[2024-01-24 11:51:11,369] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:51:11,371] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:51:11,372] [INFO] DQC Reference Directory: /var/lib/cwl/stgea4355d2-a477-4b1e-aa2e-758b2d43daf7/dqc_reference
[2024-01-24 11:51:12,702] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:51:12,703] [INFO] Task started: Prodigal
[2024-01-24 11:51:12,703] [INFO] Running command: gunzip -c /var/lib/cwl/stgbb020658-723e-4d97-8eba-db9a28810dd0/GCF_014637405.1_ASM1463740v1_genomic.fna.gz | prodigal -d GCF_014637405.1_ASM1463740v1_genomic.fna/cds.fna -a GCF_014637405.1_ASM1463740v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:51:19,864] [INFO] Task succeeded: Prodigal
[2024-01-24 11:51:19,865] [INFO] Task started: HMMsearch
[2024-01-24 11:51:19,865] [INFO] Running command: hmmsearch --tblout GCF_014637405.1_ASM1463740v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgea4355d2-a477-4b1e-aa2e-758b2d43daf7/dqc_reference/reference_markers.hmm GCF_014637405.1_ASM1463740v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:51:20,190] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:51:20,191] [INFO] Found 6/6 markers.
[2024-01-24 11:51:20,249] [INFO] Query marker FASTA was written to GCF_014637405.1_ASM1463740v1_genomic.fna/markers.fasta
[2024-01-24 11:51:20,250] [INFO] Task started: Blastn
[2024-01-24 11:51:20,250] [INFO] Running command: blastn -query GCF_014637405.1_ASM1463740v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgea4355d2-a477-4b1e-aa2e-758b2d43daf7/dqc_reference/reference_markers.fasta -out GCF_014637405.1_ASM1463740v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:51:20,882] [INFO] Task succeeded: Blastn
[2024-01-24 11:51:20,885] [INFO] Selected 24 target genomes.
[2024-01-24 11:51:20,885] [INFO] Target genome list was writen to GCF_014637405.1_ASM1463740v1_genomic.fna/target_genomes.txt
[2024-01-24 11:51:20,900] [INFO] Task started: fastANI
[2024-01-24 11:51:20,900] [INFO] Running command: fastANI --query /var/lib/cwl/stgbb020658-723e-4d97-8eba-db9a28810dd0/GCF_014637405.1_ASM1463740v1_genomic.fna.gz --refList GCF_014637405.1_ASM1463740v1_genomic.fna/target_genomes.txt --output GCF_014637405.1_ASM1463740v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:51:36,215] [INFO] Task succeeded: fastANI
[2024-01-24 11:51:36,215] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgea4355d2-a477-4b1e-aa2e-758b2d43daf7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:51:36,215] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgea4355d2-a477-4b1e-aa2e-758b2d43daf7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:51:36,229] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:51:36,229] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:51:36,230] [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
Ornithinibacillus halotolerans	strain=CGMCC 1.12408	GCA_014637405.1	1274357	1274357	type	True	100.0	1277	1282	95	conclusive
Ornithinibacillus massiliensis	strain=Marseille-P3601	GCA_018310345.1	1944633	1944633	type	True	78.6728	350	1282	95	below_threshold
Ornithinibacillus scapharcae	strain=TW25	GCA_000190475.2	1147159	1147159	type	True	78.4349	347	1282	95	below_threshold
Ornithinibacillus contaminans	strain=DSM 22953	GCA_001038425.2	694055	694055	type	True	78.2946	288	1282	95	below_threshold
Cerasibacillus terrae	strain=CC-CFT480	GCA_008039555.1	2498845	2498845	type	True	77.9082	124	1282	95	below_threshold
Ornithinibacillus halophilus	strain=IBRC-M 10683	GCA_900129485.1	930117	930117	type	True	77.7193	250	1282	95	below_threshold
Aquibacillus koreensis	strain=JCM 12387	GCA_025154055.1	279446	279446	type	True	77.4169	82	1282	95	below_threshold
Virgibacillus necropolis	strain=LMG 19488	GCA_002224365.1	163877	163877	type	True	77.3402	120	1282	95	below_threshold
Virgibacillus phasianinus	strain=LM2416	GCA_002216775.1	2017483	2017483	type	True	77.2935	96	1282	95	below_threshold
Oceanobacillus halotolerans	strain=YIM 98839	GCA_010993955.1	2663380	2663380	type	True	77.0752	139	1282	95	below_threshold
Oceanobacillus piezotolerans	strain=YLB-02	GCA_003665065.1	2448030	2448030	type	True	77.0169	125	1282	95	below_threshold
Amphibacillus cookii	strain=DSM 23721	GCA_016908375.1	767787	767787	type	True	76.8313	52	1282	95	below_threshold
Virgibacillus chiguensis	strain=CGMCC 1.6496	GCA_900129865.1	411959	411959	type	True	76.7211	111	1282	95	below_threshold
Virgibacillus alimentarius	strain=J18	GCA_000709085.1	698769	698769	type	True	76.6745	95	1282	95	below_threshold
Viridibacillus soli	strain=YIM B01967	GCA_016612995.1	2798301	2798301	type	True	76.547	50	1282	95	below_threshold
Gracilibacillus suaedae	strain=LD4P30	GCA_017599345.1	2820273	2820273	type	True	76.535	73	1282	95	below_threshold
