[2024-01-24 15:02:31,516] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:02:31,518] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:02:31,518] [INFO] DQC Reference Directory: /var/lib/cwl/stgfb962228-3505-4243-bdd0-3277afc2997b/dqc_reference
[2024-01-24 15:02:32,798] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:02:32,799] [INFO] Task started: Prodigal
[2024-01-24 15:02:32,799] [INFO] Running command: gunzip -c /var/lib/cwl/stgb4721d29-7843-4e81-96c8-699687704aec/GCF_014642895.1_ASM1464289v1_genomic.fna.gz | prodigal -d GCF_014642895.1_ASM1464289v1_genomic.fna/cds.fna -a GCF_014642895.1_ASM1464289v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:02:42,987] [INFO] Task succeeded: Prodigal
[2024-01-24 15:02:42,988] [INFO] Task started: HMMsearch
[2024-01-24 15:02:42,988] [INFO] Running command: hmmsearch --tblout GCF_014642895.1_ASM1464289v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfb962228-3505-4243-bdd0-3277afc2997b/dqc_reference/reference_markers.hmm GCF_014642895.1_ASM1464289v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:02:43,319] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:02:43,321] [INFO] Found 6/6 markers.
[2024-01-24 15:02:43,369] [INFO] Query marker FASTA was written to GCF_014642895.1_ASM1464289v1_genomic.fna/markers.fasta
[2024-01-24 15:02:43,369] [INFO] Task started: Blastn
[2024-01-24 15:02:43,369] [INFO] Running command: blastn -query GCF_014642895.1_ASM1464289v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfb962228-3505-4243-bdd0-3277afc2997b/dqc_reference/reference_markers.fasta -out GCF_014642895.1_ASM1464289v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:02:44,066] [INFO] Task succeeded: Blastn
[2024-01-24 15:02:44,069] [INFO] Selected 24 target genomes.
[2024-01-24 15:02:44,069] [INFO] Target genome list was writen to GCF_014642895.1_ASM1464289v1_genomic.fna/target_genomes.txt
[2024-01-24 15:02:44,078] [INFO] Task started: fastANI
[2024-01-24 15:02:44,078] [INFO] Running command: fastANI --query /var/lib/cwl/stgb4721d29-7843-4e81-96c8-699687704aec/GCF_014642895.1_ASM1464289v1_genomic.fna.gz --refList GCF_014642895.1_ASM1464289v1_genomic.fna/target_genomes.txt --output GCF_014642895.1_ASM1464289v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:03:01,740] [INFO] Task succeeded: fastANI
[2024-01-24 15:03:01,741] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfb962228-3505-4243-bdd0-3277afc2997b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:03:01,741] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfb962228-3505-4243-bdd0-3277afc2997b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:03:01,756] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:03:01,756] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:03:01,756] [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 dakarensis	strain=Marseille-P3469	GCA_900155625.1	1917889	1917889	type	True	98.8476	1268	1483	95	conclusive
Virgibacillus ndiopensis	strain=Marseille-P3835	GCA_900187325.1	2004408	2004408	type	True	78.142	301	1483	95	below_threshold
Virgibacillus massiliensis	strain=Vm-5	GCA_000723585.1	1462526	1462526	suspected-type	True	77.9716	139	1483	95	below_threshold
Virgibacillus massiliensis	strain=Vm-5	GCA_014905475.1	1462526	1462526	suspected-type	True	77.9246	136	1483	95	below_threshold
Virgibacillus oceani	strain=CGMCC 1.12754	GCA_014638995.1	1479511	1479511	type	True	77.8847	299	1483	95	below_threshold
Oceanobacillus massiliensis	strain=Ndiop	GCA_000285495.1	1465765	1465765	type	True	77.3921	119	1483	95	below_threshold
Virgibacillus ihumii	strain=Marseille-Q1233	GCA_902726655.1	2686091	2686091	type	True	77.3789	162	1483	95	below_threshold
Ornithinibacillus gellani	strain=LJ137	GCA_003730295.1	2293253	2293253	type	True	77.3084	90	1483	95	below_threshold
Oceanobacillus salinisoli	strain=YIM B00359	GCA_009733865.1	2678611	2678611	type	True	77.3055	124	1483	95	below_threshold
Aquibacillus koreensis	strain=JCM 12387	GCA_025154055.1	279446	279446	type	True	77.2805	59	1483	95	below_threshold
Virgibacillus litoralis	strain=DSM 21085	GCA_017873675.1	578221	578221	type	True	77.2631	188	1483	95	below_threshold
Oceanobacillus rekensis	strain=PT-11	GCA_002153375.1	937927	937927	type	True	77.2333	125	1483	95	below_threshold
Oceanobacillus polygoni	strain=SA9	GCA_008304605.1	1235259	1235259	type	True	77.2125	141	1483	95	below_threshold
Virgibacillus subterraneus	strain=CGMCC 1.7734	GCA_900110695.1	621109	621109	type	True	77.0991	175	1483	95	below_threshold
Lentibacillus amyloliquefaciens	strain=LAM0015	GCA_001307805.2	1472767	1472767	type	True	76.9859	120	1483	95	below_threshold
Oceanobacillus sojae	strain=NBRC 105379	GCA_007991515.1	582851	582851	type	True	76.9579	74	1483	95	below_threshold
