[2024-01-24 12:06:33,766] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:06:33,767] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:06:33,768] [INFO] DQC Reference Directory: /var/lib/cwl/stg982b206f-ad68-4450-9d0c-403a28137280/dqc_reference
[2024-01-24 12:06:34,997] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:06:34,997] [INFO] Task started: Prodigal
[2024-01-24 12:06:34,998] [INFO] Running command: gunzip -c /var/lib/cwl/stgdf0868d7-a16a-40ed-a87c-0c485cf0c1a8/GCF_004514475.2_ASM451447v2_genomic.fna.gz | prodigal -d GCF_004514475.2_ASM451447v2_genomic.fna/cds.fna -a GCF_004514475.2_ASM451447v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:06:51,391] [INFO] Task succeeded: Prodigal
[2024-01-24 12:06:51,391] [INFO] Task started: HMMsearch
[2024-01-24 12:06:51,391] [INFO] Running command: hmmsearch --tblout GCF_004514475.2_ASM451447v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg982b206f-ad68-4450-9d0c-403a28137280/dqc_reference/reference_markers.hmm GCF_004514475.2_ASM451447v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:06:51,730] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:06:51,731] [INFO] Found 6/6 markers.
[2024-01-24 12:06:51,777] [INFO] Query marker FASTA was written to GCF_004514475.2_ASM451447v2_genomic.fna/markers.fasta
[2024-01-24 12:06:51,778] [INFO] Task started: Blastn
[2024-01-24 12:06:51,778] [INFO] Running command: blastn -query GCF_004514475.2_ASM451447v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg982b206f-ad68-4450-9d0c-403a28137280/dqc_reference/reference_markers.fasta -out GCF_004514475.2_ASM451447v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:06:52,404] [INFO] Task succeeded: Blastn
[2024-01-24 12:06:52,408] [INFO] Selected 26 target genomes.
[2024-01-24 12:06:52,409] [INFO] Target genome list was writen to GCF_004514475.2_ASM451447v2_genomic.fna/target_genomes.txt
[2024-01-24 12:06:52,421] [INFO] Task started: fastANI
[2024-01-24 12:06:52,421] [INFO] Running command: fastANI --query /var/lib/cwl/stgdf0868d7-a16a-40ed-a87c-0c485cf0c1a8/GCF_004514475.2_ASM451447v2_genomic.fna.gz --refList GCF_004514475.2_ASM451447v2_genomic.fna/target_genomes.txt --output GCF_004514475.2_ASM451447v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:07:25,514] [INFO] Task succeeded: fastANI
[2024-01-24 12:07:25,515] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg982b206f-ad68-4450-9d0c-403a28137280/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:07:25,515] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg982b206f-ad68-4450-9d0c-403a28137280/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:07:25,538] [INFO] Found 26 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:07:25,539] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:07:25,539] [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 athensensis	strain=MEC069	GCA_004514475.2	1967502	1967502	type	True	100.0	1858	1860	95	conclusive
Paenibacillus alginolyticus	strain=DSM 5050	GCA_000422905.1	59839	59839	type	True	78.7773	250	1860	95	below_threshold
Paenibacillus albicereus	strain=UniB2	GCA_012676905.1	2726185	2726185	type	True	78.6306	233	1860	95	below_threshold
Paenibacillus phytorum	strain=LMG 31458	GCA_013141715.1	2654977	2654977	type	True	77.4432	212	1860	95	below_threshold
Paenibacillus tyrfis	strain=MSt1	GCA_000722545.1	1501230	1501230	type	True	77.3918	244	1860	95	below_threshold
Paenibacillus ferrarius	strain=CY1	GCA_002027705.1	1469647	1469647	type	True	77.3895	230	1860	95	below_threshold
Paenibacillus germinis	strain=LMG 31460	GCA_013141785.1	2654979	2654979	type	True	77.3473	222	1860	95	below_threshold
Paenibacillus aceris	strain=DSM 24950	GCA_017874035.1	869555	869555	type	True	77.3009	241	1860	95	below_threshold