Amphibacillus sediminis	strain=NBRC 103570	GCA_001552275.1	360185	360185	type	True	76.4727	55	1282	95	below_threshold
Paraliobacillus sediminis	strain=126C4	GCA_003426055.1	1885916	1885916	type	True	76.0301	59	1282	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:51:36,238] [INFO] DFAST Taxonomy check result was written to GCF_014637405.1_ASM1463740v1_genomic.fna/tc_result.tsv
[2024-01-24 11:51:36,238] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:51:36,239] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:51:36,239] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgea4355d2-a477-4b1e-aa2e-758b2d43daf7/dqc_reference/checkm_data
[2024-01-24 11:51:36,240] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:51:36,277] [INFO] Task started: CheckM
[2024-01-24 11:51:36,277] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014637405.1_ASM1463740v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014637405.1_ASM1463740v1_genomic.fna/checkm_input GCF_014637405.1_ASM1463740v1_genomic.fna/checkm_result
[2024-01-24 11:52:03,279] [INFO] Task succeeded: CheckM
[2024-01-24 11:52:03,280] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:52:03,300] [INFO] ===== Completeness check finished =====
[2024-01-24 11:52:03,300] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:52:03,301] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014637405.1_ASM1463740v1_genomic.fna/markers.fasta)
[2024-01-24 11:52:03,301] [INFO] Task started: Blastn
[2024-01-24 11:52:03,301] [INFO] Running command: blastn -query GCF_014637405.1_ASM1463740v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgea4355d2-a477-4b1e-aa2e-758b2d43daf7/dqc_reference/reference_markers_gtdb.fasta -out GCF_014637405.1_ASM1463740v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:52:04,158] [INFO] Task succeeded: Blastn
[2024-01-24 11:52:04,161] [INFO] Selected 20 target genomes.
[2024-01-24 11:52:04,162] [INFO] Target genome list was writen to GCF_014637405.1_ASM1463740v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:52:04,177] [INFO] Task started: fastANI
[2024-01-24 11:52:04,178] [INFO] Running command: fastANI --query /var/lib/cwl/stgbb020658-723e-4d97-8eba-db9a28810dd0/GCF_014637405.1_ASM1463740v1_genomic.fna.gz --refList GCF_014637405.1_ASM1463740v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014637405.1_ASM1463740v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:52:17,146] [INFO] Task succeeded: fastANI
[2024-01-24 11:52:17,157] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:52:17,158] [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_014637405.1	s__Ornithinibacillus halotolerans	100.0	1277	1282	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Ornithinibacillus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000482485.1	s__Ornithinibacillus globulus	79.1418	451	1282	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_001038485.1	s__Ornithinibacillus californiensis	78.8858	442	1282	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_000577245.1	s__Ornithinibacillus sp000577245	78.8409	451	1282	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_900184735.1	s__Ornithinibacillus globulus_B	78.8055	467	1282	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_000190475.1	s__Ornithinibacillus scapharcae	78.4354	347	1282	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_018333235.1	s__Ornithinibacillus bavariensis	78.3001	283	1282	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Ornithinibacillus	95.0	98.72	98.72	0.93	0.93	2	-
GCF_001038425.2	s__Ornithinibacillus contaminans	78.2819	289	1282	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	77.7281	249	1282	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_009728145.1	s__Ornithinibacillus caprae	77.6233	222	1282	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_900111445.1	s__Ornithinibacillus limi	77.5879	189	1282	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	77.5141	126	1282	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_016919725.1	s__Virgibacillus sp016919725	76.8634	134	1282	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_001552275.1	s__Amphibacillus_B sediminis	76.4727	55	1282	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Amphibacillus_B	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:52:17,160] [INFO] GTDB search result was written to GCF_014637405.1_ASM1463740v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:52:17,160] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:52:17,165] [INFO] DFAST_QC result json was written to GCF_014637405.1_ASM1463740v1_genomic.fna/dqc_result.json
[2024-01-24 11:52:17,165] [INFO] DFAST_QC completed!
[2024-01-24 11:52:17,165] [INFO] Total running time: 0h1m6s