[2024-01-25 18:47:50,717] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:47:50,724] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:47:50,725] [INFO] DQC Reference Directory: /var/lib/cwl/stg03507178-758e-4a82-8fe0-671e244926b1/dqc_reference
[2024-01-25 18:47:51,877] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:47:51,878] [INFO] Task started: Prodigal
[2024-01-25 18:47:51,878] [INFO] Running command: gunzip -c /var/lib/cwl/stg89f4c33a-e981-4e51-8291-451ab4a6518d/GCF_003994465.1_ASM399446v1_genomic.fna.gz | prodigal -d GCF_003994465.1_ASM399446v1_genomic.fna/cds.fna -a GCF_003994465.1_ASM399446v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:48:01,494] [INFO] Task succeeded: Prodigal
[2024-01-25 18:48:01,495] [INFO] Task started: HMMsearch
[2024-01-25 18:48:01,495] [INFO] Running command: hmmsearch --tblout GCF_003994465.1_ASM399446v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg03507178-758e-4a82-8fe0-671e244926b1/dqc_reference/reference_markers.hmm GCF_003994465.1_ASM399446v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:48:01,725] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:48:01,727] [INFO] Found 6/6 markers.
[2024-01-25 18:48:01,766] [INFO] Query marker FASTA was written to GCF_003994465.1_ASM399446v1_genomic.fna/markers.fasta
[2024-01-25 18:48:01,766] [INFO] Task started: Blastn
[2024-01-25 18:48:01,766] [INFO] Running command: blastn -query GCF_003994465.1_ASM399446v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg03507178-758e-4a82-8fe0-671e244926b1/dqc_reference/reference_markers.fasta -out GCF_003994465.1_ASM399446v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:48:02,318] [INFO] Task succeeded: Blastn
[2024-01-25 18:48:02,320] [INFO] Selected 24 target genomes.
[2024-01-25 18:48:02,321] [INFO] Target genome list was writen to GCF_003994465.1_ASM399446v1_genomic.fna/target_genomes.txt
[2024-01-25 18:48:02,353] [INFO] Task started: fastANI
[2024-01-25 18:48:02,353] [INFO] Running command: fastANI --query /var/lib/cwl/stg89f4c33a-e981-4e51-8291-451ab4a6518d/GCF_003994465.1_ASM399446v1_genomic.fna.gz --refList GCF_003994465.1_ASM399446v1_genomic.fna/target_genomes.txt --output GCF_003994465.1_ASM399446v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:48:23,431] [INFO] Task succeeded: fastANI
[2024-01-25 18:48:23,432] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg03507178-758e-4a82-8fe0-671e244926b1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:48:23,432] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg03507178-758e-4a82-8fe0-671e244926b1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:48:23,443] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:48:23,443] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:48:23,444] [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 zeisoli	strain=3-5-3	GCA_003994465.1	2496267	2496267	type	True	100.0	1457	1458	95	conclusive
Paenibacillus tuaregi	strain=Marseille-P2472	GCA_900086655.1	1816681	1816681	type	True	80.3609	696	1458	95	below_threshold
Paenibacillus shirakamiensis	strain=DSM 26806	GCA_017874255.1	1265935	1265935	type	True	78.2642	242	1458	95	below_threshold
Paenibacillus physcomitrellae	strain=XB	GCA_002240225.1	1619311	1619311	type	True	77.6893	190	1458	95	below_threshold
Paenibacillus yonginensis	strain=DCY84	GCA_001685395.1	1462996	1462996	type	True	77.6194	165	1458	95	below_threshold
Paenibacillus physcomitrellae	strain=CGMCC 1.15044	GCA_014640575.1	1619311	1619311	type	True	77.5498	186	1458	95	below_threshold
Fontibacillus solani	strain=CECT 8693	GCA_014138385.1	1572857	1572857	type	True	77.5228	164	1458	95	below_threshold
Paenibacillus antibioticophila	strain=GD11	GCA_000455265.1	1274374	1274374	type	True	77.4647	160	1458	95	below_threshold
Paenibacillus solani	strain=FJAT-22460	GCA_001277345.1	1705565	1705565	type	True	77.3777	126	1458	95	below_threshold
Paenibacillus dokdonensis	strain=YH-JAE5	GCA_004916975.1	2567944	2567944	type	True	77.3592	155	1458	95	below_threshold
Paenibacillus ihumii	strain=AT5	GCA_001403875.1	687436	687436	type	True	77.3534	191	1458	95	below_threshold
Paenibacillus ihuae	strain=GD6	GCA_001368795.1	1232431	1232431	type	True	77.3029	162	1458	95	below_threshold
Paenibacillus bouchesdurhonensis	strain=Marseille-P3071	GCA_900155685.1	1870990	1870990	type	True	77.2416	180	1458	95	below_threshold
Paenibacillus guangzhouensis	strain=KCTC 33171	GCA_009363075.1	1473112	1473112	type	True	76.9997	108	1458	95	below_threshold
Paenibacillus phytohabitans	strain=LMG 31459	GCA_013141775.1	2654978	2654978	type	True	76.9544	137	1458	95	below_threshold
Paenibacillus silagei	strain=DSM 101953	GCA_017874735.1	1670801	1670801	type	True	76.7023	142	1458	95	below_threshold
Paenibacillus turpanensis	strain=YIM B00363	GCA_011421635.1	2689078	2689078	type	True	76.3211	56	1458	95	below_threshold
Paenibacillus tarimensis	strain=DSM 19409	GCA_021532315.1	416012	416012	type	True	76.2998	63	1458	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:48:23,445] [INFO] DFAST Taxonomy check result was written to GCF_003994465.1_ASM399446v1_genomic.fna/tc_result.tsv
