[2024-01-25 17:39:35,567] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:39:35,572] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:39:35,572] [INFO] DQC Reference Directory: /var/lib/cwl/stgf6d875b5-0cbd-45d9-a25b-11712ae1b671/dqc_reference
[2024-01-25 17:39:36,716] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:39:36,717] [INFO] Task started: Prodigal
[2024-01-25 17:39:36,717] [INFO] Running command: gunzip -c /var/lib/cwl/stg2244a202-22f0-42e3-8676-974dd45dfdfa/GCF_014638995.1_ASM1463899v1_genomic.fna.gz | prodigal -d GCF_014638995.1_ASM1463899v1_genomic.fna/cds.fna -a GCF_014638995.1_ASM1463899v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:39:43,958] [INFO] Task succeeded: Prodigal
[2024-01-25 17:39:43,958] [INFO] Task started: HMMsearch
[2024-01-25 17:39:43,959] [INFO] Running command: hmmsearch --tblout GCF_014638995.1_ASM1463899v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf6d875b5-0cbd-45d9-a25b-11712ae1b671/dqc_reference/reference_markers.hmm GCF_014638995.1_ASM1463899v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:39:44,199] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:39:44,200] [INFO] Found 6/6 markers.
[2024-01-25 17:39:44,232] [INFO] Query marker FASTA was written to GCF_014638995.1_ASM1463899v1_genomic.fna/markers.fasta
[2024-01-25 17:39:44,232] [INFO] Task started: Blastn
[2024-01-25 17:39:44,233] [INFO] Running command: blastn -query GCF_014638995.1_ASM1463899v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf6d875b5-0cbd-45d9-a25b-11712ae1b671/dqc_reference/reference_markers.fasta -out GCF_014638995.1_ASM1463899v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:39:44,810] [INFO] Task succeeded: Blastn
[2024-01-25 17:39:44,813] [INFO] Selected 25 target genomes.
[2024-01-25 17:39:44,813] [INFO] Target genome list was writen to GCF_014638995.1_ASM1463899v1_genomic.fna/target_genomes.txt
[2024-01-25 17:39:44,829] [INFO] Task started: fastANI
[2024-01-25 17:39:44,829] [INFO] Running command: fastANI --query /var/lib/cwl/stg2244a202-22f0-42e3-8676-974dd45dfdfa/GCF_014638995.1_ASM1463899v1_genomic.fna.gz --refList GCF_014638995.1_ASM1463899v1_genomic.fna/target_genomes.txt --output GCF_014638995.1_ASM1463899v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:40:03,230] [INFO] Task succeeded: fastANI
[2024-01-25 17:40:03,230] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf6d875b5-0cbd-45d9-a25b-11712ae1b671/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:40:03,231] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf6d875b5-0cbd-45d9-a25b-11712ae1b671/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:40:03,242] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:40:03,242] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:40:03,242] [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 oceani	strain=CGMCC 1.12754	GCA_014638995.1	1479511	1479511	type	True	100.0	1259	1260	95	conclusive
Virgibacillus ndiopensis	strain=Marseille-P3835	GCA_900187325.1	2004408	2004408	type	True	83.1728	908	1260	95	below_threshold
Virgibacillus phasianinus	strain=LM2416	GCA_002216775.1	2017483	2017483	type	True	78.2761	197	1260	95	below_threshold
Virgibacillus dakarensis	strain=Marseille-P3469	GCA_900155625.1	1917889	1917889	type	True	77.6878	323	1260	95	below_threshold
Virgibacillus doumboii	strain=Marseille-Q1616	GCA_902806455.1	2697503	2697503	type	True	77.6228	210	1260	95	below_threshold
Virgibacillus litoralis	strain=DSM 21085	GCA_017873675.1	578221	578221	type	True	77.4973	220	1260	95	below_threshold
Virgibacillus halodenitrificans	strain=JCM 12304	GCA_001310895.1	1482	1482	type	True	77.4822	155	1260	95	below_threshold
Virgibacillus subterraneus	strain=CGMCC 1.7734	GCA_900110695.1	621109	621109	type	True	77.3687	223	1260	95	below_threshold
Virgibacillus profundi	strain=P3-H5	GCA_002287375.1	2024555	2024555	type	True	77.3585	239	1260	95	below_threshold
Oceanobacillus jordanicus	strain=GSFE11	GCA_022095695.1	2867266	2867266	type	True	77.2781	146	1260	95	below_threshold
Virgibacillus massiliensis	strain=Vm-5	GCA_000723585.1	1462526	1462526	suspected-type	True	77.2767	162	1260	95	below_threshold
Oceanobacillus salinisoli	strain=YIM B00359	GCA_009733865.1	2678611	2678611	type	True	77.1714	133	1260	95	below_threshold
Virgibacillus halotolerans	strain=DSM 25060	GCA_016908515.1	1071053	1071053	type	True	77.105	160	1260	95	below_threshold
Oceanobacillus polygoni	strain=SA9	GCA_008304605.1	1235259	1235259	type	True	76.8889	136	1260	95	below_threshold
Gracilibacillus suaedae	strain=LD4P30	GCA_017599345.1	2820273	2820273	type	True	76.8606	62	1260	95	below_threshold
Aquibacillus sediminis	strain=BH258	GCA_005870085.1	2574734	2574734	type	True	76.7887	89	1260	95	below_threshold
Pontibacillus yanchengensis	strain=Y32	GCA_000770635.1	462910	462910	type	True	76.7344	54	1260	95	below_threshold
Saliterribacillus persicus	strain=DSM 27696	GCA_003337485.1	930114	930114	type	True	76.4876	65	1260	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:40:03,243] [INFO] DFAST Taxonomy check result was written to GCF_014638995.1_ASM1463899v1_genomic.fna/tc_result.tsv
[2024-01-25 17:40:03,244] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:40:03,244] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:40:03,244] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf6d875b5-0cbd-45d9-a25b-11712ae1b671/dqc_reference/checkm_data