Paenibacillus allorhizosphaerae	strain=CIP 111802	GCA_910594985.1	2849866	2849866	type	True	77.2772	228	1860	95	below_threshold
Paenibacillus ehimensis	strain=NBRC 15659	GCA_004000785.1	79264	79264	type	True	77.2669	263	1860	95	below_threshold
Paenibacillus ginsengihumi	strain=DSM 21568	GCA_000380965.1	431596	431596	type	True	77.2147	260	1860	95	below_threshold
Paenibacillus flagellatus	strain=DXL2	GCA_003217775.1	2211139	2211139	type	True	77.2102	276	1860	95	below_threshold
Paenibacillus piri	strain=MS74	GCA_004354045.1	2547395	2547395	type	True	77.1956	261	1860	95	below_threshold
Paenibacillus ginsengarvi	strain=KCTC 13059	GCA_003626695.1	400777	400777	type	True	77.1955	226	1860	95	below_threshold
Paenibacillus thalictri	strain=N2SHLJ1	GCA_004307995.1	2527873	2527873	type	True	77.1936	220	1860	95	below_threshold
Paenibacillus koleovorans	strain=NBRC 103111	GCA_004000845.1	121608	121608	type	True	77.1471	217	1860	95	below_threshold
Paenibacillus planticolens	strain=LMG 31457	GCA_013141725.1	2654976	2654976	type	True	77.1158	291	1860	95	below_threshold
Paenibacillus eucommiae	strain=DSM 26048	GCA_017874215.1	1355755	1355755	type	True	76.9865	171	1860	95	below_threshold
Paenibacillus oceani	strain=IB182363	GCA_014705615.1	2772510	2772510	type	True	76.794	201	1860	95	below_threshold
Paenibacillus cymbidii	strain=R196	GCA_004764705.1	1639034	1639034	type	True	76.7238	303	1860	95	below_threshold
Paenibacillus donghaensis	strain=KCTC 13049	GCA_002192415.1	414771	414771	type	True	76.7188	95	1860	95	below_threshold
Paenibacillus macerans	strain=ATCC 8244	GCA_000746875.1	44252	44252	type	True	76.6456	176	1860	95	below_threshold
Paenibacillus mendelii	strain=C/2	GCA_024498075.1	206163	206163	type	True	76.5777	111	1860	95	below_threshold
Paenibacillus alkaliterrae	strain=DSM 17040	GCA_021532375.1	320909	320909	type	True	76.5481	97	1860	95	below_threshold
Paenibacillus lactis	strain=DSM 15596	GCA_017873605.1	228574	228574	type	True	76.4872	124	1860	95	below_threshold
Paenibacillus lautus	strain=NBRC 15380	GCA_004000945.1	1401	1401	suspected-type	True	76.1072	81	1860	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:07:25,540] [INFO] DFAST Taxonomy check result was written to GCF_004514475.2_ASM451447v2_genomic.fna/tc_result.tsv
[2024-01-24 12:07:25,541] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:07:25,541] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:07:25,541] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg982b206f-ad68-4450-9d0c-403a28137280/dqc_reference/checkm_data
[2024-01-24 12:07:25,542] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:07:25,599] [INFO] Task started: CheckM
[2024-01-24 12:07:25,599] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004514475.2_ASM451447v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004514475.2_ASM451447v2_genomic.fna/checkm_input GCF_004514475.2_ASM451447v2_genomic.fna/checkm_result
[2024-01-24 12:08:13,437] [INFO] Task succeeded: CheckM
[2024-01-24 12:08:13,439] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:08:13,462] [INFO] ===== Completeness check finished =====
[2024-01-24 12:08:13,462] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:08:13,463] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004514475.2_ASM451447v2_genomic.fna/markers.fasta)
[2024-01-24 12:08:13,463] [INFO] Task started: Blastn
[2024-01-24 12:08:13,463] [INFO] Running command: blastn -query GCF_004514475.2_ASM451447v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg982b206f-ad68-4450-9d0c-403a28137280/dqc_reference/reference_markers_gtdb.fasta -out GCF_004514475.2_ASM451447v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:08:14,310] [INFO] Task succeeded: Blastn
[2024-01-24 12:08:14,315] [INFO] Selected 27 target genomes.
