[2024-01-24 13:31:57,978] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:31:57,980] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:31:57,981] [INFO] DQC Reference Directory: /var/lib/cwl/stg6d845f3c-3c18-4b82-a606-559382f7bba3/dqc_reference
[2024-01-24 13:31:59,258] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:31:59,259] [INFO] Task started: Prodigal
[2024-01-24 13:31:59,259] [INFO] Running command: gunzip -c /var/lib/cwl/stg1ce3f429-0981-4e32-8dd1-f0c7ff709f3e/GCF_010993955.1_ASM1099395v1_genomic.fna.gz | prodigal -d GCF_010993955.1_ASM1099395v1_genomic.fna/cds.fna -a GCF_010993955.1_ASM1099395v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:32:06,355] [INFO] Task succeeded: Prodigal
[2024-01-24 13:32:06,355] [INFO] Task started: HMMsearch
[2024-01-24 13:32:06,355] [INFO] Running command: hmmsearch --tblout GCF_010993955.1_ASM1099395v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6d845f3c-3c18-4b82-a606-559382f7bba3/dqc_reference/reference_markers.hmm GCF_010993955.1_ASM1099395v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:32:06,599] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:32:06,601] [INFO] Found 6/6 markers.
[2024-01-24 13:32:06,628] [INFO] Query marker FASTA was written to GCF_010993955.1_ASM1099395v1_genomic.fna/markers.fasta
[2024-01-24 13:32:06,629] [INFO] Task started: Blastn
[2024-01-24 13:32:06,629] [INFO] Running command: blastn -query GCF_010993955.1_ASM1099395v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6d845f3c-3c18-4b82-a606-559382f7bba3/dqc_reference/reference_markers.fasta -out GCF_010993955.1_ASM1099395v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:07,245] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:07,248] [INFO] Selected 26 target genomes.
[2024-01-24 13:32:07,249] [INFO] Target genome list was writen to GCF_010993955.1_ASM1099395v1_genomic.fna/target_genomes.txt
[2024-01-24 13:32:07,259] [INFO] Task started: fastANI
[2024-01-24 13:32:07,260] [INFO] Running command: fastANI --query /var/lib/cwl/stg1ce3f429-0981-4e32-8dd1-f0c7ff709f3e/GCF_010993955.1_ASM1099395v1_genomic.fna.gz --refList GCF_010993955.1_ASM1099395v1_genomic.fna/target_genomes.txt --output GCF_010993955.1_ASM1099395v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:32:26,165] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:26,165] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6d845f3c-3c18-4b82-a606-559382f7bba3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:32:26,166] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6d845f3c-3c18-4b82-a606-559382f7bba3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:32:26,181] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:32:26,181] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:32:26,181] [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
Oceanobacillus halotolerans	strain=YIM 98839	GCA_010993955.1	2663380	2663380	type	True	100.0	1096	1097	95	conclusive
Virgibacillus ndiopensis	strain=Marseille-P3835	GCA_900187325.1	2004408	2004408	type	True	77.264	177	1097	95	below_threshold
Oceanobacillus halophilus	strain=DSM 23996	GCA_003628505.1	930130	930130	type	True	77.2557	134	1097	95	below_threshold
Ornithinibacillus massiliensis	strain=Marseille-P3601	GCA_018310345.1	1944633	1944633	type	True	77.2058	132	1097	95	below_threshold
Virgibacillus massiliensis	strain=Vm-5	GCA_014905475.1	1462526	1462526	suspected-type	True	77.1842	134	1097	95	below_threshold
Virgibacillus massiliensis	strain=Vm-5	GCA_000723585.1	1462526	1462526	suspected-type	True	77.1837	131	1097	95	below_threshold
Ornithinibacillus halophilus	strain=IBRC-M 10683	GCA_900129485.1	930117	930117	type	True	77.1586	180	1097	95	below_threshold
Ornithinibacillus halotolerans	strain=CGMCC 1.12408	GCA_014637405.1	1274357	1274357	type	True	77.0721	137	1097	95	below_threshold
Virgibacillus chiguensis	strain=CGMCC 1.6496	GCA_900129865.1	411959	411959	type	True	77.0317	117	1097	95	below_threshold
Oceanobacillus jordanicus	strain=GSFE11	GCA_022095695.1	2867266	2867266	type	True	76.9668	130	1097	95	below_threshold
Oceanobacillus zhaokaii	strain=160	GCA_003352005.1	2052660	2052660	type	True	76.868	123	1097	95	below_threshold
Lentibacillus persicus	strain=DSM 22530	GCA_900112705.1	640948	640948	type	True	76.8466	78	1097	95	below_threshold
Bacillus shivajii	strain=JCM 32183	GCA_020519665.1	1983719	1983719	type	True	76.7925	50	1097	95	below_threshold
Aquibacillus sediminis	strain=BH258	GCA_005870085.1	2574734	2574734	type	True	76.7092	119	1097	95	below_threshold
Virgibacillus pantothenticus	strain=DSM 26	GCA_001189575.1	1473	1473	type	True	76.6858	117	1097	95	below_threshold
Virgibacillus pantothenticus	strain=DSM 26	GCA_900156795.1	1473	1473	type	True	76.6726	125	1097	95	below_threshold
Cerasibacillus quisquiliarum	strain=NBRC 102429	GCA_007991195.1	227865	227865	type	True	76.5742	70	1097	95	below_threshold
Cerasibacillus quisquiliarum	strain=DSM 15825	GCA_014202495.1	227865	227865	type	True	76.4902	72	1097	95	below_threshold
Niallia alba	strain=UniB3	GCA_012933555.1	2729105	2729105	type	True	76.4076	52	1097	95	below_threshold
