[2024-01-25 19:39:05,612] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:39:05,614] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:39:05,614] [INFO] DQC Reference Directory: /var/lib/cwl/stgc3dea032-5ca4-4a95-8309-bba8a060eb5f/dqc_reference
[2024-01-25 19:39:06,794] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:39:06,795] [INFO] Task started: Prodigal
[2024-01-25 19:39:06,795] [INFO] Running command: gunzip -c /var/lib/cwl/stga6a7d9da-1a40-413f-8580-6737f79e6918/GCF_017874115.1_ASM1787411v1_genomic.fna.gz | prodigal -d GCF_017874115.1_ASM1787411v1_genomic.fna/cds.fna -a GCF_017874115.1_ASM1787411v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:39:13,999] [INFO] Task succeeded: Prodigal
[2024-01-25 19:39:13,999] [INFO] Task started: HMMsearch
[2024-01-25 19:39:14,000] [INFO] Running command: hmmsearch --tblout GCF_017874115.1_ASM1787411v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc3dea032-5ca4-4a95-8309-bba8a060eb5f/dqc_reference/reference_markers.hmm GCF_017874115.1_ASM1787411v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:39:14,246] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:39:14,247] [INFO] Found 6/6 markers.
[2024-01-25 19:39:14,277] [INFO] Query marker FASTA was written to GCF_017874115.1_ASM1787411v1_genomic.fna/markers.fasta
[2024-01-25 19:39:14,278] [INFO] Task started: Blastn
[2024-01-25 19:39:14,278] [INFO] Running command: blastn -query GCF_017874115.1_ASM1787411v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc3dea032-5ca4-4a95-8309-bba8a060eb5f/dqc_reference/reference_markers.fasta -out GCF_017874115.1_ASM1787411v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:39:14,841] [INFO] Task succeeded: Blastn
[2024-01-25 19:39:14,844] [INFO] Selected 26 target genomes.
[2024-01-25 19:39:14,845] [INFO] Target genome list was writen to GCF_017874115.1_ASM1787411v1_genomic.fna/target_genomes.txt
[2024-01-25 19:39:14,857] [INFO] Task started: fastANI
[2024-01-25 19:39:14,857] [INFO] Running command: fastANI --query /var/lib/cwl/stga6a7d9da-1a40-413f-8580-6737f79e6918/GCF_017874115.1_ASM1787411v1_genomic.fna.gz --refList GCF_017874115.1_ASM1787411v1_genomic.fna/target_genomes.txt --output GCF_017874115.1_ASM1787411v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:39:34,867] [INFO] Task succeeded: fastANI
[2024-01-25 19:39:34,868] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc3dea032-5ca4-4a95-8309-bba8a060eb5f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:39:34,868] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc3dea032-5ca4-4a95-8309-bba8a060eb5f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:39:34,879] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:39:34,879] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:39:34,879] [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
Virgibacillus natechei	strain=DSM 25609	GCA_017874115.1	1216297	1216297	type	True	100.0	1247	1249	95	conclusive
Virgibacillus profundi	strain=P3-H5	GCA_002287375.1	2024555	2024555	type	True	77.8161	290	1249	95	below_threshold
Virgibacillus indicus	strain=P2-C2	GCA_002266285.1	2024554	2024554	type	True	77.5691	216	1249	95	below_threshold
Oceanobacillus jordanicus	strain=GSFE11	GCA_022095695.1	2867266	2867266	type	True	77.0174	142	1249	95	below_threshold
Virgibacillus pantothenticus	strain=DSM 26	GCA_900156795.1	1473	1473	type	True	76.9186	118	1249	95	below_threshold
Oceanobacillus arenosus	strain=CAU 1183	GCA_003369575.1	1229153	1229153	type	True	76.9045	150	1249	95	below_threshold
Virgibacillus pantothenticus	strain=DSM 26	GCA_018075365.1	1473	1473	type	True	76.858	118	1249	95	below_threshold
Virgibacillus pantothenticus	strain=DSM 26	GCA_001189575.1	1473	1473	type	True	76.8309	116	1249	95	below_threshold
Oceanobacillus chungangensis	strain=CAU 1051	GCA_003369565.1	1229152	1229152	type	True	76.7755	163	1249	95	below_threshold
Oceanobacillus senegalensis	strain=Marseille-P3587	GCA_900176885.1	1936063	1936063	type	True	76.6527	126	1249	95	below_threshold
Oceanobacillus salinisoli	strain=YIM B00359	GCA_009733865.1	2678611	2678611	type	True	76.6193	167	1249	95	below_threshold
Oceanobacillus bengalensis	strain=MCCC 1K00260	GCA_003628445.1	1435466	1435466	type	True	76.6172	148	1249	95	below_threshold
Virgibacillus chiguensis	strain=CGMCC 1.6496	GCA_900129865.1	411959	411959	type	True	76.6163	105	1249	95	below_threshold
Ornithinibacillus scapharcae	strain=TW25	GCA_000190475.2	1147159	1147159	type	True	76.3881	94	1249	95	below_threshold
Cerasibacillus quisquiliarum	strain=NBRC 102429	GCA_007991195.1	227865	227865	type	True	76.2982	56	1249	95	below_threshold
Cerasibacillus quisquiliarum	strain=DSM 15825	GCA_014202495.1	227865	227865	type	True	76.2535	56	1249	95	below_threshold
Paraliobacillus zengyii	strain=X-1125	GCA_003268595.1	2213194	2213194	type	True	76.1403	68	1249	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:39:34,880] [INFO] DFAST Taxonomy check result was written to GCF_017874115.1_ASM1787411v1_genomic.fna/tc_result.tsv
[2024-01-25 19:39:34,881] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:39:34,881] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:39:34,881] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc3dea032-5ca4-4a95-8309-bba8a060eb5f/dqc_reference/checkm_data
[2024-01-25 19:39:34,882] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:39:34,920] [INFO] Task started: CheckM
[2024-01-25 19:39:34,920] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017874115.1_ASM1787411v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017874115.1_ASM1787411v1_genomic.fna/checkm_input GCF_017874115.1_ASM1787411v1_genomic.fna/checkm_result
[2024-01-25 19:40:00,509] [INFO] Task succeeded: CheckM
[2024-01-25 19:40:00,509] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:40:00,551] [INFO] ===== Completeness check finished =====
[2024-01-25 19:40:00,551] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:40:00,552] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017874115.1_ASM1787411v1_genomic.fna/markers.fasta)
[2024-01-25 19:40:00,552] [INFO] Task started: Blastn
[2024-01-25 19:40:00,552] [INFO] Running command: blastn -query GCF_017874115.1_ASM1787411v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc3dea032-5ca4-4a95-8309-bba8a060eb5f/dqc_reference/reference_markers_gtdb.fasta -out GCF_017874115.1_ASM1787411v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:40:01,351] [INFO] Task succeeded: Blastn
[2024-01-25 19:40:01,354] [INFO] Selected 31 target genomes.
