[2024-01-24 11:43:41,113] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:43:41,115] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:43:41,115] [INFO] DQC Reference Directory: /var/lib/cwl/stgf7f63651-b7c4-437d-a88a-b52f2258ea42/dqc_reference
[2024-01-24 11:43:42,502] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:43:42,503] [INFO] Task started: Prodigal
[2024-01-24 11:43:42,503] [INFO] Running command: gunzip -c /var/lib/cwl/stg2d05f246-a605-4e64-9d66-72d54792edb0/GCF_902726655.1_PRJEB35829_genomic.fna.gz | prodigal -d GCF_902726655.1_PRJEB35829_genomic.fna/cds.fna -a GCF_902726655.1_PRJEB35829_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:43:52,689] [INFO] Task succeeded: Prodigal
[2024-01-24 11:43:52,689] [INFO] Task started: HMMsearch
[2024-01-24 11:43:52,689] [INFO] Running command: hmmsearch --tblout GCF_902726655.1_PRJEB35829_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf7f63651-b7c4-437d-a88a-b52f2258ea42/dqc_reference/reference_markers.hmm GCF_902726655.1_PRJEB35829_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:43:53,061] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:43:53,062] [INFO] Found 6/6 markers.
[2024-01-24 11:43:53,097] [INFO] Query marker FASTA was written to GCF_902726655.1_PRJEB35829_genomic.fna/markers.fasta
[2024-01-24 11:43:53,097] [INFO] Task started: Blastn
[2024-01-24 11:43:53,097] [INFO] Running command: blastn -query GCF_902726655.1_PRJEB35829_genomic.fna/markers.fasta -db /var/lib/cwl/stgf7f63651-b7c4-437d-a88a-b52f2258ea42/dqc_reference/reference_markers.fasta -out GCF_902726655.1_PRJEB35829_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:43:53,707] [INFO] Task succeeded: Blastn
[2024-01-24 11:43:53,710] [INFO] Selected 24 target genomes.
[2024-01-24 11:43:53,710] [INFO] Target genome list was writen to GCF_902726655.1_PRJEB35829_genomic.fna/target_genomes.txt
[2024-01-24 11:43:53,723] [INFO] Task started: fastANI
[2024-01-24 11:43:53,723] [INFO] Running command: fastANI --query /var/lib/cwl/stg2d05f246-a605-4e64-9d66-72d54792edb0/GCF_902726655.1_PRJEB35829_genomic.fna.gz --refList GCF_902726655.1_PRJEB35829_genomic.fna/target_genomes.txt --output GCF_902726655.1_PRJEB35829_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:44:13,690] [INFO] Task succeeded: fastANI
[2024-01-24 11:44:13,690] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf7f63651-b7c4-437d-a88a-b52f2258ea42/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:44:13,690] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf7f63651-b7c4-437d-a88a-b52f2258ea42/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:44:13,708] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:44:13,708] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:44:13,708] [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 ihumii	strain=Marseille-Q1233	GCA_902726655.1	2686091	2686091	type	True	100.0	1286	1288	95	conclusive
Virgibacillus doumboii	strain=Marseille-Q1616	GCA_902806455.1	2697503	2697503	type	True	78.6603	295	1288	95	below_threshold
Virgibacillus phasianinus	strain=LM2416	GCA_002216775.1	2017483	2017483	type	True	78.4502	170	1288	95	below_threshold
Lentibacillus jeotgali	strain=Grbi	GCA_000224785.2	558169	558169	type	True	78.2747	202	1288	95	below_threshold
Lentibacillus cibarius	strain=NKC220-2	GCA_005887555.1	2583219	2583219	type	True	78.0014	151	1288	95	below_threshold
Virgibacillus dakarensis	strain=Marseille-P3469	GCA_900155625.1	1917889	1917889	type	True	77.5101	177	1288	95	below_threshold
Ornithinibacillus contaminans	strain=DSM 22953	GCA_001038425.2	694055	694055	type	True	77.1789	95	1288	95	below_threshold
Virgibacillus halodenitrificans	strain=JCM 12304	GCA_001310895.1	1482	1482	type	True	77.1487	109	1288	95	below_threshold
Virgibacillus oceani	strain=CGMCC 1.12754	GCA_014638995.1	1479511	1479511	type	True	77.131	169	1288	95	below_threshold
Virgibacillus profundi	strain=P3-H5	GCA_002287375.1	2024555	2024555	type	True	76.9205	162	1288	95	below_threshold
Virgibacillus halotolerans	strain=DSM 25060	GCA_016908515.1	1071053	1071053	type	True	76.8151	125	1288	95	below_threshold
Oceanobacillus salinisoli	strain=YIM B00359	GCA_009733865.1	2678611	2678611	type	True	76.8062	113	1288	95	below_threshold
Oceanobacillus arenosus	strain=CAU 1183	GCA_003369575.1	1229153	1229153	type	True	76.7866	80	1288	95	below_threshold
Gracilibacillus suaedae	strain=LD4P30	GCA_017599345.1	2820273	2820273	type	True	76.7604	53	1288	95	below_threshold
Ornithinibacillus halotolerans	strain=CGMCC 1.12408	GCA_014637405.1	1274357	1274357	type	True	76.7517	77	1288	95	below_threshold
Oceanobacillus polygoni	strain=SA9	GCA_008304605.1	1235259	1235259	type	True	76.7044	106	1288	95	below_threshold
Gracilibacillus lacisalsi	strain=DSM 19029	GCA_000377765.1	393087	393087	type	True	76.5315	55	1288	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:44:13,710] [INFO] DFAST Taxonomy check result was written to GCF_902726655.1_PRJEB35829_genomic.fna/tc_result.tsv