Paraliobacillus sediminis	strain=126C4	GCA_003426055.1	1885916	1885916	type	True	75.8716	64	1097	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:32:26,183] [INFO] DFAST Taxonomy check result was written to GCF_010993955.1_ASM1099395v1_genomic.fna/tc_result.tsv
[2024-01-24 13:32:26,183] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:32:26,183] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:32:26,184] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6d845f3c-3c18-4b82-a606-559382f7bba3/dqc_reference/checkm_data
[2024-01-24 13:32:26,185] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:32:26,218] [INFO] Task started: CheckM
[2024-01-24 13:32:26,218] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_010993955.1_ASM1099395v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_010993955.1_ASM1099395v1_genomic.fna/checkm_input GCF_010993955.1_ASM1099395v1_genomic.fna/checkm_result
[2024-01-24 13:32:52,071] [INFO] Task succeeded: CheckM
[2024-01-24 13:32:52,072] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:32:52,088] [INFO] ===== Completeness check finished =====
[2024-01-24 13:32:52,089] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:32:52,089] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_010993955.1_ASM1099395v1_genomic.fna/markers.fasta)
[2024-01-24 13:32:52,089] [INFO] Task started: Blastn
[2024-01-24 13:32:52,089] [INFO] Running command: blastn -query GCF_010993955.1_ASM1099395v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6d845f3c-3c18-4b82-a606-559382f7bba3/dqc_reference/reference_markers_gtdb.fasta -out GCF_010993955.1_ASM1099395v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:52,920] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:52,924] [INFO] Selected 27 target genomes.
[2024-01-24 13:32:52,924] [INFO] Target genome list was writen to GCF_010993955.1_ASM1099395v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:32:52,943] [INFO] Task started: fastANI
[2024-01-24 13:32:52,944] [INFO] Running command: fastANI --query /var/lib/cwl/stg1ce3f429-0981-4e32-8dd1-f0c7ff709f3e/GCF_010993955.1_ASM1099395v1_genomic.fna.gz --refList GCF_010993955.1_ASM1099395v1_genomic.fna/target_genomes_gtdb.txt --output GCF_010993955.1_ASM1099395v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:33:15,061] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:15,078] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:33:15,078] [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_010993955.1	s__YIM-98839 sp010993955	100.0	1096	1097	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__YIM-98839	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_009728145.1	s__Ornithinibacillus caprae	77.588	190	1097	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_900166595.1	s__Virgibacillus dokdonensis	77.5534	116	1097	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_016919725.1	s__Virgibacillus sp016919725	77.482	142	1097	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_003628505.1	s__Oceanobacillus halophilus	77.2842	130	1097	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_900258515.1	s__Virgibacillus_E sp900258515	77.2823	173	1097	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	77.2756	179	1097	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	77.2115	135	1097	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_001038485.1	s__Ornithinibacillus californiensis	77.1848	140	1097	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	77.1284	184	1097	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_014637405.1	s__Ornithinibacillus halotolerans	77.0895	136	1097	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_900162615.1	s__Virgibacillus proomii_A	77.0119	117	1097	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_003268595.1	s__Paraliobacillus_A zengyii	76.9514	67	1097	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Paraliobacillus_A	95.0	99.46	99.36	0.95	0.93	3	-
GCF_018916875.1	s__Virgibacillus proomii_B	76.9319	97	1097	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_900184735.1	s__Ornithinibacillus globulus_B	76.9212	146	1097	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_900114645.1	s__Gracilibacillus orientalis	76.9105	76	1097	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Gracilibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900112705.1	s__Lentibacillus persicus	76.8723	79	1097	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_003352005.1	s__Oceanobacillus zhaokaii	76.8499	122	1097	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Oceanobacillus	95.0	99.81	99.81	1.00	1.00	2	-
GCF_005870085.1	s__BH258 sp005870085	76.7274	120	1097	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__BH258	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014202495.1	s__Cerasibacillus quisquiliarum	76.5177	71	1097	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Cerasibacillus	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:33:15,088] [INFO] GTDB search result was written to GCF_010993955.1_ASM1099395v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:33:15,089] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:33:15,095] [INFO] DFAST_QC result json was written to GCF_010993955.1_ASM1099395v1_genomic.fna/dqc_result.json
[2024-01-24 13:33:15,095] [INFO] DFAST_QC completed!
[2024-01-24 13:33:15,095] [INFO] Total running time: 0h1m17s