[2024-01-25 20:06:05,708] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:06:05,710] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:06:05,710] [INFO] DQC Reference Directory: /var/lib/cwl/stge12e1d16-0902-444a-9ae4-76d7a86cff17/dqc_reference
[2024-01-25 20:06:06,855] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:06:06,855] [INFO] Task started: Prodigal
[2024-01-25 20:06:06,856] [INFO] Running command: gunzip -c /var/lib/cwl/stg8133eaaf-852e-4dc8-82ef-b5319fb5639f/GCF_016908515.1_ASM1690851v1_genomic.fna.gz | prodigal -d GCF_016908515.1_ASM1690851v1_genomic.fna/cds.fna -a GCF_016908515.1_ASM1690851v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:06:15,433] [INFO] Task succeeded: Prodigal
[2024-01-25 20:06:15,433] [INFO] Task started: HMMsearch
[2024-01-25 20:06:15,434] [INFO] Running command: hmmsearch --tblout GCF_016908515.1_ASM1690851v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge12e1d16-0902-444a-9ae4-76d7a86cff17/dqc_reference/reference_markers.hmm GCF_016908515.1_ASM1690851v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:06:15,677] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:06:15,678] [INFO] Found 6/6 markers.
[2024-01-25 20:06:15,714] [INFO] Query marker FASTA was written to GCF_016908515.1_ASM1690851v1_genomic.fna/markers.fasta
[2024-01-25 20:06:15,714] [INFO] Task started: Blastn
[2024-01-25 20:06:15,714] [INFO] Running command: blastn -query GCF_016908515.1_ASM1690851v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge12e1d16-0902-444a-9ae4-76d7a86cff17/dqc_reference/reference_markers.fasta -out GCF_016908515.1_ASM1690851v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:06:16,269] [INFO] Task succeeded: Blastn
[2024-01-25 20:06:16,272] [INFO] Selected 24 target genomes.
[2024-01-25 20:06:16,272] [INFO] Target genome list was writen to GCF_016908515.1_ASM1690851v1_genomic.fna/target_genomes.txt
[2024-01-25 20:06:16,298] [INFO] Task started: fastANI
[2024-01-25 20:06:16,298] [INFO] Running command: fastANI --query /var/lib/cwl/stg8133eaaf-852e-4dc8-82ef-b5319fb5639f/GCF_016908515.1_ASM1690851v1_genomic.fna.gz --refList GCF_016908515.1_ASM1690851v1_genomic.fna/target_genomes.txt --output GCF_016908515.1_ASM1690851v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:06:33,275] [INFO] Task succeeded: fastANI
[2024-01-25 20:06:33,275] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge12e1d16-0902-444a-9ae4-76d7a86cff17/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:06:33,275] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge12e1d16-0902-444a-9ae4-76d7a86cff17/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:06:33,286] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:06:33,286] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:06:33,286] [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 halotolerans	strain=DSM 25060	GCA_016908515.1	1071053	1071053	type	True	100.0	1443	1443	95	conclusive
Virgibacillus profundi	strain=P3-H5	GCA_002287375.1	2024555	2024555	type	True	77.9796	261	1443	95	below_threshold
Virgibacillus necropolis	strain=LMG 19488	GCA_002224365.1	163877	163877	type	True	77.5602	191	1443	95	below_threshold
Virgibacillus indicus	strain=P2-C2	GCA_002266285.1	2024554	2024554	type	True	77.497	220	1443	95	below_threshold
Oceanobacillus rekensis	strain=PT-11	GCA_002153375.1	937927	937927	type	True	77.4335	158	1443	95	below_threshold
Oceanobacillus damuensis	strain=PT-20	GCA_001618145.1	937928	937928	type	True	77.3034	146	1443	95	below_threshold
Oceanobacillus zhaokaii	strain=160	GCA_003352005.1	2052660	2052660	type	True	77.2919	174	1443	95	below_threshold
Oceanobacillus polygoni	strain=SA9	GCA_008304605.1	1235259	1235259	type	True	77.2506	178	1443	95	below_threshold
Oceanobacillus profundus	strain=CL-MP28	GCA_008087205.1	372463	372463	type	True	77.1991	165	1443	95	below_threshold
Oceanobacillus profundus	strain=DSM 18246	GCA_003515705.1	372463	372463	type	True	77.1584	164	1443	95	below_threshold
Virgibacillus doumboii	strain=Marseille-Q1616	GCA_902806455.1	2697503	2697503	type	True	76.9621	135	1443	95	below_threshold
Virgibacillus oceani	strain=CGMCC 1.12754	GCA_014638995.1	1479511	1479511	type	True	76.7979	174	1443	95	below_threshold
Oceanobacillus salinisoli	strain=YIM B00359	GCA_009733865.1	2678611	2678611	type	True	76.6403	133	1443	95	below_threshold
Oceanobacillus senegalensis	strain=Marseille-P3587	GCA_900176885.1	1936063	1936063	type	True	76.6163	127	1443	95	below_threshold
Oceanobacillus jeddahense	strain=S5	GCA_000750635.1	1462527	1462527	type	True	76.4151	91	1443	95	below_threshold
Gracilibacillus suaedae	strain=LD4P30	GCA_017599345.1	2820273	2820273	type	True	76.2669	62	1443	95	below_threshold
Heyndrickxia oleronia	strain=DSM 9356	GCA_025263665.1	38875	38875	type	True	76.2241	51	1443	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:06:33,288] [INFO] DFAST Taxonomy check result was written to GCF_016908515.1_ASM1690851v1_genomic.fna/tc_result.tsv