[2024-01-25 19:40:01,354] [INFO] Target genome list was writen to GCF_017874115.1_ASM1787411v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:40:01,380] [INFO] Task started: fastANI
[2024-01-25 19:40:01,380] [INFO] Running command: fastANI --query /var/lib/cwl/stga6a7d9da-1a40-413f-8580-6737f79e6918/GCF_017874115.1_ASM1787411v1_genomic.fna.gz --refList GCF_017874115.1_ASM1787411v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017874115.1_ASM1787411v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:40:25,100] [INFO] Task succeeded: fastANI
[2024-01-25 19:40:25,113] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:40:25,114] [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_017874115.1	s__Virgibacillus_H natechei	100.0	1247	1249	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Virgibacillus_H	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002287375.1	s__Virgibacillus_G profundi	77.8652	284	1249	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Virgibacillus_G	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002266285.1	s__Virgibacillus_G indicus	77.6218	209	1249	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Virgibacillus_G	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000612865.1	s__Virgibacillus picturae	77.1741	139	1249	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Virgibacillus	95.0	97.99	95.34	0.93	0.90	5	-
GCF_900187325.1	s__Virgibacillus_E ndiopensis	77.1068	167	1249	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Virgibacillus_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001310895.1	s__Virgibacillus halodenitrificans	77.0271	158	1249	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Virgibacillus	95.0	98.29	98.21	0.89	0.88	7	-
GCF_000724085.1	s__Virgibacillus manasiensis	77.0043	140	1249	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Virgibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110695.1	s__Lentibacillus subterraneus	76.9914	196	1249	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Lentibacillus	95.0	98.85	98.85	0.91	0.91	2	-
GCF_008304605.1	s__Oceanobacillus polygoni	76.8593	197	1249	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Oceanobacillus	95.0	99.99	99.99	1.00	1.00	2	-
GCF_003369575.1	s__Oceanobacillus arenosus	76.8578	150	1249	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Oceanobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018075365.1	s__Virgibacillus pantothenticus	76.8399	119	1249	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Virgibacillus	95.0	99.44	97.53	0.92	0.86	18	-
GCF_018333235.1	s__Ornithinibacillus bavariensis	76.8191	88	1249	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Ornithinibacillus	95.0	98.72	98.72	0.93	0.93	2	-
GCF_000482485.1	s__Ornithinibacillus globulus	76.7983	117	1249	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Ornithinibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003369565.1	s__Oceanobacillus chungangensis	76.7763	165	1249	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Oceanobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003628445.1	s__Oceanobacillus bengalensis	76.6861	139	1249	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Oceanobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900176885.1	s__Oceanobacillus senegalensis	76.6829	123	1249	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Oceanobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009733865.1	s__Oceanobacillus salinisoli	76.6523	159	1249	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Oceanobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129865.1	s__Virgibacillus chiguensis	76.6376	104	1249	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Virgibacillus	95.5968	98.02	97.78	0.91	0.87	3	-
GCF_900166595.1	s__Virgibacillus dokdonensis	76.543	116	1249	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Virgibacillus	95.5968	98.95	98.88	0.93	0.90	3	-
GCF_900184735.1	s__Ornithinibacillus globulus_B	76.4346	108	1249	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Ornithinibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000190475.1	s__Ornithinibacillus scapharcae	76.3881	94	1249	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Ornithinibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014202495.1	s__Cerasibacillus quisquiliarum	76.2535	56	1249	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Cerasibacillus	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-25 19:40:25,115] [INFO] GTDB search result was written to GCF_017874115.1_ASM1787411v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:40:25,116] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:40:25,119] [INFO] DFAST_QC result json was written to GCF_017874115.1_ASM1787411v1_genomic.fna/dqc_result.json
[2024-01-25 19:40:25,119] [INFO] DFAST_QC completed!
[2024-01-25 19:40:25,119] [INFO] Total running time: 0h1m20s