[2024-01-25 18:48:23,445] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:48:23,446] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:48:23,446] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg03507178-758e-4a82-8fe0-671e244926b1/dqc_reference/checkm_data
[2024-01-25 18:48:23,447] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:48:23,491] [INFO] Task started: CheckM
[2024-01-25 18:48:23,491] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003994465.1_ASM399446v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003994465.1_ASM399446v1_genomic.fna/checkm_input GCF_003994465.1_ASM399446v1_genomic.fna/checkm_result
[2024-01-25 18:48:55,582] [INFO] Task succeeded: CheckM
[2024-01-25 18:48:55,583] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:48:55,602] [INFO] ===== Completeness check finished =====
[2024-01-25 18:48:55,603] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:48:55,603] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003994465.1_ASM399446v1_genomic.fna/markers.fasta)
[2024-01-25 18:48:55,603] [INFO] Task started: Blastn
[2024-01-25 18:48:55,603] [INFO] Running command: blastn -query GCF_003994465.1_ASM399446v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg03507178-758e-4a82-8fe0-671e244926b1/dqc_reference/reference_markers_gtdb.fasta -out GCF_003994465.1_ASM399446v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:48:56,379] [INFO] Task succeeded: Blastn
[2024-01-25 18:48:56,382] [INFO] Selected 22 target genomes.
[2024-01-25 18:48:56,382] [INFO] Target genome list was writen to GCF_003994465.1_ASM399446v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:48:56,407] [INFO] Task started: fastANI
[2024-01-25 18:48:56,407] [INFO] Running command: fastANI --query /var/lib/cwl/stg89f4c33a-e981-4e51-8291-451ab4a6518d/GCF_003994465.1_ASM399446v1_genomic.fna.gz --refList GCF_003994465.1_ASM399446v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003994465.1_ASM399446v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:49:17,799] [INFO] Task succeeded: fastANI
[2024-01-25 18:49:17,811] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:49:17,811] [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_003994465.1	s__Paenibacillus_A zeisoli	100.0	1457	1458	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_A	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900086655.1	s__Paenibacillus_A tuaregi	80.3832	693	1458	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_017874255.1	s__Paenibacillus_A shirakamiensis	78.2642	242	1458	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	77.7822	216	1458	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_002240225.1	s__Paenibacillus_A physcomitrellae	77.6893	190	1458	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_001685395.1	s__Paenibacillus_A yonginensis	77.6194	165	1458	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_000455265.1	s__Paenibacillus_A antibioticophila	77.4693	159	1458	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_018403325.1	s__Paenibacillus_A vini	77.4347	211	1458	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_A	95.0	98.00	98.00	0.91	0.91	2	-
GCF_003931855.1	s__Paenibacillus_A lentus	77.3758	155	1458	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_001403875.1	s__Paenibacillus_A ihumii	77.3534	191	1458	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_001368795.1	s__Paenibacillus ihuae	77.2848	163	1458	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900155685.1	s__Paenibacillus_A bouchesdurhonensis	77.2416	180	1458	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_014639155.1	s__Paenibacillus_A segetis	77.1774	158	1458	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_008084145.1	s__Paenibacillus_A faecis	77.0755	198	1458	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_A	95.0	97.85	97.85	0.92	0.92	2	-
GCF_009363075.1	s__Paenibacillus_K guangzhouensis	76.9997	108	1458	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_002257645.1	s__Paenibacillus sp002257645	76.9748	176	1458	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002272015.1	s__Paenibacillus campinasensis	76.7869	142	1458	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	99.23	99.19	0.91	0.90	3	-
GCF_017874765.1	s__Paenibacillus rhizoplanae	76.7462	145	1458	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017874735.1	s__Paenibacillus silagei	76.7189	141	1458	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	96.84	96.20	0.88	0.87	3	-
GCF_011421635.1	s__Paenibacillus_AK turpanensis	76.3211	56	1458	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__YIM-B00363;g__Paenibacillus_AK	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:49:17,812] [INFO] GTDB search result was written to GCF_003994465.1_ASM399446v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:49:17,813] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:49:17,817] [INFO] DFAST_QC result json was written to GCF_003994465.1_ASM399446v1_genomic.fna/dqc_result.json
[2024-01-25 18:49:17,817] [INFO] DFAST_QC completed!
[2024-01-25 18:49:17,817] [INFO] Total running time: 0h1m27s