Lentibacillus halodurans	strain=CGMCC 1.3702	GCA_900112045.1	237679	237679	type	True	76.9466	149	1483	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:03:01,759] [INFO] DFAST Taxonomy check result was written to GCF_014642895.1_ASM1464289v1_genomic.fna/tc_result.tsv
[2024-01-24 15:03:01,759] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:03:01,760] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:03:01,760] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfb962228-3505-4243-bdd0-3277afc2997b/dqc_reference/checkm_data
[2024-01-24 15:03:01,761] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:03:01,812] [INFO] Task started: CheckM
[2024-01-24 15:03:01,812] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014642895.1_ASM1464289v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014642895.1_ASM1464289v1_genomic.fna/checkm_input GCF_014642895.1_ASM1464289v1_genomic.fna/checkm_result
[2024-01-24 15:03:39,279] [INFO] Task succeeded: CheckM
[2024-01-24 15:03:39,281] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:03:39,306] [INFO] ===== Completeness check finished =====
[2024-01-24 15:03:39,306] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:03:39,307] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014642895.1_ASM1464289v1_genomic.fna/markers.fasta)
[2024-01-24 15:03:39,307] [INFO] Task started: Blastn
[2024-01-24 15:03:39,307] [INFO] Running command: blastn -query GCF_014642895.1_ASM1464289v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfb962228-3505-4243-bdd0-3277afc2997b/dqc_reference/reference_markers_gtdb.fasta -out GCF_014642895.1_ASM1464289v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:03:40,139] [INFO] Task succeeded: Blastn
[2024-01-24 15:03:40,142] [INFO] Selected 23 target genomes.
[2024-01-24 15:03:40,142] [INFO] Target genome list was writen to GCF_014642895.1_ASM1464289v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:03:40,158] [INFO] Task started: fastANI
[2024-01-24 15:03:40,158] [INFO] Running command: fastANI --query /var/lib/cwl/stgb4721d29-7843-4e81-96c8-699687704aec/GCF_014642895.1_ASM1464289v1_genomic.fna.gz --refList GCF_014642895.1_ASM1464289v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014642895.1_ASM1464289v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:03:56,124] [INFO] Task succeeded: fastANI
[2024-01-24 15:03:56,145] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:03:56,146] [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
GCA_014642895.1	s__Virgibacillus_E populi	100.0	1474	1483	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	conclusive
GCF_900258515.1	s__Virgibacillus_E sp900258515	79.14	456	1483	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_900187325.1	s__Virgibacillus_E ndiopensis	78.135	301	1483	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	77.8609	303	1483	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_014905415.1	s__Virgibacillus salexigens	77.8414	139	1483	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_000285495.1	s__Oceanobacillus massiliensis	77.4399	119	1483	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Oceanobacillus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000612865.1	s__Virgibacillus picturae	77.3411	110	1483	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_009733865.1	s__Oceanobacillus salinisoli	77.3031	128	1483	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_016919725.1	s__Virgibacillus sp016919725	77.2898	147	1483	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_017873675.1	s__Lentibacillus litoralis	77.2785	188	1483	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_900111445.1	s__Ornithinibacillus limi	77.2774	138	1483	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_003730295.1	s__LJ137 sp003730295	77.2769	91	1483	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__LJ137	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008304605.1	s__Oceanobacillus polygoni	77.2468	140	1483	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_002153375.1	s__Oceanobacillus rekensis	77.236	126	1483	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_900112045.1	s__Lentibacillus halodurans	76.9637	148	1483	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Lentibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004145795.1	s__Lentibacillus lipolyticus	76.6394	103	1483	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Lentibacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:03:56,148] [INFO] GTDB search result was written to GCF_014642895.1_ASM1464289v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:03:56,149] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:03:56,161] [INFO] DFAST_QC result json was written to GCF_014642895.1_ASM1464289v1_genomic.fna/dqc_result.json
[2024-01-24 15:03:56,161] [INFO] DFAST_QC completed!
[2024-01-24 15:03:56,161] [INFO] Total running time: 0h1m25s