[2024-01-24 11:59:06,692] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:59:06,694] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:59:06,694] [INFO] DQC Reference Directory: /var/lib/cwl/stgf82a37b9-7dc3-40c3-93eb-08ca20cb07f4/dqc_reference
[2024-01-24 11:59:07,973] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:59:07,974] [INFO] Task started: Prodigal
[2024-01-24 11:59:07,974] [INFO] Running command: gunzip -c /var/lib/cwl/stg5837e3d0-363e-499c-a7b1-40dd64d26ca8/GCF_900086655.1_PRJEB13948_genomic.fna.gz | prodigal -d GCF_900086655.1_PRJEB13948_genomic.fna/cds.fna -a GCF_900086655.1_PRJEB13948_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:59:23,937] [INFO] Task succeeded: Prodigal
[2024-01-24 11:59:23,938] [INFO] Task started: HMMsearch
[2024-01-24 11:59:23,938] [INFO] Running command: hmmsearch --tblout GCF_900086655.1_PRJEB13948_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf82a37b9-7dc3-40c3-93eb-08ca20cb07f4/dqc_reference/reference_markers.hmm GCF_900086655.1_PRJEB13948_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:59:24,317] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:59:24,319] [INFO] Found 6/6 markers.
[2024-01-24 11:59:24,368] [INFO] Query marker FASTA was written to GCF_900086655.1_PRJEB13948_genomic.fna/markers.fasta
[2024-01-24 11:59:24,369] [INFO] Task started: Blastn
[2024-01-24 11:59:24,369] [INFO] Running command: blastn -query GCF_900086655.1_PRJEB13948_genomic.fna/markers.fasta -db /var/lib/cwl/stgf82a37b9-7dc3-40c3-93eb-08ca20cb07f4/dqc_reference/reference_markers.fasta -out GCF_900086655.1_PRJEB13948_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:59:24,987] [INFO] Task succeeded: Blastn
[2024-01-24 11:59:24,991] [INFO] Selected 26 target genomes.
[2024-01-24 11:59:24,991] [INFO] Target genome list was writen to GCF_900086655.1_PRJEB13948_genomic.fna/target_genomes.txt
[2024-01-24 11:59:25,006] [INFO] Task started: fastANI
[2024-01-24 11:59:25,006] [INFO] Running command: fastANI --query /var/lib/cwl/stg5837e3d0-363e-499c-a7b1-40dd64d26ca8/GCF_900086655.1_PRJEB13948_genomic.fna.gz --refList GCF_900086655.1_PRJEB13948_genomic.fna/target_genomes.txt --output GCF_900086655.1_PRJEB13948_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:59:53,144] [INFO] Task succeeded: fastANI
[2024-01-24 11:59:53,145] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf82a37b9-7dc3-40c3-93eb-08ca20cb07f4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:59:53,145] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf82a37b9-7dc3-40c3-93eb-08ca20cb07f4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:59:53,166] [INFO] Found 26 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:59:53,166] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:59:53,166] [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 tuaregi	strain=Marseille-P2472	GCA_900086655.1	1816681	1816681	type	True	100.0	1888	1888	95	conclusive
Paenibacillus zeisoli	strain=3-5-3	GCA_003994465.1	2496267	2496267	type	True	80.1698	701	1888	95	below_threshold
Paenibacillus faecalis	strain=Marseille-P3787	GCA_900289175.1	2079532	2079532	type	True	78.467	139	1888	95	below_threshold
Paenibacillus tianjinensis	strain=TB2019	GCA_017086365.1	2810347	2810347	type	True	78.3814	166	1888	95	below_threshold
Paenibacillus shirakamiensis	strain=DSM 26806	GCA_017874255.1	1265935	1265935	type	True	78.3426	223	1888	95	below_threshold
Paenibacillus pabuli	strain=NBRC 13638	GCA_001514495.1	1472	1472	suspected-type	True	78.2508	175	1888	95	below_threshold
Paenibacillus physcomitrellae	strain=XB	GCA_002240225.1	1619311	1619311	type	True	77.9603	202	1888	95	below_threshold
Paenibacillus ihumii	strain=AT5	GCA_001403875.1	687436	687436	type	True	77.9006	226	1888	95	below_threshold
