[2024-01-24 11:05:03,926] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:05:03,927] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:05:03,927] [INFO] DQC Reference Directory: /var/lib/cwl/stg0da7bd62-b68e-4bf9-ba30-8eee03da3520/dqc_reference
[2024-01-24 11:05:05,764] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:05:05,765] [INFO] Task started: Prodigal
[2024-01-24 11:05:05,765] [INFO] Running command: gunzip -c /var/lib/cwl/stgc2c1fb43-cb23-46d2-b9e2-7160d8dff520/GCF_003217775.1_ASM321777v1_genomic.fna.gz | prodigal -d GCF_003217775.1_ASM321777v1_genomic.fna/cds.fna -a GCF_003217775.1_ASM321777v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:05:24,030] [INFO] Task succeeded: Prodigal
[2024-01-24 11:05:24,030] [INFO] Task started: HMMsearch
[2024-01-24 11:05:24,030] [INFO] Running command: hmmsearch --tblout GCF_003217775.1_ASM321777v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0da7bd62-b68e-4bf9-ba30-8eee03da3520/dqc_reference/reference_markers.hmm GCF_003217775.1_ASM321777v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:05:24,373] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:05:24,374] [INFO] Found 6/6 markers.
[2024-01-24 11:05:24,439] [INFO] Query marker FASTA was written to GCF_003217775.1_ASM321777v1_genomic.fna/markers.fasta
[2024-01-24 11:05:24,439] [INFO] Task started: Blastn
[2024-01-24 11:05:24,439] [INFO] Running command: blastn -query GCF_003217775.1_ASM321777v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0da7bd62-b68e-4bf9-ba30-8eee03da3520/dqc_reference/reference_markers.fasta -out GCF_003217775.1_ASM321777v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:05:25,042] [INFO] Task succeeded: Blastn
[2024-01-24 11:05:25,045] [INFO] Selected 17 target genomes.
[2024-01-24 11:05:25,045] [INFO] Target genome list was writen to GCF_003217775.1_ASM321777v1_genomic.fna/target_genomes.txt
[2024-01-24 11:05:25,054] [INFO] Task started: fastANI
[2024-01-24 11:05:25,054] [INFO] Running command: fastANI --query /var/lib/cwl/stgc2c1fb43-cb23-46d2-b9e2-7160d8dff520/GCF_003217775.1_ASM321777v1_genomic.fna.gz --refList GCF_003217775.1_ASM321777v1_genomic.fna/target_genomes.txt --output GCF_003217775.1_ASM321777v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:05:48,030] [INFO] Task succeeded: fastANI
[2024-01-24 11:05:48,030] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0da7bd62-b68e-4bf9-ba30-8eee03da3520/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:05:48,031] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0da7bd62-b68e-4bf9-ba30-8eee03da3520/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:05:48,041] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:05:48,041] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:05:48,041] [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 flagellatus	strain=DXL2	GCA_003217775.1	2211139	2211139	type	True	100.0	2391	2393	95	conclusive
Paenibacillus mesophilus	strain=SYSU K30004	GCA_005938385.1	2582849	2582849	type	True	80.2448	929	2393	95	below_threshold
Paenibacillus hemerocallicola	strain=KCTC 33185	GCA_006265175.1	1172614	1172614	type	True	79.9241	970	2393	95	below_threshold
Paenibacillus ginsengarvi	strain=KCTC 13059	GCA_003626695.1	400777	400777	type	True	79.3134	814	2393	95	below_threshold
Paenibacillus oceani	strain=IB182363	GCA_014705615.1	2772510	2772510	type	True	79.2255	847	2393	95	below_threshold
Paenibacillus ehimensis	strain=NBRC 15659	GCA_004000785.1	79264	79264	type	True	78.3473	408	2393	95	below_threshold
Paenibacillus koleovorans	strain=NBRC 103111	GCA_004000845.1	121608	121608	type	True	77.7017	459	2393	95	below_threshold
Paenibacillus macerans	strain=ATCC 8244	GCA_000746875.1	44252	44252	type	True	77.6779	231	2393	95	below_threshold
Paenibacillus ginsengihumi	strain=DSM 21568	GCA_000380965.1	431596	431596	type	True	77.6272	390	2393	95	below_threshold
Paenibacillus artemisiicola	strain=MWE-103	GCA_017652985.1	1172618	1172618	type	True	77.3255	443	2393	95	below_threshold
Thermobacillus composti	strain=KWC4	GCA_000227705.3	377615	377615	type	True	77.1497	305	2393	95	below_threshold
Paenibacillus doosanensis	strain=CAU 1055	GCA_025060755.1	1229154	1229154	type	True	77.141	358	2393	95	below_threshold
Thermobacillus xylanilyticus	strain=XE	GCA_907165215.1	76633	76633	type	True	77.1279	301	2393	95	below_threshold
Paenibacillus piri	strain=MS74	GCA_004354045.1	2547395	2547395	type	True	77.0501	242	2393	95	below_threshold
Paenibacillus albicereus	strain=UniB2	GCA_012676905.1	2726185	2726185	type	True	77.0488	358	2393	95	below_threshold
Paenibacillus tyrfis	strain=MSt1	GCA_000722545.1	1501230	1501230	type	True	77.0146	355	2393	95	below_threshold
Paenibacillus rhizovicinus	strain=14171R-81	GCA_010365285.1	2704463	2704463	type	True	76.3717	253	2393	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:05:48,043] [INFO] DFAST Taxonomy check result was written to GCF_003217775.1_ASM321777v1_genomic.fna/tc_result.tsv
