[2024-01-24 13:58:10,230] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:58:10,232] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:58:10,232] [INFO] DQC Reference Directory: /var/lib/cwl/stgd7bf0a0e-34f5-4670-bfe4-36f4e79a7049/dqc_reference
[2024-01-24 13:58:11,361] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:58:11,362] [INFO] Task started: Prodigal
[2024-01-24 13:58:11,362] [INFO] Running command: gunzip -c /var/lib/cwl/stg955b2deb-6553-4404-bd00-75d5355bbedd/GCF_016908495.1_ASM1690849v1_genomic.fna.gz | prodigal -d GCF_016908495.1_ASM1690849v1_genomic.fna/cds.fna -a GCF_016908495.1_ASM1690849v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:58:20,269] [INFO] Task succeeded: Prodigal
[2024-01-24 13:58:20,269] [INFO] Task started: HMMsearch
[2024-01-24 13:58:20,269] [INFO] Running command: hmmsearch --tblout GCF_016908495.1_ASM1690849v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd7bf0a0e-34f5-4670-bfe4-36f4e79a7049/dqc_reference/reference_markers.hmm GCF_016908495.1_ASM1690849v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:58:20,509] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:58:20,510] [INFO] Found 6/6 markers.
[2024-01-24 13:58:20,547] [INFO] Query marker FASTA was written to GCF_016908495.1_ASM1690849v1_genomic.fna/markers.fasta
[2024-01-24 13:58:20,547] [INFO] Task started: Blastn
[2024-01-24 13:58:20,547] [INFO] Running command: blastn -query GCF_016908495.1_ASM1690849v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd7bf0a0e-34f5-4670-bfe4-36f4e79a7049/dqc_reference/reference_markers.fasta -out GCF_016908495.1_ASM1690849v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:21,101] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:21,104] [INFO] Selected 25 target genomes.
[2024-01-24 13:58:21,104] [INFO] Target genome list was writen to GCF_016908495.1_ASM1690849v1_genomic.fna/target_genomes.txt
[2024-01-24 13:58:21,133] [INFO] Task started: fastANI
[2024-01-24 13:58:21,134] [INFO] Running command: fastANI --query /var/lib/cwl/stg955b2deb-6553-4404-bd00-75d5355bbedd/GCF_016908495.1_ASM1690849v1_genomic.fna.gz --refList GCF_016908495.1_ASM1690849v1_genomic.fna/target_genomes.txt --output GCF_016908495.1_ASM1690849v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:58:38,109] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:38,110] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd7bf0a0e-34f5-4670-bfe4-36f4e79a7049/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:58:38,110] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd7bf0a0e-34f5-4670-bfe4-36f4e79a7049/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:58:38,122] [INFO] Found 22 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:58:38,122] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:58:38,123] [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 pakistanensis	strain=DSM 24834	GCA_016908495.1	992288	992288	type	True	100.0	1689	1690	95	conclusive
Rossellomorea arthrocnemi	strain=EAR8	GCA_904424705.1	2769542	2769542	type	True	77.7629	188	1690	95	below_threshold
Rossellomorea aquimaris	strain=TF12	GCA_001648555.1	189382	189382	suspected-type	True	77.6704	218	1690	95	below_threshold
Heyndrickxia vini	strain=JCM 19841	GCA_016772275.1	1476025	1476025	type	True	77.2621	126	1690	95	below_threshold
Margalitia shackletonii	strain=LMG 18435	GCA_001420715.1	157838	157838	type	True	77.2325	135	1690	95	below_threshold
Margalitia shackletonii	strain=LMG 18435	GCA_011008805.1	157838	157838	type	True	77.2294	132	1690	95	below_threshold
Bacillus dafuensis	strain=FJAT-25496	GCA_007995155.1	1742359	1742359	type	True	77.1682	150	1690	95	below_threshold
Heyndrickxia oleronia	strain=DSM 9356	GCA_017809215.1	38875	38875	type	True	77.1223	125	1690	95	below_threshold
Heyndrickxia oleronia	strain=DSM 9356	GCA_025263665.1	38875	38875	type	True	77.1152	130	1690	95	below_threshold
Cytobacillus depressus	strain=BZ1	GCA_008923245.1	1602942	1602942	type	True	77.0997	128	1690	95	below_threshold
Heyndrickxia oleronia	strain=DSM 9356	GCA_002009555.1	38875	38875	type	True	77.0775	115	1690	95	below_threshold
Neobacillus drentensis	strain=FJAT-10044	GCA_001636415.1	220684	220684	type	True	76.8733	102	1690	95	below_threshold
Sutcliffiella halmapala	strain=DSM 8723	GCA_002019665.1	79882	79882	type	True	76.7731	112	1690	95	below_threshold
Bacillus kwashiorkori	strain=SIT6	GCA_001375515.1	1522318	1522318	type	True	76.7654	57	1690	95	below_threshold
Gottfriedia solisilvae	strain=NEAU-cbsb5	GCA_002128405.1	1516104	1516104	type	True	76.618	84	1690	95	below_threshold
Gottfriedia solisilvae	strain=CGMCC 1.14993	GCA_014640495.1	1516104	1516104	type	True	76.618	84	1690	95	below_threshold
Niallia circulans	strain=NBRC 13626	GCA_001591585.1	1397	1397	suspected-type	True	76.6046	108	1690	95	below_threshold
Oceanobacillus senegalensis	strain=Marseille-P3587	GCA_900176885.1	1936063	1936063	type	True	76.5426	51	1690	95	below_threshold
Cytobacillus luteolus	strain=DSM 22388	GCA_017873715.1	682179	682179	type	True	76.4648	101	1690	95	below_threshold
Cytobacillus luteolus	strain=YIM 93174	GCA_014982515.1	682179	682179	type	True	76.3976	98	1690	95	below_threshold
Metabacillus crassostreae	strain=DSM 24486	GCA_016908395.1	929098	929098	type	True	76.3085	121	1690	95	below_threshold
Anaerobacillus alkaliphilus	strain=B16-10	GCA_004116265.1	1548597	1548597	type	True	76.0711	66	1690	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:58:38,124] [INFO] DFAST Taxonomy check result was written to GCF_016908495.1_ASM1690849v1_genomic.fna/tc_result.tsv
[2024-01-24 13:58:38,124] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:58:38,124] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:58:38,125] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd7bf0a0e-34f5-4670-bfe4-36f4e79a7049/dqc_reference/checkm_data
