[2024-01-24 14:46:35,386] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:46:35,388] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:46:35,389] [INFO] DQC Reference Directory: /var/lib/cwl/stg03c3554d-4708-4cfa-90bb-1b2d8edc457b/dqc_reference
[2024-01-24 14:46:36,623] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:46:36,624] [INFO] Task started: Prodigal
[2024-01-24 14:46:36,624] [INFO] Running command: gunzip -c /var/lib/cwl/stg6a3258bd-7a17-499a-8dc7-522933375d3e/GCF_003285015.1_ASM328501v1_genomic.fna.gz | prodigal -d GCF_003285015.1_ASM328501v1_genomic.fna/cds.fna -a GCF_003285015.1_ASM328501v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:47:05,946] [INFO] Task succeeded: Prodigal
[2024-01-24 14:47:05,947] [INFO] Task started: HMMsearch
[2024-01-24 14:47:05,947] [INFO] Running command: hmmsearch --tblout GCF_003285015.1_ASM328501v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg03c3554d-4708-4cfa-90bb-1b2d8edc457b/dqc_reference/reference_markers.hmm GCF_003285015.1_ASM328501v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:47:06,398] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:47:06,400] [INFO] Found 6/6 markers.
[2024-01-24 14:47:06,481] [INFO] Query marker FASTA was written to GCF_003285015.1_ASM328501v1_genomic.fna/markers.fasta
[2024-01-24 14:47:06,481] [INFO] Task started: Blastn
[2024-01-24 14:47:06,481] [INFO] Running command: blastn -query GCF_003285015.1_ASM328501v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg03c3554d-4708-4cfa-90bb-1b2d8edc457b/dqc_reference/reference_markers.fasta -out GCF_003285015.1_ASM328501v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:47:07,116] [INFO] Task succeeded: Blastn
[2024-01-24 14:47:07,121] [INFO] Selected 24 target genomes.
[2024-01-24 14:47:07,121] [INFO] Target genome list was writen to GCF_003285015.1_ASM328501v1_genomic.fna/target_genomes.txt
[2024-01-24 14:47:07,136] [INFO] Task started: fastANI
[2024-01-24 14:47:07,136] [INFO] Running command: fastANI --query /var/lib/cwl/stg6a3258bd-7a17-499a-8dc7-522933375d3e/GCF_003285015.1_ASM328501v1_genomic.fna.gz --refList GCF_003285015.1_ASM328501v1_genomic.fna/target_genomes.txt --output GCF_003285015.1_ASM328501v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:47:36,916] [INFO] Task succeeded: fastANI
[2024-01-24 14:47:36,917] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg03c3554d-4708-4cfa-90bb-1b2d8edc457b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:47:36,917] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg03c3554d-4708-4cfa-90bb-1b2d8edc457b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:47:36,939] [INFO] Found 24 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:47:36,940] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:47:36,940] [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 contaminans	strain=CKOBP-6	GCA_003285015.1	450362	450362	type	True	100.0	3364	3366	95	conclusive
Paenibacillus ginsengarvi	strain=KCTC 13059	GCA_003626695.1	400777	400777	type	True	77.8308	396	3366	95	below_threshold
Paenibacillus oceani	strain=IB182363	GCA_014705615.1	2772510	2772510	type	True	77.762	378	3366	95	below_threshold
Paenibacillus hemerocallicola	strain=KCTC 33185	GCA_006265175.1	1172614	1172614	type	True	77.5975	417	3366	95	below_threshold
Paenibacillus flagellatus	strain=DXL2	GCA_003217775.1	2211139	2211139	type	True	77.4448	400	3366	95	below_threshold
Paenibacillus piri	strain=MS74	GCA_004354045.1	2547395	2547395	type	True	77.2645	285	3366	95	below_threshold
Cohnella faecalis	strain=K2E09-144	GCA_003570905.1	2315694	2315694	type	True	77.17	181	3366	95	below_threshold
Paenibacillus beijingensis	strain=DSM 24997	GCA_000961095.1	1126833	1126833	type	True	77.027	173	3366	95	below_threshold
Paenibacillus darwinianus	strain=Br	GCA_000598065.1	1380763	1380763	type	True	76.9617	122	3366	95	below_threshold
Paenibacillus ehimensis	strain=NBRC 15659	GCA_004000785.1	79264	79264	type	True	76.957	288	3366	95	below_threshold
Paenibacillus doosanensis	strain=CAU 1055	GCA_025060755.1	1229154	1229154	type	True	76.9494	314	3366	95	below_threshold
Paenibacillus cymbidii	strain=R196	GCA_004764705.1	1639034	1639034	type	True	76.9336	417	3366	95	below_threshold
Paenibacillus lycopersici	strain=12200R-189	GCA_010119935.1	2704462	2704462	type	True	76.6896	239	3366	95	below_threshold
Paenibacillus rigui	strain=JCM 16352	GCA_002234615.1	554312	554312	type	True	76.5643	180	3366	95	below_threshold
Paenibacillus validus	strain=NBRC 15382	GCA_004000985.1	44253	44253	type	True	76.5366	195	3366	95	below_threshold
Paenibacillus macerans	strain=ATCC 8244	GCA_000746875.1	44252	44252	type	True	76.486	160	3366	95	below_threshold
Paenibacillus ginsengihumi	strain=DSM 21568	GCA_000380965.1	431596	431596	type	True	76.4787	230	3366	95	below_threshold
Paenibacillus sonchi	strain=LMG 24727	GCA_016772475.1	373687	373687	type	True	76.476	121	3366	95	below_threshold
Paenibacillus thermoaerophilus	strain=DSM 26310	GCA_005938195.1	1215385	1215385	type	True	76.4366	175	3366	95	below_threshold
Cohnella candidum	strain=18JY8-7	GCA_003713065.1	2674991	2674991	type	True	76.384	139	3366	95	below_threshold
Paenibacillus bouchesdurhonensis	strain=Marseille-P3071	GCA_900155685.1	1870990	1870990	type	True	76.319	90	3366	95	below_threshold
Paenibacillus timonensis	strain=DSM 16943	GCA_022427145.1	225915	225915	type	True	76.3086	132	3366	95	below_threshold
Paenibacillus albicereus	strain=UniB2	GCA_012676905.1	2726185	2726185	type	True	76.1886	145	3366	95	below_threshold
Paenibacillus turpanensis	strain=YIM B00363	GCA_011421635.1	2689078	2689078	type	True	76.1389	135	3366	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:47:36,945] [INFO] DFAST Taxonomy check result was written to GCF_003285015.1_ASM328501v1_genomic.fna/tc_result.tsv
