[2024-01-24 13:48:59,612] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:48:59,613] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:48:59,614] [INFO] DQC Reference Directory: /var/lib/cwl/stga3a5f8b8-ec73-4c90-bb9f-eb02aedf3c98/dqc_reference
[2024-01-24 13:49:01,021] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:01,022] [INFO] Task started: Prodigal
[2024-01-24 13:49:01,022] [INFO] Running command: gunzip -c /var/lib/cwl/stg58aeea39-ab16-4fd6-ad0f-d13757028fc3/GCF_023036475.1_ASM2303647v1_genomic.fna.gz | prodigal -d GCF_023036475.1_ASM2303647v1_genomic.fna/cds.fna -a GCF_023036475.1_ASM2303647v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:49:09,140] [INFO] Task succeeded: Prodigal
[2024-01-24 13:49:09,140] [INFO] Task started: HMMsearch
[2024-01-24 13:49:09,140] [INFO] Running command: hmmsearch --tblout GCF_023036475.1_ASM2303647v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga3a5f8b8-ec73-4c90-bb9f-eb02aedf3c98/dqc_reference/reference_markers.hmm GCF_023036475.1_ASM2303647v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:49:09,452] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:49:09,454] [INFO] Found 6/6 markers.
[2024-01-24 13:49:09,492] [INFO] Query marker FASTA was written to GCF_023036475.1_ASM2303647v1_genomic.fna/markers.fasta
[2024-01-24 13:49:09,493] [INFO] Task started: Blastn
[2024-01-24 13:49:09,493] [INFO] Running command: blastn -query GCF_023036475.1_ASM2303647v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga3a5f8b8-ec73-4c90-bb9f-eb02aedf3c98/dqc_reference/reference_markers.fasta -out GCF_023036475.1_ASM2303647v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:10,111] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:10,114] [INFO] Selected 27 target genomes.
[2024-01-24 13:49:10,115] [INFO] Target genome list was writen to GCF_023036475.1_ASM2303647v1_genomic.fna/target_genomes.txt
[2024-01-24 13:49:10,124] [INFO] Task started: fastANI
[2024-01-24 13:49:10,124] [INFO] Running command: fastANI --query /var/lib/cwl/stg58aeea39-ab16-4fd6-ad0f-d13757028fc3/GCF_023036475.1_ASM2303647v1_genomic.fna.gz --refList GCF_023036475.1_ASM2303647v1_genomic.fna/target_genomes.txt --output GCF_023036475.1_ASM2303647v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:49:27,760] [INFO] Task succeeded: fastANI
[2024-01-24 13:49:27,760] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga3a5f8b8-ec73-4c90-bb9f-eb02aedf3c98/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:49:27,761] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga3a5f8b8-ec73-4c90-bb9f-eb02aedf3c98/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:49:27,778] [INFO] Found 24 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:49:27,778] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:49:27,778] [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
Bacillus mesophilus	strain=DSM 101000	GCA_016908955.1	1808955	1808955	type	True	79.8796	524	1313	95	below_threshold
Bacillus mesophilus	strain=SA4	GCA_011008845.1	1808955	1808955	type	True	79.8439	530	1313	95	below_threshold
Bacillus suaedaesalsae	strain=RD4P76	GCA_016890225.1	2810349	2810349	type	True	78.1514	253	1313	95	below_threshold
Heyndrickxia vini	strain=JCM 19841	GCA_016772275.1	1476025	1476025	type	True	77.4241	62	1313	95	below_threshold
Neobacillus drentensis	strain=FJAT-10044	GCA_001636415.1	220684	220684	type	True	77.2947	63	1313	95	below_threshold
Metabacillus crassostreae	strain=DSM 24486	GCA_016908395.1	929098	929098	type	True	77.2269	110	1313	95	below_threshold
Metabacillus iocasae	strain=DSM 104297	GCA_016909075.1	2291674	2291674	type	True	77.1621	107	1313	95	below_threshold
