[2024-01-25 18:09:20,351] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:09:20,352] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:09:20,352] [INFO] DQC Reference Directory: /var/lib/cwl/stg4646b72f-28c6-4199-a313-1d176666ab06/dqc_reference
[2024-01-25 18:09:21,489] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:09:21,490] [INFO] Task started: Prodigal
[2024-01-25 18:09:21,491] [INFO] Running command: gunzip -c /var/lib/cwl/stg6ad7cfd2-6b08-4170-90fc-ce27e56a2d49/GCF_002287375.1_ASM228737v1_genomic.fna.gz | prodigal -d GCF_002287375.1_ASM228737v1_genomic.fna/cds.fna -a GCF_002287375.1_ASM228737v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:09:29,564] [INFO] Task succeeded: Prodigal
[2024-01-25 18:09:29,564] [INFO] Task started: HMMsearch
[2024-01-25 18:09:29,564] [INFO] Running command: hmmsearch --tblout GCF_002287375.1_ASM228737v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4646b72f-28c6-4199-a313-1d176666ab06/dqc_reference/reference_markers.hmm GCF_002287375.1_ASM228737v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:09:29,810] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:09:29,811] [INFO] Found 6/6 markers.
[2024-01-25 18:09:29,848] [INFO] Query marker FASTA was written to GCF_002287375.1_ASM228737v1_genomic.fna/markers.fasta
[2024-01-25 18:09:29,849] [INFO] Task started: Blastn
[2024-01-25 18:09:29,849] [INFO] Running command: blastn -query GCF_002287375.1_ASM228737v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4646b72f-28c6-4199-a313-1d176666ab06/dqc_reference/reference_markers.fasta -out GCF_002287375.1_ASM228737v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:09:30,405] [INFO] Task succeeded: Blastn
[2024-01-25 18:09:30,408] [INFO] Selected 24 target genomes.
[2024-01-25 18:09:30,409] [INFO] Target genome list was writen to GCF_002287375.1_ASM228737v1_genomic.fna/target_genomes.txt
[2024-01-25 18:09:30,424] [INFO] Task started: fastANI
[2024-01-25 18:09:30,425] [INFO] Running command: fastANI --query /var/lib/cwl/stg6ad7cfd2-6b08-4170-90fc-ce27e56a2d49/GCF_002287375.1_ASM228737v1_genomic.fna.gz --refList GCF_002287375.1_ASM228737v1_genomic.fna/target_genomes.txt --output GCF_002287375.1_ASM228737v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:09:49,812] [INFO] Task succeeded: fastANI
[2024-01-25 18:09:49,813] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4646b72f-28c6-4199-a313-1d176666ab06/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:09:49,813] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4646b72f-28c6-4199-a313-1d176666ab06/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:09:49,824] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:09:49,824] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:09:49,824] [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 profundi	strain=P3-H5	GCA_002287375.1	2024555	2024555	type	True	100.0	1415	1416	95	conclusive
Virgibacillus indicus	strain=P2-C2	GCA_002266285.1	2024554	2024554	type	True	80.462	622	1416	95	below_threshold
Virgibacillus halotolerans	strain=DSM 25060	GCA_016908515.1	1071053	1071053	type	True	78.0773	249	1416	95	below_threshold
Oceanobacillus jordanicus	strain=GSFE11	GCA_022095695.1	2867266	2867266	type	True	77.981	201	1416	95	below_threshold
Virgibacillus natechei	strain=DSM 25609	GCA_017874115.1	1216297	1216297	type	True	77.8681	298	1416	95	below_threshold
Oceanobacillus arenosus	strain=CAU 1183	GCA_003369575.1	1229153	1229153	type	True	77.7291	195	1416	95	below_threshold
Virgibacillus ndiopensis	strain=Marseille-P3835	GCA_900187325.1	2004408	2004408	type	True	77.6909	241	1416	95	below_threshold
Virgibacillus doumboii	strain=Marseille-Q1616	GCA_902806455.1	2697503	2697503	type	True	77.5258	216	1416	95	below_threshold
Virgibacillus massiliensis	strain=Vm-5	GCA_000723585.1	1462526	1462526	suspected-type	True	77.5254	168	1416	95	below_threshold
Virgibacillus massiliensis	strain=Vm-5	GCA_014905475.1	1462526	1462526	suspected-type	True	77.5248	168	1416	95	below_threshold
Oceanobacillus bengalensis	strain=MCCC 1K00260	GCA_003628445.1	1435466	1435466	type	True	77.481	185	1416	95	below_threshold
Oceanobacillus damuensis	strain=PT-20	GCA_001618145.1	937928	937928	type	True	77.4732	203	1416	95	below_threshold
Virgibacillus oceani	strain=CGMCC 1.12754	GCA_014638995.1	1479511	1479511	type	True	77.426	233	1416	95	below_threshold
Oceanobacillus polygoni	strain=SA9	GCA_008304605.1	1235259	1235259	type	True	77.4061	231	1416	95	below_threshold
Oceanobacillus senegalensis	strain=Marseille-P3587	GCA_900176885.1	1936063	1936063	type	True	77.338	159	1416	95	below_threshold
Virgibacillus litoralis	strain=DSM 21085	GCA_017873675.1	578221	578221	type	True	77.1502	217	1416	95	below_threshold
Oceanobacillus piezotolerans	strain=YLB-02	GCA_003665065.1	2448030	2448030	type	True	76.927	153	1416	95	below_threshold
Bacillus aquiflavi	strain=3H-10	GCA_019915265.1	2672567	2672567	type	True	76.1047	51	1416	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:09:49,826] [INFO] DFAST Taxonomy check result was written to GCF_002287375.1_ASM228737v1_genomic.fna/tc_result.tsv
