28:37,945] [INFO] Selected 26 target genomes.
[2024-01-24 13:28:37,946] [INFO] Target genome list was writen to GCF_927798095.1_CIP111893_genomic.fna/target_genomes.txt
[2024-01-24 13:28:37,958] [INFO] Task started: fastANI
[2024-01-24 13:28:37,958] [INFO] Running command: fastANI --query /var/lib/cwl/stg1f417458-7a84-4c90-a57a-4439b9915bdd/GCF_927798095.1_CIP111893_genomic.fna.gz --refList GCF_927798095.1_CIP111893_genomic.fna/target_genomes.txt --output GCF_927798095.1_CIP111893_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:29:05,224] [INFO] Task succeeded: fastANI
[2024-01-24 13:29:05,225] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc999696e-58ed-4bcd-92f4-3f6c2e8212c3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:29:05,226] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc999696e-58ed-4bcd-92f4-3f6c2e8212c3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:29:05,249] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:29:05,249] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:29:05,249] [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 oenotherae	strain=DT7-4	GCA_019443105.1	1435645	1435645	type	True	82.81	1130	1980	95	below_threshold
Paenibacillus baekrokdamisoli	strain=KCTC 33723	GCA_003945345.1	1712516	1712516	type	True	78.0209	261	1980	95	below_threshold
Paenibacillus baekrokdamisoli	strain=CECT 8890	GCA_014191785.1	1712516	1712516	type	True	77.9105	260	1980	95	below_threshold
Paenibacillus nasutitermitis	strain=CGMCC 1.15178	GCA_014641075.1	1652958	1652958	type	True	77.8696	298	1980	95	below_threshold
Paenibacillus rhizovicinus	strain=14171R-81	GCA_010365285.1	2704463	2704463	type	True	77.8456	261	1980	95	below_threshold
Paenibacillus lignilyticus	strain=DLE-14	GCA_017942085.1	1172615	1172615	type	True	77.8317	268	1980	95	below_threshold
Paenibacillus mendelii	strain=C/2	GCA_024498075.1	206163	206163	type	True	77.8224	321	1980	95	below_threshold
Paenibacillus beijingensis	strain=DSM 24997	GCA_000961095.1	1126833	1126833	type	True	77.7857	161	1980	95	below_threshold
Paenibacillus lycopersici	strain=12200R-189	GCA_010119935.1	2704462	2704462	type	True	77.7086	276	1980	95	below_threshold
Paenibacillus taihuensis	strain=CGMCC 1.10966	GCA_003386535.1	1156355	1156355	type	True	77.6782	270	1980	95	below_threshold
Paenibacillus glycinis	strain=T1	GCA_009909185.1	2697035	2697035	type	True	77.6715	252	1980	95	below_threshold
Paenibacillus alkaliterrae	strain=DSM 17040	GCA_021532375.1	320909	320909	type	True	77.445	172	1980	95	below_threshold
Paenibacillus artemisiicola	strain=MWE-103	GCA_017652985.1	1172618	1172618	type	True	77.3187	228	1980	95	below_threshold
Paenibacillus phyllosphaerae	strain=CECT 5862	GCA_014192105.1	274593	274593	type	True	77.2662	256	1980	95	below_threshold
Paenibacillus protaetiae	strain=FW100M-2	GCA_004135365.1	2509456	2509456	type	True	77.2198	140	1980	95	below_threshold
Paenibacillus abyssi	strain=CGMCC 1.12987	GCA_014640295.1	1340531	1340531	type	True	77.12	184	1980	95	below_threshold
Paenibacillus aceti	strain=L14	GCA_003614185.1	1820010	1820010	type	True	76.7926	79	1980	95	below_threshold
Paenibacillus bovis	strain=BD3526	GCA_001421015.2	1616788	1616788	type	True	76.6734	63	1980	95	below_threshold
Paenibacillus chondroitinus	strain=NBRC 15376	GCA_004000765.1	59842	59842	type	True	76.6317	57	1980	95	below_threshold
Paenibacillus silvestris	strain=5J-6	GCA_009882985.1	2606219	2606219	type	True	76.5425	66	1980	95	below_threshold
Paenibacillus aceti	strain=CGMCC 1.15420	GCA_014642755.1	1820010	1820010	type	True	76.5038	79	1980	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:29:05,255] [INFO] DFAST Taxonomy check result was written to GCF_927798095.1_CIP111893_genomic.fna/tc_result.tsv
[2024-01-24 13:29:05,256] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:29:05,256] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:29:05,256] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc999696e-58ed-4bcd-92f4-3f6c2e8212c3/dqc_reference/checkm_data
[2024-01-24 13:29:05,258] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:29:05,318] [INFO] Task started: CheckM
[2024-01-24 13:29:05,318] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_927798095.1_CIP111893_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_927798095.1_CIP111893_genomic.fna/checkm_input GCF_927798095.1_CIP111893_genomic.fna/checkm_result
[2024-01-24 13:29:57,008] [INFO] Task succeeded: CheckM
[2024-01-24 13:29:57,010] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:29:57,039] [INFO] ===== Completeness check finished =====
[2024-01-24 13:29:57,040] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:29:57,040] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_927798095.1_CIP111893_genomic.fna/markers.fasta)
[2024-01-24 13:29:57,041] [INFO] Task started: Blastn
[2024-01-24 13:29:57,041] [INFO] Running command: blastn -query GCF_927798095.1_CIP111893_genomic.fna/markers.fasta -db /var/lib/cwl/stgc999696e-58ed-4bcd-92f4-3f6c2e8212c3/dqc_reference/reference_markers_gtdb.fasta -out GCF_927798095.1_CIP111893_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:29:57,842] [INFO] Task succeeded: Blastn
[2024-01-24 13:29:57,845] [INFO] Selected 28 target genomes.