Sutcliffiella deserti	strain=DG-18	GCA_020037475.1	2875501	2875501	type	True	77.14	79	1313	95	below_threshold
Neobacillus novalis	strain=FJAT-14227	GCA_001636395.1	220687	220687	type	True	77.1083	63	1313	95	below_threshold
Cytobacillus solani	strain=FJAT-18043	GCA_001420595.1	1637975	1637975	type	True	77.0914	79	1313	95	below_threshold
Neobacillus thermocopriae	strain=SgZ-7	GCA_010975035.1	1215031	1215031	type	True	76.958	56	1313	95	below_threshold
Metabacillus litoralis	strain=SW-211	GCA_007994985.1	152268	152268	suspected-type	True	76.9128	126	1313	95	below_threshold
Heyndrickxia oleronia	strain=DSM 9356	GCA_002009555.1	38875	38875	type	True	76.8663	67	1313	95	below_threshold
Metabacillus fastidiosus	strain=NBRC 101226	GCA_001591625.1	1458	1458	type	True	76.7663	80	1313	95	below_threshold
Bacillus suaedae	strain=YZJH907-2	GCA_017939705.1	2822140	2822140	type	True	76.7227	70	1313	95	below_threshold
Heyndrickxia oleronia	strain=DSM 9356	GCA_017809215.1	38875	38875	type	True	76.6886	73	1313	95	below_threshold
Heyndrickxia oleronia	strain=DSM 9356	GCA_025263665.1	38875	38875	type	True	76.5948	75	1313	95	below_threshold
Neobacillus novalis	strain=NBRC 102450	GCA_001591805.1	220687	220687	type	True	76.5574	61	1313	95	below_threshold
Gottfriedia solisilvae	strain=NEAU-cbsb5	GCA_002128405.1	1516104	1516104	type	True	76.5279	94	1313	95	below_threshold
Bacillus taeanensis	strain=BH030017	GCA_003318295.1	273032	273032	type	True	76.5234	83	1313	95	below_threshold
Gottfriedia solisilvae	strain=CGMCC 1.14993	GCA_014640495.1	1516104	1516104	type	True	76.5124	94	1313	95	below_threshold
Neobacillus sedimentimangrovi	strain=FJAT-2464	GCA_010614825.1	2699460	2699460	type	True	76.4876	63	1313	95	below_threshold
Peribacillus asahii	strain=MA001	GCA_003570725.1	228899	228899	suspected-type	True	76.423	72	1313	95	below_threshold
Pseudalkalibacillus decolorationis	strain=DSM 14890	GCA_024609785.1	163879	163879	type	True	75.8752	57	1313	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:49:27,812] [INFO] DFAST Taxonomy check result was written to GCF_023036475.1_ASM2303647v1_genomic.fna/tc_result.tsv
[2024-01-24 13:49:27,813] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:49:27,813] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:49:27,813] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga3a5f8b8-ec73-4c90-bb9f-eb02aedf3c98/dqc_reference/checkm_data
[2024-01-24 13:49:27,814] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:49:27,863] [INFO] Task started: CheckM
[2024-01-24 13:49:27,863] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_023036475.1_ASM2303647v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_023036475.1_ASM2303647v1_genomic.fna/checkm_input GCF_023036475.1_ASM2303647v1_genomic.fna/checkm_result
[2024-01-24 13:49:58,398] [INFO] Task succeeded: CheckM
[2024-01-24 13:49:58,399] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:49:58,419] [INFO] ===== Completeness check finished =====
[2024-01-24 13:49:58,420] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:49:58,420] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_023036475.1_ASM2303647v1_genomic.fna/markers.fasta)
[2024-01-24 13:49:58,420] [INFO] Task started: Blastn
[2024-01-24 13:49:58,421] [INFO] Running command: blastn -query GCF_023036475.1_ASM2303647v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga3a5f8b8-ec73-4c90-bb9f-eb02aedf3c98/dqc_reference/reference_markers_gtdb.fasta -out GCF_023036475.1_ASM2303647v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:59,247] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:59,251] [INFO] Selected 29 target genomes.