[2024-01-24 12:08:14,315] [INFO] Target genome list was writen to GCF_004514475.2_ASM451447v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:08:14,336] [INFO] Task started: fastANI
[2024-01-24 12:08:14,336] [INFO] Running command: fastANI --query /var/lib/cwl/stgdf0868d7-a16a-40ed-a87c-0c485cf0c1a8/GCF_004514475.2_ASM451447v2_genomic.fna.gz --refList GCF_004514475.2_ASM451447v2_genomic.fna/target_genomes_gtdb.txt --output GCF_004514475.2_ASM451447v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:08:46,340] [INFO] Task succeeded: fastANI
[2024-01-24 12:08:46,368] [INFO] Found 27 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:08:46,369] [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_004514475.1	s__MEC069 sp004514475	99.97	1801	1860	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__MEC069	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014534655.1	s__Paenibacillus_E sp014534655	77.9653	305	1860	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_010820665.1	s__Paenibacillus_E sp010820665	77.9021	177	1860	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_001426375.1	s__Paenibacillus_E sp001426375	77.5783	189	1860	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_E	95.0	98.92	98.92	0.95	0.95	2	-
GCF_001399685.1	s__Paenibacillus_G sp001399685	77.5363	239	1860	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_G	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013141715.1	s__Paenibacillus_E phytorum	77.4376	208	1860	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_E	95.0	95.60	95.60	0.80	0.80	2	-
GCF_000829455.1	s__VKM-B-2647 sp000829455	77.417	290	1860	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_002027705.1	s__Paenibacillus_E ferrarius	77.3899	229	1860	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_000722545.1	s__Paenibacillus_G tyrfis	77.3798	242	1860	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_G	95.0	98.07	98.07	0.93	0.93	2	-
GCF_013204855.1	s__Paenibacillus_E alba	77.3491	240	1860	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_900104695.1	s__Paenibacillus_AI sp900104695	77.3267	182	1860	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_AI	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007829615.1	s__Paenibacillus_E sp007829615	77.2988	236	1860	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_017874035.1	s__Paenibacillus_E aceris	77.295	240	1860	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_E	95.0	99.99	99.99	1.00	1.00	2	-
GCF_910594985.1	s__Paenibacillus_G sp910594985	77.2792	227	1860	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_G	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004000785.1	s__Paenibacillus_G ehimensis	77.2689	262	1860	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_G	95.0	99.10	99.10	0.93	0.93	2	-
GCF_003217775.1	s__Paenibacillus_AB flagellatus	77.2261	275	1860	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_004307995.1	s__Paenibacillus_AF thalictri	77.193	221	1860	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_AF	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004000845.1	s__Paenibacillus_AA koleovorans	77.1596	216	1860	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_004354045.1	s__Paenibacillus_S piri	77.1565	260	1860	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_013141725.1	s__Paenibacillus_E planticolens	77.1395	290	1860	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_900101595.1	s__Paenibacillus_G sp900101595	77.0813	241	1860	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_G	95.0	100.00	100.00	0.99	0.99	2	-
GCF_005938385.1	s__Paenibacillus_AB mesophilus	76.9235	200	1860	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_003285015.1	s__Paenibacillus_V contaminans	76.9156	220	1860	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_V	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014705615.1	s__Paenibacillus_AB sp014705615	76.7976	199	1860	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_008084145.1	s__Paenibacillus_A faecis	76.5943	130	1860	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_009870825.1	s__Paenibacillus albilobatus	76.5362	128	1860	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	99.80	99.80	0.98	0.98	2	-
GCF_004000945.1	s__Paenibacillus lautus	76.1863	81	1860	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	96.53	96.53	0.89	0.89	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:08:46,370] [INFO] GTDB search result was written to GCF_004514475.2_ASM451447v2_genomic.fna/result_gtdb.tsv
[2024-01-24 12:08:46,371] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:08:46,376] [INFO] DFAST_QC result json was written to GCF_004514475.2_ASM451447v2_genomic.fna/dqc_result.json
[2024-01-24 12:08:46,376] [INFO] DFAST_QC completed!
[2024-01-24 12:08:46,376] [INFO] Total running time: 0h2m13s