[2024-01-24 11:05:48,043] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:05:48,043] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:05:48,043] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0da7bd62-b68e-4bf9-ba30-8eee03da3520/dqc_reference/checkm_data
[2024-01-24 11:05:48,044] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:05:48,108] [INFO] Task started: CheckM
[2024-01-24 11:05:48,108] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003217775.1_ASM321777v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003217775.1_ASM321777v1_genomic.fna/checkm_input GCF_003217775.1_ASM321777v1_genomic.fna/checkm_result
[2024-01-24 11:06:35,836] [INFO] Task succeeded: CheckM
[2024-01-24 11:06:35,837] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:06:35,854] [INFO] ===== Completeness check finished =====
[2024-01-24 11:06:35,854] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:06:35,854] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003217775.1_ASM321777v1_genomic.fna/markers.fasta)
[2024-01-24 11:06:35,854] [INFO] Task started: Blastn
[2024-01-24 11:06:35,854] [INFO] Running command: blastn -query GCF_003217775.1_ASM321777v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0da7bd62-b68e-4bf9-ba30-8eee03da3520/dqc_reference/reference_markers_gtdb.fasta -out GCF_003217775.1_ASM321777v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:06:36,780] [INFO] Task succeeded: Blastn
[2024-01-24 11:06:36,782] [INFO] Selected 14 target genomes.
[2024-01-24 11:06:36,782] [INFO] Target genome list was writen to GCF_003217775.1_ASM321777v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:06:36,789] [INFO] Task started: fastANI
[2024-01-24 11:06:36,789] [INFO] Running command: fastANI --query /var/lib/cwl/stgc2c1fb43-cb23-46d2-b9e2-7160d8dff520/GCF_003217775.1_ASM321777v1_genomic.fna.gz --refList GCF_003217775.1_ASM321777v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003217775.1_ASM321777v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:06:55,650] [INFO] Task succeeded: fastANI
[2024-01-24 11:06:55,659] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:06:55,659] [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_003217775.1	s__Paenibacillus_AB flagellatus	100.0	2391	2393	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_AB	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_005938385.1	s__Paenibacillus_AB mesophilus	80.2448	929	2393	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_AB	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006265175.1	s__Paenibacillus_AB hemerocallicola	79.9244	971	2393	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_AB	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003626695.1	s__Paenibacillus_AB ginsengarvi	79.3281	811	2393	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_AB	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014705615.1	s__Paenibacillus_AB sp014705615	79.2307	847	2393	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_AB	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000829455.1	s__VKM-B-2647 sp000829455	78.3249	452	2393	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__VKM-B-2647	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004000845.1	s__Paenibacillus_AA koleovorans	77.7073	458	2393	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_AA	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000380965.1	s__Paenibacillus_M ginsengihumi	77.6557	386	2393	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_M	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900113915.1	s__Paenibacillus_Z sp900113915	77.4626	451	2393	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_018403265.1	s__J31TS4 sp018403265	77.1559	364	2393	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_004514475.1	s__MEC069 sp004514475	77.1237	284	2393	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__MEC069	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004354045.1	s__Paenibacillus_S piri	77.0501	242	2393	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_019091135.1	s__Cohnella sp019091135	76.6852	343	2393	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Cohnella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010365285.1	s__Paenibacillus_Z rhizovicinus	76.3656	253	2393	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_Z	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:06:55,660] [INFO] GTDB search result was written to GCF_003217775.1_ASM321777v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:06:55,661] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:06:55,664] [INFO] DFAST_QC result json was written to GCF_003217775.1_ASM321777v1_genomic.fna/dqc_result.json
[2024-01-24 11:06:55,664] [INFO] DFAST_QC completed!
[2024-01-24 11:06:55,664] [INFO] Total running time: 0h1m52s