[2024-01-24 13:49:59,252] [INFO] Target genome list was writen to GCF_023036475.1_ASM2303647v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:49:59,304] [INFO] Task started: fastANI
[2024-01-24 13:49:59,304] [INFO] Running command: fastANI --query /var/lib/cwl/stg58aeea39-ab16-4fd6-ad0f-d13757028fc3/GCF_023036475.1_ASM2303647v1_genomic.fna.gz --refList GCF_023036475.1_ASM2303647v1_genomic.fna/target_genomes_gtdb.txt --output GCF_023036475.1_ASM2303647v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:50:22,521] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:22,543] [INFO] Found 29 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:50:22,543] [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_011008845.1	s__Bacillus_BS mesophilus	79.8639	528	1313	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__SA4;g__Bacillus_BS	95.0	100.00	100.00	1.00	1.00	2	-
GCF_016890225.1	s__Bacillus_BS sp016890225	78.1711	255	1313	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__SA4;g__Bacillus_BS	95.0	N/A	N/A	N/A	N/A	1	-
GCA_008364785.1	s__Bacillus_BS sp008364785	78.1358	261	1313	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__SA4;g__Bacillus_BS	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018613415.1	s__Neobacillus sp018613415	77.5104	77	1313	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Neobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016772275.1	s__Heyndrickxia vini	77.4298	61	1313	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_C;g__Heyndrickxia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017873715.1	s__Bacillus_BV luteolus	77.3984	158	1313	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_L;g__Bacillus_BV	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002335755.1	s__FJAT-45066 sp002335755	77.3702	106	1313	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_I;g__FJAT-45066	95.0	99.38	99.38	0.94	0.94	2	-
GCF_018613195.1	s__Mesobacillus sp018613195	77.3544	57	1313	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Mesobacillus	95.0	98.95	98.95	0.85	0.85	2	-
GCF_001274725.1	s__Cytobacillus globisporus	77.35	75	1313	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Cytobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016908395.1	s__Metabacillus crassostreae	77.2875	106	1313	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007678255.1	s__Neobacillus sp007678255	77.2632	71	1313	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Neobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002276165.1	s__Cytobacillus kochii	77.2215	79	1313	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Cytobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016909075.1	s__Priestia iocasae	77.2161	108	1313	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_H;g__Priestia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001866655.1	s__Neobacillus sp001866655	77.1166	78	1313	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Neobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001420595.1	s__Cytobacillus solani	77.0914	79	1313	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Cytobacillus	95.0	99.54	99.49	0.95	0.94	3	-
GCF_003667865.1	s__Bacillus_BQ marisflavi_A	76.9833	114	1313	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_B;g__Bacillus_BQ	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014856545.1	s__Mesobacillus sp014856545	76.9789	53	1313	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Mesobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010975035.1	s__Neobacillus thermocopriae	76.958	56	1313	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Neobacillus	95.0	95.41	95.38	0.92	0.91	3	-
GCF_007994985.1	s__Metabacillus litoralis	76.9295	126	1313	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003944835.1	s__HMF5848 sp003944835	76.9093	76	1313	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__HMF5848;g__HMF5848	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001591565.1	s__Priestia flexa	76.894	73	1313	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_H;g__Priestia	95.0	99.12	98.83	0.89	0.87	15	-
GCA_018333075.1	s__Heyndrickxia sporothermodurans_A	76.843	63	1313	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_C;g__Heyndrickxia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001591445.1	s__Neobacillus drentensis	76.8363	56	1313	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Neobacillus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003259415.1	s__Metabacillus sp003259415	76.7883	97	1313	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004799755.1	s__Fredinandcohnia timonensis_A	76.7829	104	1313	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_L;g__Fredinandcohnia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002571225.1	s__Bacillus_A sp002571225	76.6465	92	1313	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000299035.1	s__Bacillus_A bingmayongensis	76.6385	80	1313	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	95.0	97.40	97.40	0.86	0.86	2	-
GCF_001591805.1	s__Neobacillus novalis	76.5574	61	1313	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Neobacillus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002128405.1	s__Gottfriedia solisilvae	76.5279	94	1313	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Gottfriedia	95.0	98.14	96.28	0.93	0.87	3	-
--------------------------------------------------------------------------------
[2024-01-24 13:50:22,545] [INFO] GTDB search result was written to GCF_023036475.1_ASM2303647v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:50:22,546] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:50:22,551] [INFO] DFAST_QC result json was written to GCF_023036475.1_ASM2303647v1_genomic.fna/dqc_result.json
[2024-01-24 13:50:22,552] [INFO] DFAST_QC completed!
[2024-01-24 13:50:22,552] [INFO] Total running time: 0h1m23s