[2024-01-24 15:27:02,024] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:27:02,026] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:27:02,027] [INFO] DQC Reference Directory: /var/lib/cwl/stg7f264ec3-712c-47c8-9117-bead1c91c20b/dqc_reference
[2024-01-24 15:27:03,188] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:27:03,189] [INFO] Task started: Prodigal
[2024-01-24 15:27:03,189] [INFO] Running command: gunzip -c /var/lib/cwl/stg3bd12b05-c252-45dd-bcb3-184909e77c27/GCF_017873675.1_ASM1787367v1_genomic.fna.gz | prodigal -d GCF_017873675.1_ASM1787367v1_genomic.fna/cds.fna -a GCF_017873675.1_ASM1787367v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:27:11,117] [INFO] Task succeeded: Prodigal
[2024-01-24 15:27:11,118] [INFO] Task started: HMMsearch
[2024-01-24 15:27:11,118] [INFO] Running command: hmmsearch --tblout GCF_017873675.1_ASM1787367v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7f264ec3-712c-47c8-9117-bead1c91c20b/dqc_reference/reference_markers.hmm GCF_017873675.1_ASM1787367v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:27:11,397] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:27:11,399] [INFO] Found 6/6 markers.
[2024-01-24 15:27:11,437] [INFO] Query marker FASTA was written to GCF_017873675.1_ASM1787367v1_genomic.fna/markers.fasta
[2024-01-24 15:27:11,438] [INFO] Task started: Blastn
[2024-01-24 15:27:11,438] [INFO] Running command: blastn -query GCF_017873675.1_ASM1787367v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7f264ec3-712c-47c8-9117-bead1c91c20b/dqc_reference/reference_markers.fasta -out GCF_017873675.1_ASM1787367v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:27:12,029] [INFO] Task succeeded: Blastn
[2024-01-24 15:27:12,034] [INFO] Selected 25 target genomes.
[2024-01-24 15:27:12,034] [INFO] Target genome list was writen to GCF_017873675.1_ASM1787367v1_genomic.fna/target_genomes.txt
[2024-01-24 15:27:12,115] [INFO] Task started: fastANI
[2024-01-24 15:27:12,115] [INFO] Running command: fastANI --query /var/lib/cwl/stg3bd12b05-c252-45dd-bcb3-184909e77c27/GCF_017873675.1_ASM1787367v1_genomic.fna.gz --refList GCF_017873675.1_ASM1787367v1_genomic.fna/target_genomes.txt --output GCF_017873675.1_ASM1787367v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:27:32,126] [INFO] Task succeeded: fastANI
[2024-01-24 15:27:32,126] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7f264ec3-712c-47c8-9117-bead1c91c20b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:27:32,127] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7f264ec3-712c-47c8-9117-bead1c91c20b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:27:32,142] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:27:32,142] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:27:32,142] [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 litoralis	strain=DSM 21085	GCA_017873675.1	578221	578221	type	True	100.0	1264	1269	95	conclusive
Virgibacillus subterraneus	strain=CGMCC 1.7734	GCA_900110695.1	621109	621109	type	True	92.7156	1066	1269	95	below_threshold
Virgibacillus doumboii	strain=Marseille-Q1616	GCA_902806455.1	2697503	2697503	type	True	78.3235	409	1269	95	below_threshold
Virgibacillus indicus	strain=P2-C2	GCA_002266285.1	2024554	2024554	type	True	77.3406	196	1269	95	below_threshold
Gracilibacillus salitolerans	strain=SCU50	GCA_009650095.1	2663022	2663022	type	True	77.3275	80	1269	95	below_threshold
Virgibacillus oceani	strain=CGMCC 1.12754	GCA_014638995.1	1479511	1479511	type	True	77.1843	233	1269	95	below_threshold
Virgibacillus profundi	strain=P3-H5	GCA_002287375.1	2024555	2024555	type	True	77.1263	225	1269	95	below_threshold
Ornithinibacillus halophilus	strain=IBRC-M 10683	GCA_900129485.1	930117	930117	type	True	77.0621	131	1269	95	below_threshold
Ornithinibacillus contaminans	strain=DSM 22953	GCA_001038425.2	694055	694055	type	True	76.9606	118	1269	95	below_threshold
Oceanobacillus arenosus	strain=CAU 1183	GCA_003369575.1	1229153	1229153	type	True	76.948	115	1269	95	below_threshold
Virgibacillus dakarensis	strain=Marseille-P3469	GCA_900155625.1	1917889	1917889	type	True	76.9283	201	1269	95	below_threshold
Virgibacillus halodenitrificans	strain=JCM 12304	GCA_001310895.1	1482	1482	type	True	76.9033	137	1269	95	below_threshold
Lentibacillus halodurans	strain=CGMCC 1.3702	GCA_900112045.1	237679	237679	type	True	76.8648	179	1269	95	below_threshold
Oceanobacillus piezotolerans	strain=YLB-02	GCA_003665065.1	2448030	2448030	type	True	76.7921	95	1269	95	below_threshold
Lentibacillus kapialis	strain=JCM 12580	GCA_014646635.1	340214	340214	type	True	76.7892	134	1269	95	below_threshold
Gracilibacillus suaedae	strain=LD4P30	GCA_017599345.1	2820273	2820273	type	True	76.7761	60	1269	95	below_threshold
Gracilibacillus lacisalsi	strain=DSM 19029	GCA_000377765.1	393087	393087	type	True	76.2944	68	1269	95	below_threshold
Gracilibacillus saliphilus	strain=YIM 91119	GCA_010994085.1	543890	543890	type	True	76.1812	68	1269	95	below_threshold
Gracilibacillus thailandensis	strain=TP2-8	GCA_010994055.1	563735	563735	type	True	76.1438	59	1269	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:27:32,149] [INFO] DFAST Taxonomy check result was written to GCF_017873675.1_ASM1787367v1_genomic.fna/tc_result.tsv