[2024-01-25 18:09:49,828] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:09:49,828] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:09:49,828] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4646b72f-28c6-4199-a313-1d176666ab06/dqc_reference/checkm_data
[2024-01-25 18:09:49,829] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:09:49,873] [INFO] Task started: CheckM
[2024-01-25 18:09:49,873] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002287375.1_ASM228737v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002287375.1_ASM228737v1_genomic.fna/checkm_input GCF_002287375.1_ASM228737v1_genomic.fna/checkm_result
[2024-01-25 18:10:18,225] [INFO] Task succeeded: CheckM
[2024-01-25 18:10:18,226] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:10:18,245] [INFO] ===== Completeness check finished =====
[2024-01-25 18:10:18,246] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:10:18,246] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002287375.1_ASM228737v1_genomic.fna/markers.fasta)
[2024-01-25 18:10:18,246] [INFO] Task started: Blastn
[2024-01-25 18:10:18,246] [INFO] Running command: blastn -query GCF_002287375.1_ASM228737v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4646b72f-28c6-4199-a313-1d176666ab06/dqc_reference/reference_markers_gtdb.fasta -out GCF_002287375.1_ASM228737v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:10:19,042] [INFO] Task succeeded: Blastn
[2024-01-25 18:10:19,046] [INFO] Selected 22 target genomes.
[2024-01-25 18:10:19,046] [INFO] Target genome list was writen to GCF_002287375.1_ASM228737v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:10:19,061] [INFO] Task started: fastANI
[2024-01-25 18:10:19,061] [INFO] Running command: fastANI --query /var/lib/cwl/stg6ad7cfd2-6b08-4170-90fc-ce27e56a2d49/GCF_002287375.1_ASM228737v1_genomic.fna.gz --refList GCF_002287375.1_ASM228737v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002287375.1_ASM228737v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:10:35,736] [INFO] Task succeeded: fastANI
[2024-01-25 18:10:35,748] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:10:35,749] [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_002287375.1	s__Virgibacillus_G profundi	100.0	1415	1416	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	conclusive
GCF_002266285.1	s__Virgibacillus_G indicus	80.4245	627	1416	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Virgibacillus_G	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016908515.1	s__Virgibacillus_I halotolerans	78.0743	246	1416	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	-
GCF_017874115.1	s__Virgibacillus_H natechei	77.886	293	1416	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Virgibacillus_H	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900258515.1	s__Virgibacillus_E sp900258515	77.7505	202	1416	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_003369575.1	s__Oceanobacillus arenosus	77.7128	196	1416	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	77.6404	241	1416	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_000612865.1	s__Virgibacillus picturae	77.5709	187	1416	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_000724085.1	s__Virgibacillus manasiensis	77.5695	194	1416	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_014905415.1	s__Virgibacillus salexigens	77.515	173	1416	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_001618145.1	s__Oceanobacillus damuensis	77.4918	201	1416	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_003628445.1	s__Oceanobacillus bengalensis	77.457	183	1416	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_014638995.1	s__Virgibacillus_E oceani	77.4501	232	1416	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	77.4308	229	1416	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_900176885.1	s__Oceanobacillus senegalensis	77.3402	158	1416	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_900166595.1	s__Virgibacillus dokdonensis	77.2847	140	1416	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_000577245.1	s__Ornithinibacillus sp000577245	77.2347	145	1416	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	77.2137	206	1416	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_017873675.1	s__Lentibacillus litoralis	77.1522	216	1416	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_003665065.1	s__Oceanobacillus piezotolerans	76.9115	154	1416	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Oceanobacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:10:35,753] [INFO] GTDB search result was written to GCF_002287375.1_ASM228737v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:10:35,754] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:10:35,762] [INFO] DFAST_QC result json was written to GCF_002287375.1_ASM228737v1_genomic.fna/dqc_result.json
[2024-01-25 18:10:35,763] [INFO] DFAST_QC completed!
[2024-01-25 18:10:35,763] [INFO] Total running time: 0h1m15s