[2024-01-24 14:47:36,946] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:47:36,946] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:47:36,946] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg03c3554d-4708-4cfa-90bb-1b2d8edc457b/dqc_reference/checkm_data
[2024-01-24 14:47:36,947] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:47:37,043] [INFO] Task started: CheckM
[2024-01-24 14:47:37,043] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003285015.1_ASM328501v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003285015.1_ASM328501v1_genomic.fna/checkm_input GCF_003285015.1_ASM328501v1_genomic.fna/checkm_result
[2024-01-24 14:48:55,343] [INFO] Task succeeded: CheckM
[2024-01-24 14:48:55,344] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:48:55,369] [INFO] ===== Completeness check finished =====
[2024-01-24 14:48:55,369] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:48:55,370] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003285015.1_ASM328501v1_genomic.fna/markers.fasta)
[2024-01-24 14:48:55,370] [INFO] Task started: Blastn
[2024-01-24 14:48:55,370] [INFO] Running command: blastn -query GCF_003285015.1_ASM328501v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg03c3554d-4708-4cfa-90bb-1b2d8edc457b/dqc_reference/reference_markers_gtdb.fasta -out GCF_003285015.1_ASM328501v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:48:56,276] [INFO] Task succeeded: Blastn
[2024-01-24 14:48:56,280] [INFO] Selected 22 target genomes.
[2024-01-24 14:48:56,281] [INFO] Target genome list was writen to GCF_003285015.1_ASM328501v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:48:56,303] [INFO] Task started: fastANI
[2024-01-24 14:48:56,304] [INFO] Running command: fastANI --query /var/lib/cwl/stg6a3258bd-7a17-499a-8dc7-522933375d3e/GCF_003285015.1_ASM328501v1_genomic.fna.gz --refList GCF_003285015.1_ASM328501v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003285015.1_ASM328501v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:49:25,945] [INFO] Task succeeded: fastANI
[2024-01-24 14:49:26,007] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:49:26,007] [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_003285015.1	s__Paenibacillus_V contaminans	100.0	3364	3366	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	conclusive
GCF_006265175.1	s__Paenibacillus_AB hemerocallicola	77.589	417	3366	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_003217775.1	s__Paenibacillus_AB flagellatus	77.3999	407	3366	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_001399685.1	s__Paenibacillus_G sp001399685	77.3797	302	3366	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_910593845.1	s__Paenibacillus_G solanacearum	77.3052	301	3366	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_004354045.1	s__Paenibacillus_S piri	77.2445	287	3366	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_018998565.1	s__Paenibacillus_G sp018998565	77.0219	311	3366	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_000961095.1	s__Paenibacillus_O beijingensis	77.0084	172	3366	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_004764705.1	s__R196 sp004764705	76.8831	421	3366	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__R196	95.0	95.77	95.77	0.86	0.86	2	-
GCF_004514475.1	s__MEC069 sp004514475	76.8807	211	3366	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_010119935.1	s__Paenibacillus_Z lycopersici	76.6879	241	3366	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_000250655.1	s__Paenibacillus_G mucilaginosus	76.6639	197	3366	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_G	95.0	98.86	98.79	0.96	0.95	3	-
GCF_007786445.1	s__Paenibacillus_G sp007786445	76.593	204	3366	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_002234615.1	s__Paenibacillus_S rigui	76.5869	179	3366	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_004000985.1	s__Paenibacillus_G validus	76.5378	193	3366	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_G	95.0	99.29	99.15	0.90	0.89	6	-
GCF_000380965.1	s__Paenibacillus_M ginsengihumi	76.4787	230	3366	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_018918005.1	s__MSJ-34 sp018918005	76.4779	204	3366	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__MSJ-34	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005938195.1	s__Paenibacillus_W thermoaerophilus	76.4683	176	3366	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Reconcilibacillaceae;g__Paenibacillus_W	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003713065.1	s__Cohnella candidum	76.3869	138	3366	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Cohnella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009725205.1	s__Paenibacillus_A timonensis	76.3817	114	3366	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_A	95.0	98.34	98.12	0.92	0.92	3	-
GCF_900155685.1	s__Paenibacillus_A bouchesdurhonensis	76.2465	89	3366	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_011421635.1	s__Paenibacillus_AK turpanensis	76.1389	135	3366	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	-
--------------------------------------------------------------------------------
[2024-01-24 14:49:26,010] [INFO] GTDB search result was written to GCF_003285015.1_ASM328501v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:49:26,011] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:49:26,015] [INFO] DFAST_QC result json was written to GCF_003285015.1_ASM328501v1_genomic.fna/dqc_result.json
[2024-01-24 14:49:26,016] [INFO] DFAST_QC completed!
[2024-01-24 14:49:26,016] [INFO] Total running time: 0h2m51s