[2024-01-24 15:27:32,150] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:27:32,150] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:27:32,150] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7f264ec3-712c-47c8-9117-bead1c91c20b/dqc_reference/checkm_data
[2024-01-24 15:27:32,151] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:27:32,189] [INFO] Task started: CheckM
[2024-01-24 15:27:32,189] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017873675.1_ASM1787367v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017873675.1_ASM1787367v1_genomic.fna/checkm_input GCF_017873675.1_ASM1787367v1_genomic.fna/checkm_result
[2024-01-24 15:28:02,272] [INFO] Task succeeded: CheckM
[2024-01-24 15:28:02,273] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:28:02,295] [INFO] ===== Completeness check finished =====
[2024-01-24 15:28:02,296] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:28:02,296] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017873675.1_ASM1787367v1_genomic.fna/markers.fasta)
[2024-01-24 15:28:02,296] [INFO] Task started: Blastn
[2024-01-24 15:28:02,297] [INFO] Running command: blastn -query GCF_017873675.1_ASM1787367v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7f264ec3-712c-47c8-9117-bead1c91c20b/dqc_reference/reference_markers_gtdb.fasta -out GCF_017873675.1_ASM1787367v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:28:03,039] [INFO] Task succeeded: Blastn
[2024-01-24 15:28:03,042] [INFO] Selected 23 target genomes.
[2024-01-24 15:28:03,042] [INFO] Target genome list was writen to GCF_017873675.1_ASM1787367v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:28:03,064] [INFO] Task started: fastANI
[2024-01-24 15:28:03,064] [INFO] Running command: fastANI --query /var/lib/cwl/stg3bd12b05-c252-45dd-bcb3-184909e77c27/GCF_017873675.1_ASM1787367v1_genomic.fna.gz --refList GCF_017873675.1_ASM1787367v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017873675.1_ASM1787367v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:28:19,797] [INFO] Task succeeded: fastANI
[2024-01-24 15:28:19,819] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:28:19,819] [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_017873675.1	s__Lentibacillus litoralis	100.0	1264	1269	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Lentibacillus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900110695.1	s__Lentibacillus subterraneus	92.7246	1065	1269	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_902806455.1	s__Lentibacillus doumboii	78.2796	415	1269	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_900187325.1	s__Virgibacillus_E ndiopensis	77.4008	256	1269	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_002266285.1	s__Virgibacillus_G indicus	77.341	196	1269	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_900258515.1	s__Virgibacillus_E sp900258515	77.2693	236	1269	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_014638995.1	s__Virgibacillus_E oceani	77.2078	230	1269	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_016919725.1	s__Virgibacillus sp016919725	77.2013	146	1269	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Virgibacillus	95.0	99.34	99.27	0.95	0.91	5	-
GCF_009728145.1	s__Ornithinibacillus caprae	77.0118	160	1269	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_900129485.1	s__Ornithinibacillus halophilus	77.0096	132	1269	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_003369575.1	s__Oceanobacillus arenosus	76.9467	116	1269	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_900111445.1	s__Ornithinibacillus limi	76.9115	151	1269	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_001310895.1	s__Virgibacillus halodenitrificans	76.8841	138	1269	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_900112045.1	s__Lentibacillus halodurans	76.8648	180	1269	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_003612345.1	s__Virgibacillus sp003612345	76.8304	99	1269	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Virgibacillus	95.0	100.00	100.00	1.00	0.99	4	-
GCF_000725285.1	s__Virgibacillus sp000725285	76.8111	155	1269	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_003665065.1	s__Oceanobacillus piezotolerans	76.7899	95	1269	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_013373365.1	s__Lentibacillus sp013373365	76.6338	170	1269	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_000482485.1	s__Ornithinibacillus globulus	76.6275	129	1269	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_000377765.1	s__Gracilibacillus lacisalsi	76.2944	68	1269	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Gracilibacillus	95.0	95.88	95.36	0.83	0.81	4	-
--------------------------------------------------------------------------------
[2024-01-24 15:28:19,821] [INFO] GTDB search result was written to GCF_017873675.1_ASM1787367v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:28:19,821] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:28:19,825] [INFO] DFAST_QC result json was written to GCF_017873675.1_ASM1787367v1_genomic.fna/dqc_result.json
[2024-01-24 15:28:19,825] [INFO] DFAST_QC completed!
[2024-01-24 15:28:19,825] [INFO] Total running time: 0h1m18s