Paenibacillus graminis	strain=RSA19	GCA_000520655.1	189425	189425	type	True	77.8393	179	1888	95	below_threshold
Paenibacillus segetis	strain=CGMCC 1.12769	GCA_014639155.1	1325360	1325360	type	True	77.7995	166	1888	95	below_threshold
Paenibacillus sediminis	strain=DSM 23491	GCA_017873765.1	664909	664909	type	True	77.771	93	1888	95	below_threshold
Paenibacillus caui	strain=81-11	GCA_019904135.1	2873927	2873927	type	True	77.7041	201	1888	95	below_threshold
Paenibacillus riograndensis	strain=SBR5	GCA_000224945.2	483937	483937	type	True	77.704	163	1888	95	below_threshold
Paenibacillus antibioticophila	strain=GD11	GCA_000455265.1	1274374	1274374	type	True	77.6014	196	1888	95	below_threshold
Paenibacillus xylanivorans	strain=A59	GCA_001280595.1	1705561	1705561	type	True	77.4744	156	1888	95	below_threshold
Paenibacillus pinistramenti	strain=ASL46	GCA_005869875.1	1768003	1768003	type	True	77.4344	213	1888	95	below_threshold
Paenibacillus timonensis	strain=DSM 16943	GCA_022427145.1	225915	225915	type	True	77.4076	189	1888	95	below_threshold
Paenibacillus brevis	strain=MSJ-6	GCA_018919145.1	2841508	2841508	type	True	77.3655	187	1888	95	below_threshold
Paenibacillus physcomitrellae	strain=CGMCC 1.15044	GCA_014640575.1	1619311	1619311	type	True	77.3633	197	1888	95	below_threshold
Paenibacillus lactis	strain=DSM 15596	GCA_017873605.1	228574	228574	type	True	77.3441	196	1888	95	below_threshold
Paenibacillus silvae	strain=CGMCC 1.12770	GCA_014639235.1	1325358	1325358	type	True	77.3331	151	1888	95	below_threshold
Paenibacillus glucanolyticus	strain=NBRC 15330	GCA_004000885.1	59843	59843	type	True	77.2315	175	1888	95	below_threshold
Paenibacillus dakarensis	strain=FF9	GCA_001373415.1	1527293	1527293	type	True	77.1786	138	1888	95	below_threshold
Paenibacillus aceti	strain=CGMCC 1.15420	GCA_014642755.1	1820010	1820010	type	True	77.0915	197	1888	95	below_threshold
Paenibacillus silagei	strain=DSM 101953	GCA_017874735.1	1670801	1670801	type	True	76.9913	183	1888	95	below_threshold
Paenibacillus piscarius	strain=P121	GCA_022234545.1	1089681	1089681	type	True	76.9518	176	1888	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:59:53,168] [INFO] DFAST Taxonomy check result was written to GCF_900086655.1_PRJEB13948_genomic.fna/tc_result.tsv
[2024-01-24 11:59:53,169] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:59:53,169] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:59:53,170] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf82a37b9-7dc3-40c3-93eb-08ca20cb07f4/dqc_reference/checkm_data
[2024-01-24 11:59:53,171] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:59:53,225] [INFO] Task started: CheckM
[2024-01-24 11:59:53,225] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900086655.1_PRJEB13948_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900086655.1_PRJEB13948_genomic.fna/checkm_input GCF_900086655.1_PRJEB13948_genomic.fna/checkm_result
[2024-01-24 12:00:43,015] [INFO] Task succeeded: CheckM
[2024-01-24 12:00:43,017] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.38%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:00:43,037] [INFO] ===== Completeness check finished =====
[2024-01-24 12:00:43,038] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:00:43,038] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900086655.1_PRJEB13948_genomic.fna/markers.fasta)
[2024-01-24 12:00:43,039] [INFO] Task started: Blastn
[2024-01-24 12:00:43,039] [INFO] Running command: blastn -query GCF_900086655.1_PRJEB13948_genomic.fna/markers.fasta -db /var/lib/cwl/stgf82a37b9-7dc3-40c3-93eb-08ca20cb07f4/dqc_reference/reference_markers_gtdb.fasta -out GCF_900086655.1_PRJEB13948_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:00:43,820] [INFO] Task succeeded: Blastn
[2024-01-24 12:00:43,825] [INFO] Selected 24 target genomes.