[2024-01-25 20:06:33,288] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:06:33,288] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:06:33,289] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge12e1d16-0902-444a-9ae4-76d7a86cff17/dqc_reference/checkm_data
[2024-01-25 20:06:33,289] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:06:33,337] [INFO] Task started: CheckM
[2024-01-25 20:06:33,337] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016908515.1_ASM1690851v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016908515.1_ASM1690851v1_genomic.fna/checkm_input GCF_016908515.1_ASM1690851v1_genomic.fna/checkm_result
[2024-01-25 20:07:02,616] [INFO] Task succeeded: CheckM
[2024-01-25 20:07:02,617] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:07:02,637] [INFO] ===== Completeness check finished =====
[2024-01-25 20:07:02,637] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:07:02,637] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016908515.1_ASM1690851v1_genomic.fna/markers.fasta)
[2024-01-25 20:07:02,637] [INFO] Task started: Blastn
[2024-01-25 20:07:02,637] [INFO] Running command: blastn -query GCF_016908515.1_ASM1690851v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge12e1d16-0902-444a-9ae4-76d7a86cff17/dqc_reference/reference_markers_gtdb.fasta -out GCF_016908515.1_ASM1690851v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:07:03,438] [INFO] Task succeeded: Blastn
[2024-01-25 20:07:03,442] [INFO] Selected 25 target genomes.
[2024-01-25 20:07:03,442] [INFO] Target genome list was writen to GCF_016908515.1_ASM1690851v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:07:03,493] [INFO] Task started: fastANI
[2024-01-25 20:07:03,493] [INFO] Running command: fastANI --query /var/lib/cwl/stg8133eaaf-852e-4dc8-82ef-b5319fb5639f/GCF_016908515.1_ASM1690851v1_genomic.fna.gz --refList GCF_016908515.1_ASM1690851v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016908515.1_ASM1690851v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:07:20,886] [INFO] Task succeeded: fastANI
[2024-01-25 20:07:20,899] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:07:20,900] [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_016908515.1	s__Virgibacillus_I halotolerans	100.0	1443	1443	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Virgibacillus_I	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002287375.1	s__Virgibacillus_G profundi	78.0195	258	1443	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	-
GCF_002224365.1	s__Virgibacillus_F necropolis	77.5462	188	1443	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_002153375.1	s__Oceanobacillus rekensis	77.4335	158	1443	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	77.3381	168	1443	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_003352005.1	s__Oceanobacillus zhaokaii	77.2765	175	1443	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_001618145.1	s__Oceanobacillus damuensis	77.2569	145	1443	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_900187325.1	s__Virgibacillus_E ndiopensis	77.2551	178	1443	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_008304605.1	s__Oceanobacillus polygoni	77.2512	178	1443	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_003515705.1	s__Oceanobacillus profundus	77.1423	166	1443	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Oceanobacillus	95.0	99.49	99.20	0.93	0.85	4	-
GCF_001310895.1	s__Virgibacillus halodenitrificans	77.0425	144	1443	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_000724085.1	s__Virgibacillus manasiensis	77.0201	143	1443	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_902806455.1	s__Lentibacillus doumboii	76.9546	137	1443	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_014638995.1	s__Virgibacillus_E oceani	76.8504	170	1443	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_000821065.1	s__Oceanobacillus oncorhynchi	76.7769	90	1443	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Oceanobacillus	95.0	98.79	98.49	0.90	0.88	3	-
GCF_900176885.1	s__Oceanobacillus senegalensis	76.6595	127	1443	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_009733865.1	s__Oceanobacillus salinisoli	76.6395	133	1443	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_001659985.1	s__Oceanobacillus sp001659985	76.5434	130	1443	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_900162615.1	s__Virgibacillus proomii_A	76.536	125	1443	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_000750635.1	s__Oceanobacillus jeddahense	76.5201	89	1443	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Oceanobacillus	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-25 20:07:20,901] [INFO] GTDB search result was written to GCF_016908515.1_ASM1690851v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:07:20,902] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:07:20,905] [INFO] DFAST_QC result json was written to GCF_016908515.1_ASM1690851v1_genomic.fna/dqc_result.json
[2024-01-25 20:07:20,905] [INFO] DFAST_QC completed!
[2024-01-25 20:07:20,906] [INFO] Total running time: 0h1m15s