[2024-01-24 12:28:35,040] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:28:35,042] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:28:35,042] [INFO] DQC Reference Directory: /var/lib/cwl/stg28f48ffc-d9b1-4934-9f75-bbbc9dd876e1/dqc_reference
[2024-01-24 12:28:36,244] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:28:36,244] [INFO] Task started: Prodigal
[2024-01-24 12:28:36,244] [INFO] Running command: gunzip -c /var/lib/cwl/stg6f0366f2-5603-4279-bfd2-34f73616988a/GCF_020037475.1_ASM2003747v1_genomic.fna.gz | prodigal -d GCF_020037475.1_ASM2003747v1_genomic.fna/cds.fna -a GCF_020037475.1_ASM2003747v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:28:43,451] [INFO] Task succeeded: Prodigal
[2024-01-24 12:28:43,451] [INFO] Task started: HMMsearch
[2024-01-24 12:28:43,451] [INFO] Running command: hmmsearch --tblout GCF_020037475.1_ASM2003747v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg28f48ffc-d9b1-4934-9f75-bbbc9dd876e1/dqc_reference/reference_markers.hmm GCF_020037475.1_ASM2003747v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:28:43,703] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:28:43,705] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg6f0366f2-5603-4279-bfd2-34f73616988a/GCF_020037475.1_ASM2003747v1_genomic.fna.gz]
[2024-01-24 12:28:43,747] [INFO] Query marker FASTA was written to GCF_020037475.1_ASM2003747v1_genomic.fna/markers.fasta
[2024-01-24 12:28:43,748] [INFO] Task started: Blastn
[2024-01-24 12:28:43,748] [INFO] Running command: blastn -query GCF_020037475.1_ASM2003747v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg28f48ffc-d9b1-4934-9f75-bbbc9dd876e1/dqc_reference/reference_markers.fasta -out GCF_020037475.1_ASM2003747v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:28:44,366] [INFO] Task succeeded: Blastn
[2024-01-24 12:28:44,370] [INFO] Selected 20 target genomes.
[2024-01-24 12:28:44,370] [INFO] Target genome list was writen to GCF_020037475.1_ASM2003747v1_genomic.fna/target_genomes.txt
[2024-01-24 12:28:44,504] [INFO] Task started: fastANI
[2024-01-24 12:28:44,505] [INFO] Running command: fastANI --query /var/lib/cwl/stg6f0366f2-5603-4279-bfd2-34f73616988a/GCF_020037475.1_ASM2003747v1_genomic.fna.gz --refList GCF_020037475.1_ASM2003747v1_genomic.fna/target_genomes.txt --output GCF_020037475.1_ASM2003747v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:28:58,662] [INFO] Task succeeded: fastANI
[2024-01-24 12:28:58,663] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg28f48ffc-d9b1-4934-9f75-bbbc9dd876e1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:28:58,663] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg28f48ffc-d9b1-4934-9f75-bbbc9dd876e1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:28:58,677] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:28:58,677] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:28:58,677] [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
Sutcliffiella deserti	strain=DG-18	GCA_020037475.1	2875501	2875501	type	True	100.0	1141	1141	95	conclusive
Sutcliffiella halmapala	strain=DSM 8723	GCA_002019665.1	79882	79882	type	True	79.8195	420	1141	95	below_threshold
Sutcliffiella cohnii	strain=NBRC 15565	GCA_001591425.1	33932	33932	type	True	77.7864	145	1141	95	below_threshold
Sutcliffiella cohnii	strain=DSM 6307	GCA_002250055.1	33932	33932	type	True	77.6883	158	1141	95	below_threshold
Bacillus alkalisoli	strain=FJAT-45122	GCA_002797415.1	2011008	2011008	type	True	77.6746	182	1141	95	below_threshold
Bacillus paranthracis	strain=Mn5	GCA_001883995.1	2026186	2026186	type	True	77.3958	56	1141	95	below_threshold
Bacillus dafuensis	strain=FJAT-25496	GCA_007995155.1	1742359	1742359	type	True	77.27	69	1141	95	below_threshold
Bacillus proteolyticus	strain=TD42	GCA_001884065.1	2026192	2026192	type	True	77.1997	60	1141	95	below_threshold
Priestia endophytica	strain=DSM 13796	GCA_900115845.1	135735	135735	type	True	77.0962	60	1141	95	below_threshold
Bacillus mycoides	strain=DSM 2048	GCA_022630575.1	1405	1405	type	True	77.0627	70	1141	95	below_threshold
Metabacillus iocasae	strain=DSM 104297	GCA_016909075.1	2291674	2291674	type	True	76.9483	78	1141	95	below_threshold
Bacillus mycoides	strain=DSM 2048	GCA_000003925.1	1405	1405	type	True	76.8106	65	1141	95	below_threshold
Metabacillus flavus	strain=KIGAM252	GCA_018283675.1	2823519	2823519	type	True	76.7723	51	1141	95	below_threshold
Bacillus pakistanensis	strain=DSM 24834	GCA_016908495.1	992288	992288	type	True	76.6218	86	1141	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:28:58,679] [INFO] DFAST Taxonomy check result was written to GCF_020037475.1_ASM2003747v1_genomic.fna/tc_result.tsv
[2024-01-24 12:28:58,679] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:28:58,680] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:28:58,680] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg28f48ffc-d9b1-4934-9f75-bbbc9dd876e1/dqc_reference/checkm_data