[2024-01-24 13:58:38,125] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:58:38,174] [INFO] Task started: CheckM
[2024-01-24 13:58:38,174] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016908495.1_ASM1690849v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016908495.1_ASM1690849v1_genomic.fna/checkm_input GCF_016908495.1_ASM1690849v1_genomic.fna/checkm_result
[2024-01-24 13:59:07,800] [INFO] Task succeeded: CheckM
[2024-01-24 13:59:07,801] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:59:07,821] [INFO] ===== Completeness check finished =====
[2024-01-24 13:59:07,822] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:59:07,822] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016908495.1_ASM1690849v1_genomic.fna/markers.fasta)
[2024-01-24 13:59:07,822] [INFO] Task started: Blastn
[2024-01-24 13:59:07,822] [INFO] Running command: blastn -query GCF_016908495.1_ASM1690849v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd7bf0a0e-34f5-4670-bfe4-36f4e79a7049/dqc_reference/reference_markers_gtdb.fasta -out GCF_016908495.1_ASM1690849v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:59:08,583] [INFO] Task succeeded: Blastn
[2024-01-24 13:59:08,586] [INFO] Selected 25 target genomes.
[2024-01-24 13:59:08,586] [INFO] Target genome list was writen to GCF_016908495.1_ASM1690849v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:59:08,598] [INFO] Task started: fastANI
[2024-01-24 13:59:08,598] [INFO] Running command: fastANI --query /var/lib/cwl/stg955b2deb-6553-4404-bd00-75d5355bbedd/GCF_016908495.1_ASM1690849v1_genomic.fna.gz --refList GCF_016908495.1_ASM1690849v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016908495.1_ASM1690849v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:59:26,930] [INFO] Task succeeded: fastANI
[2024-01-24 13:59:26,943] [INFO] Found 23 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:59:26,943] [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_016908495.1	s__Bacillus_BW pakistanensis	100.0	1689	1690	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_B;g__Bacillus_BW	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_008364765.1	s__Rossellomorea sp008364765	78.3517	246	1690	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_B;g__Rossellomorea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008180865.1	s__Rossellomorea aquimaris_D	78.1075	218	1690	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_B;g__Rossellomorea	95.0	97.97	97.96	0.89	0.89	3	-
GCF_002563655.1	s__Rossellomorea sp002563655	77.7573	175	1690	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_B;g__Rossellomorea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012911895.1	s__Rossellomorea sp012911895	77.7457	169	1690	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_B;g__Rossellomorea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003315075.1	s__Rossellomorea aquimaris_C	77.7408	190	1690	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_B;g__Rossellomorea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001648555.1	s__Rossellomorea aquimaris	77.7011	218	1690	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_B;g__Rossellomorea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001591825.1	s__Rossellomorea vietnamensis	77.6326	161	1690	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_B;g__Rossellomorea	95.0	97.54	97.34	0.88	0.87	6	-
GCF_000299035.1	s__Bacillus_A bingmayongensis	77.4885	94	1690	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_003667865.1	s__Bacillus_BQ marisflavi_A	77.4703	181	1690	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_003667825.1	s__Metabacillus litoralis_B	77.269	115	1690	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus	95.0	98.61	98.61	0.90	0.90	2	-
GCF_016772275.1	s__Heyndrickxia vini	77.2638	126	1690	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_014874135.1	s__Neobacillus sp014874135	77.2443	113	1690	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_001420715.1	s__Margalitia shackletonii	77.2325	135	1690	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_C;g__Margalitia	95.0	99.16	98.74	0.93	0.89	4	-
GCF_017809215.1	s__Heyndrickxia oleronia	77.1223	125	1690	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_C;g__Heyndrickxia	95.0	98.68	97.33	0.92	0.89	7	-
GCF_008923245.1	s__Cytobacillus depressus	77.0997	128	1690	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_003400205.1	s__Fredinandcohnia sp003400205	77.0088	96	1690	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_004799755.1	s__Fredinandcohnia timonensis_A	76.8476	102	1690	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_002019665.1	s__Sutcliffiella_A halmapala	76.7731	112	1690	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_I;g__Sutcliffiella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007679095.1	s__DE0126 sp007679095	76.6373	78	1690	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_C;g__DE0126	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017873715.1	s__Bacillus_BV luteolus	76.4805	98	1690	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_011393025.1	s__URHB0009 sp011393025	76.4613	97	1690	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__URHB0009	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002551815.1	s__Bacillus_A sp002551815	76.2066	102	1690	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	95.0	99.80	99.69	0.94	0.92	5	-
--------------------------------------------------------------------------------
[2024-01-24 13:59:26,944] [INFO] GTDB search result was written to GCF_016908495.1_ASM1690849v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:59:26,945] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:59:26,949] [INFO] DFAST_QC result json was written to GCF_016908495.1_ASM1690849v1_genomic.fna/dqc_result.json
[2024-01-24 13:59:26,949] [INFO] DFAST_QC completed!
[2024-01-24 13:59:26,949] [INFO] Total running time: 0h1m17s