[2024-01-24 11:44:13,710] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:44:13,710] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:44:13,711] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf7f63651-b7c4-437d-a88a-b52f2258ea42/dqc_reference/checkm_data
[2024-01-24 11:44:13,712] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:44:13,751] [INFO] Task started: CheckM
[2024-01-24 11:44:13,751] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_902726655.1_PRJEB35829_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_902726655.1_PRJEB35829_genomic.fna/checkm_input GCF_902726655.1_PRJEB35829_genomic.fna/checkm_result
[2024-01-24 11:44:48,885] [INFO] Task succeeded: CheckM
[2024-01-24 11:44:48,887] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:44:48,908] [INFO] ===== Completeness check finished =====
[2024-01-24 11:44:48,908] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:44:48,909] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_902726655.1_PRJEB35829_genomic.fna/markers.fasta)
[2024-01-24 11:44:48,909] [INFO] Task started: Blastn
[2024-01-24 11:44:48,909] [INFO] Running command: blastn -query GCF_902726655.1_PRJEB35829_genomic.fna/markers.fasta -db /var/lib/cwl/stgf7f63651-b7c4-437d-a88a-b52f2258ea42/dqc_reference/reference_markers_gtdb.fasta -out GCF_902726655.1_PRJEB35829_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:44:49,644] [INFO] Task succeeded: Blastn
[2024-01-24 11:44:49,648] [INFO] Selected 24 target genomes.
[2024-01-24 11:44:49,649] [INFO] Target genome list was writen to GCF_902726655.1_PRJEB35829_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:44:49,675] [INFO] Task started: fastANI
[2024-01-24 11:44:49,676] [INFO] Running command: fastANI --query /var/lib/cwl/stg2d05f246-a605-4e64-9d66-72d54792edb0/GCF_902726655.1_PRJEB35829_genomic.fna.gz --refList GCF_902726655.1_PRJEB35829_genomic.fna/target_genomes_gtdb.txt --output GCF_902726655.1_PRJEB35829_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:45:05,546] [INFO] Task succeeded: fastANI
[2024-01-24 11:45:05,561] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:45:05,562] [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_902726655.1	s__Lentibacillus ihumii	100.0	1286	1288	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_900162695.1	s__Lentibacillus siamensis	80.5599	723	1288	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_902806455.1	s__Lentibacillus doumboii	78.6259	301	1288	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_002216775.1	s__Virgibacillus_F phasianinus	78.3106	170	1288	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_000224785.1	s__Lentibacillus jeotgali	78.2348	203	1288	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_001307805.1	s__Lentibacillus amyloliquefaciens	78.1678	205	1288	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_005887555.1	s__Lentibacillus cibarius	78.0711	151	1288	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Lentibacillus	95.0	98.44	97.49	0.90	0.85	3	-
GCA_001311805.1	s__Lentibacillus juripiscarius	77.6077	131	1288	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_900162615.1	s__Virgibacillus proomii_A	77.4878	85	1288	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_001038425.2	s__Ornithinibacillus contaminans	77.3595	96	1288	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	77.1487	109	1288	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_014638995.1	s__Virgibacillus_E oceani	77.131	169	1288	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_002287375.1	s__Virgibacillus_G profundi	76.9332	162	1288	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	-
GCA_014642895.1	s__Virgibacillus_E populi	76.9232	178	1288	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	-
GCA_004145795.1	s__Lentibacillus lipolyticus	76.8978	138	1288	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_009733865.1	s__Oceanobacillus salinisoli	76.8058	114	1288	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Oceanobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017656265.1	s__Melghiribacillus sp017656265	76.7888	52	1288	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Alkalibacillaceae;g__Melghiribacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003369575.1	s__Oceanobacillus arenosus	76.7856	80	1288	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_008304605.1	s__Oceanobacillus polygoni	76.7159	107	1288	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Oceanobacillus	95.0	99.99	99.99	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 11:45:05,563] [INFO] GTDB search result was written to GCF_902726655.1_PRJEB35829_genomic.fna/result_gtdb.tsv
[2024-01-24 11:45:05,564] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:45:05,568] [INFO] DFAST_QC result json was written to GCF_902726655.1_PRJEB35829_genomic.fna/dqc_result.json
[2024-01-24 11:45:05,568] [INFO] DFAST_QC completed!
[2024-01-24 11:45:05,569] [INFO] Total running time: 0h1m24s