[2024-01-24 12:28:58,681] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:28:58,718] [INFO] Task started: CheckM
[2024-01-24 12:28:58,718] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_020037475.1_ASM2003747v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_020037475.1_ASM2003747v1_genomic.fna/checkm_input GCF_020037475.1_ASM2003747v1_genomic.fna/checkm_result
[2024-01-24 12:29:25,891] [INFO] Task succeeded: CheckM
[2024-01-24 12:29:25,892] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:29:25,916] [INFO] ===== Completeness check finished =====
[2024-01-24 12:29:25,916] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:29:25,917] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_020037475.1_ASM2003747v1_genomic.fna/markers.fasta)
[2024-01-24 12:29:25,917] [INFO] Task started: Blastn
[2024-01-24 12:29:25,917] [INFO] Running command: blastn -query GCF_020037475.1_ASM2003747v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg28f48ffc-d9b1-4934-9f75-bbbc9dd876e1/dqc_reference/reference_markers_gtdb.fasta -out GCF_020037475.1_ASM2003747v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:29:26,807] [INFO] Task succeeded: Blastn
[2024-01-24 12:29:26,812] [INFO] Selected 20 target genomes.
[2024-01-24 12:29:26,812] [INFO] Target genome list was writen to GCF_020037475.1_ASM2003747v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:29:26,905] [INFO] Task started: fastANI
[2024-01-24 12:29:26,906] [INFO] Running command: fastANI --query /var/lib/cwl/stg6f0366f2-5603-4279-bfd2-34f73616988a/GCF_020037475.1_ASM2003747v1_genomic.fna.gz --refList GCF_020037475.1_ASM2003747v1_genomic.fna/target_genomes_gtdb.txt --output GCF_020037475.1_ASM2003747v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:29:40,972] [INFO] Task succeeded: fastANI
[2024-01-24 12:29:40,990] [INFO] Found 19 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:29:40,990] [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_002019665.1	s__Sutcliffiella_A halmapala	79.8429	418	1141	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_016908565.1	s__Sutcliffiella_A tianshenii	79.2729	374	1141	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_012524115.1	s__Sutcliffiella_A sp012524115	79.0359	294	1141	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	-
GCA_001648575.1	s__Sutcliffiella_A horikoshii	78.9704	275	1141	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_002157855.1	s__Sutcliffiella_A horikoshii_C	78.8893	302	1141	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_I;g__Sutcliffiella_A	95.0	96.53	95.82	0.92	0.90	4	-
GCA_001636495.1	s__Sutcliffiella_A horikoshii_A	78.865	316	1141	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_008180725.1	s__Sutcliffiella_A horikoshii_B	78.8304	305	1141	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_001293645.1	s__Sutcliffiella_A sp001293645	78.8035	313	1141	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_012911845.1	s__Sutcliffiella_A sp012911845	78.6949	291	1141	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_002335755.1	s__FJAT-45066 sp002335755	77.8116	176	1141	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_002250055.1	s__Sutcliffiella cohnii	77.7488	155	1141	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_I;g__Sutcliffiella	95.0	100.00	100.00	0.97	0.97	2	-
GCF_016909075.1	s__Priestia iocasae	76.9483	78	1141	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_002584985.1	s__Bacillus_A sp002584985	76.9152	63	1141	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	95.0	99.52	99.41	0.96	0.94	8	-
GCF_002975175.1	s__Bacillus_A sp002975175	76.8747	66	1141	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_007673305.1	s__Bacillus_A mycoides_C	76.7905	71	1141	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	95.0	95.83	95.78	0.82	0.81	3	-
GCF_014874135.1	s__Neobacillus sp014874135	76.7154	57	1141	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_016908495.1	s__Bacillus_BW pakistanensis	76.6218	86	1141	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	-
GCF_016820555.1	s__FJAT-46582 sp016820555	76.5291	65	1141	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Domibacillaceae;g__FJAT-46582	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001884235.1	s__Bacillus_A paramycoides	76.515	66	1141	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	95.0	97.72	97.18	0.88	0.85	10	-
--------------------------------------------------------------------------------
[2024-01-24 12:29:40,992] [INFO] GTDB search result was written to GCF_020037475.1_ASM2003747v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:29:40,992] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:29:41,288] [INFO] DFAST_QC result json was written to GCF_020037475.1_ASM2003747v1_genomic.fna/dqc_result.json
[2024-01-24 12:29:41,289] [INFO] DFAST_QC completed!
[2024-01-24 12:29:41,289] [INFO] Total running time: 0h1m6s