[2024-01-24 12:00:43,825] [INFO] Target genome list was writen to GCF_900086655.1_PRJEB13948_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:00:43,843] [INFO] Task started: fastANI
[2024-01-24 12:00:43,844] [INFO] Running command: fastANI --query /var/lib/cwl/stg5837e3d0-363e-499c-a7b1-40dd64d26ca8/GCF_900086655.1_PRJEB13948_genomic.fna.gz --refList GCF_900086655.1_PRJEB13948_genomic.fna/target_genomes_gtdb.txt --output GCF_900086655.1_PRJEB13948_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:01:09,183] [INFO] Task succeeded: fastANI
[2024-01-24 12:01:09,202] [INFO] Found 24 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:01:09,203] [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_900086655.1	s__Paenibacillus_A tuaregi	100.0	1888	1888	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_A	95.0	98.53	97.06	0.96	0.92	3	conclusive
GCF_003994465.1	s__Paenibacillus_A zeisoli	80.1658	702	1888	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_003060825.1	s__Paenibacillus_A sp003060825	78.9197	243	1888	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_003863965.1	s__Paenibacillus_A oralis	78.4856	240	1888	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_013401555.1	s__Paenibacillus sp900110055	78.4012	179	1888	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	97.27	96.55	0.92	0.89	5	-
GCF_000758705.1	s__Paenibacillus graminis	78.399	209	1888	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001685395.1	s__Paenibacillus_A yonginensis	78.3685	209	1888	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_017874255.1	s__Paenibacillus_A shirakamiensis	78.34	222	1888	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_001514495.1	s__Paenibacillus pabuli	78.1988	176	1888	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000758605.1	s__Paenibacillus sp000758605	77.9805	191	1888	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001403875.1	s__Paenibacillus_A ihumii	77.8961	227	1888	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_002240225.1	s__Paenibacillus_A physcomitrellae	77.8549	201	1888	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_014639155.1	s__Paenibacillus_A segetis	77.7809	170	1888	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_017873765.1	s__Paenibacillus_AG sediminis	77.771	93	1888	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_AG	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014192015.1	s__Paenibacillus rhizosphaerae	77.739	214	1888	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000455265.1	s__Paenibacillus_A antibioticophila	77.6081	198	1888	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_A	95.0	97.82	95.80	0.91	0.82	4	-
GCF_900109515.1	s__Paenibacillus sp900109515	77.4633	141	1888	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	95.23	95.20	0.85	0.85	7	-
GCF_003614185.1	s__Paenibacillus_A aceti	77.4208	208	1888	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_018919145.1	s__Paenibacillus_A sp018919145	77.3729	190	1888	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_017873605.1	s__Paenibacillus lactis	77.3339	199	1888	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	97.99	97.11	0.89	0.86	16	-
GCF_001373415.1	s__Paenibacillus dakarensis	77.257	142	1888	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900766135.1	s__Paenibacillus_A sp900766135	77.2296	191	1888	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_001955925.1	s__Paenibacillus sp001955925	77.1483	176	1888	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	98.91	98.91	0.92	0.92	2	-
GCF_017874735.1	s__Paenibacillus silagei	76.963	185	1888	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	96.84	96.20	0.88	0.87	3	-
--------------------------------------------------------------------------------
[2024-01-24 12:01:09,204] [INFO] GTDB search result was written to GCF_900086655.1_PRJEB13948_genomic.fna/result_gtdb.tsv
[2024-01-24 12:01:09,205] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:01:09,210] [INFO] DFAST_QC result json was written to GCF_900086655.1_PRJEB13948_genomic.fna/dqc_result.json
[2024-01-24 12:01:09,211] [INFO] DFAST_QC completed!
[2024-01-24 12:01:09,211] [INFO] Total running time: 0h2m3s