[2024-01-24 13:29:57,845] [INFO] Target genome list was writen to GCF_927798095.1_CIP111893_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:29:57,876] [INFO] Task started: fastANI
[2024-01-24 13:29:57,876] [INFO] Running command: fastANI --query /var/lib/cwl/stg1f417458-7a84-4c90-a57a-4439b9915bdd/GCF_927798095.1_CIP111893_genomic.fna.gz --refList GCF_927798095.1_CIP111893_genomic.fna/target_genomes_gtdb.txt --output GCF_927798095.1_CIP111893_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:30:27,976] [INFO] Task succeeded: fastANI
[2024-01-24 13:30:27,999] [INFO] Found 28 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:30:28,000] [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_900116125.1	s__Paenibacillus_Z sp900116125	78.2228	258	1980	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_Z	95.0	95.31	95.31	0.87	0.87	2	-
GCF_003945345.1	s__Paenibacillus_Z baekrokdamisoli	77.9844	265	1980	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_Z	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014641075.1	s__Paenibacillus_Z nasutitermitis	77.8579	299	1980	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_010365285.1	s__Paenibacillus_Z rhizovicinus	77.8487	260	1980	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_003268025.1	s__Paenibacillus_Z montanisoli	77.8457	265	1980	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_016908135.1	s__Paenibacillus_Z mendelii	77.7821	326	1980	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_900110075.1	s__Paenibacillus_Z sp900110075	77.7528	269	1980	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_004342525.1	s__Paenibacillus_Z sp004342525	77.739	250	1980	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_000961095.1	s__Paenibacillus_O beijingensis	77.7309	161	1980	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_O	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010119935.1	s__Paenibacillus_Z lycopersici	77.7086	276	1980	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_003386535.1	s__Paenibacillus_Z taihuensis	77.6782	270	1980	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_009909185.1	s__Paenibacillus_Z glycinis	77.6715	252	1980	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_900106745.1	s__Paenibacillus_Z sp900106745	77.6689	298	1980	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_017874275.1	s__Paenibacillus_Z sepulcri	77.5589	331	1980	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_005222705.1	s__Paenibacillus_C sp005222705	77.3968	177	1980	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_009737085.1	s__Paenibacillus_C sp009737085	77.3253	184	1980	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_900113915.1	s__Paenibacillus_Z sp900113915	77.3041	235	1980	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_Z	95.0	96.39	96.39	0.86	0.86	2	-
GCF_015326965.1	s__Paenibacillus sp001860525	77.2849	98	1980	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	96.48	95.93	0.88	0.85	4	-
GCF_012935325.2	s__Paenibacillus_C sp012935325	77.284	206	1980	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_000758545.1	s__Paenibacillus sp000758545	77.2548	63	1980	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	97.87	97.65	0.91	0.90	4	-
GCF_004135365.1	s__Paenibacillus_C protaetiae	77.2198	140	1980	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_009789195.1	s__Paenibacillus_T sp009789195	77.1216	173	1980	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_T	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014640295.1	s__Paenibacillus_D abyssi	77.0932	186	1980	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004345425.1	s__Paenibacillus_C sp004345425	76.7945	177	1980	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_C	95.0	99.19	99.19	0.96	0.96	2	-
GCF_003614185.1	s__Paenibacillus_A aceti	76.7926	79	1980	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_001421015.2	s__Paenibacillus_J bovis	76.7112	63	1980	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_J	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009882985.1	s__Paenibacillus_E silvestris	76.5829	66	1980	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_015845845.1	s__Paenibacillus_B dendritiformis_C	76.293	102	1980	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_B	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:30:28,002] [INFO] GTDB search result was written to GCF_927798095.1_CIP111893_genomic.fna/result_gtdb.tsv
[2024-01-24 13:30:28,003] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:30:28,008] [INFO] DFAST_QC result json was written to GCF_927798095.1_CIP111893_genomic.fna/dqc_result.json
[2024-01-24 13:30:28,009] [INFO] DFAST_QC completed!
[2024-01-24 13:30:28,009] [INFO] Total running time: 0h2m10s