[2024-01-25 17:40:03,245] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:40:03,284] [INFO] Task started: CheckM
[2024-01-25 17:40:03,284] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014638995.1_ASM1463899v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014638995.1_ASM1463899v1_genomic.fna/checkm_input GCF_014638995.1_ASM1463899v1_genomic.fna/checkm_result
[2024-01-25 17:40:29,436] [INFO] Task succeeded: CheckM
[2024-01-25 17:40:29,436] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:40:29,466] [INFO] ===== Completeness check finished =====
[2024-01-25 17:40:29,466] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:40:29,467] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014638995.1_ASM1463899v1_genomic.fna/markers.fasta)
[2024-01-25 17:40:29,467] [INFO] Task started: Blastn
[2024-01-25 17:40:29,467] [INFO] Running command: blastn -query GCF_014638995.1_ASM1463899v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf6d875b5-0cbd-45d9-a25b-11712ae1b671/dqc_reference/reference_markers_gtdb.fasta -out GCF_014638995.1_ASM1463899v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:40:30,330] [INFO] Task succeeded: Blastn
[2024-01-25 17:40:30,333] [INFO] Selected 23 target genomes.
[2024-01-25 17:40:30,333] [INFO] Target genome list was writen to GCF_014638995.1_ASM1463899v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:40:30,365] [INFO] Task started: fastANI
[2024-01-25 17:40:30,366] [INFO] Running command: fastANI --query /var/lib/cwl/stg2244a202-22f0-42e3-8676-974dd45dfdfa/GCF_014638995.1_ASM1463899v1_genomic.fna.gz --refList GCF_014638995.1_ASM1463899v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014638995.1_ASM1463899v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:40:47,549] [INFO] Task succeeded: fastANI
[2024-01-25 17:40:47,561] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:40:47,561] [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_014638995.1	s__Virgibacillus_E oceani	100.0	1259	1260	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	conclusive
GCF_900187325.1	s__Virgibacillus_E ndiopensis	83.1767	909	1260	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_002216775.1	s__Virgibacillus_F phasianinus	78.2881	195	1260	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Virgibacillus_F	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900258515.1	s__Virgibacillus_E sp900258515	78.0247	315	1260	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	-
GCA_014642895.1	s__Virgibacillus_E populi	77.777	306	1260	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Virgibacillus_E	95.0	98.98	98.88	0.86	0.85	5	-
GCF_902806455.1	s__Lentibacillus doumboii	77.6184	211	1260	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Lentibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000725285.1	s__Virgibacillus sp000725285	77.5152	156	1260	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_002224365.1	s__Virgibacillus_F necropolis	77.5114	213	1260	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Virgibacillus_F	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017873675.1	s__Lentibacillus litoralis	77.4971	220	1260	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Lentibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001310895.1	s__Virgibacillus halodenitrificans	77.4632	154	1260	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_900129485.1	s__Ornithinibacillus halophilus	77.4613	136	1260	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_014905415.1	s__Virgibacillus salexigens	77.412	160	1260	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Virgibacillus	95.0	99.53	99.42	0.93	0.91	9	-
GCF_002287375.1	s__Virgibacillus_G profundi	77.3703	238	1260	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_900110695.1	s__Lentibacillus subterraneus	77.368	223	1260	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_000724085.1	s__Virgibacillus manasiensis	77.1522	138	1260	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_900129865.1	s__Virgibacillus chiguensis	77.0797	112	1260	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_016908515.1	s__Virgibacillus_I halotolerans	77.0731	160	1260	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Virgibacillus_I	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000482485.1	s__Ornithinibacillus globulus	77.0496	143	1260	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_000770635.1	s__Pontibacillus yanchengensis	76.6941	55	1260	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Halobacillaceae;g__Pontibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003337485.1	s__Saliterribacillus persicus	76.4876	65	1260	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Saliterribacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:40:47,562] [INFO] GTDB search result was written to GCF_014638995.1_ASM1463899v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:40:47,563] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:40:47,567] [INFO] DFAST_QC result json was written to GCF_014638995.1_ASM1463899v1_genomic.fna/dqc_result.json
[2024-01-25 17:40:47,567] [INFO] DFAST_QC completed!
[2024-01-25 17:40:47,567] [INFO] Total running time: 0h1m12s