[2024-01-24 13:31:35,221] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:31:35,224] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:31:35,225] [INFO] DQC Reference Directory: /var/lib/cwl/stgd94a845b-64ef-42d0-9f41-53c0a505b750/dqc_reference
[2024-01-24 13:31:36,690] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:31:36,691] [INFO] Task started: Prodigal
[2024-01-24 13:31:36,691] [INFO] Running command: gunzip -c /var/lib/cwl/stgd416677f-55f7-4c9f-add5-856cb111185a/GCF_017874935.1_ASM1787493v1_genomic.fna.gz | prodigal -d GCF_017874935.1_ASM1787493v1_genomic.fna/cds.fna -a GCF_017874935.1_ASM1787493v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:31:46,665] [INFO] Task succeeded: Prodigal
[2024-01-24 13:31:46,666] [INFO] Task started: HMMsearch
[2024-01-24 13:31:46,666] [INFO] Running command: hmmsearch --tblout GCF_017874935.1_ASM1787493v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd94a845b-64ef-42d0-9f41-53c0a505b750/dqc_reference/reference_markers.hmm GCF_017874935.1_ASM1787493v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:31:47,032] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:31:47,033] [INFO] Found 6/6 markers.
[2024-01-24 13:31:47,073] [INFO] Query marker FASTA was written to GCF_017874935.1_ASM1787493v1_genomic.fna/markers.fasta
[2024-01-24 13:31:47,074] [INFO] Task started: Blastn
[2024-01-24 13:31:47,074] [INFO] Running command: blastn -query GCF_017874935.1_ASM1787493v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd94a845b-64ef-42d0-9f41-53c0a505b750/dqc_reference/reference_markers.fasta -out GCF_017874935.1_ASM1787493v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:31:47,719] [INFO] Task succeeded: Blastn
[2024-01-24 13:31:47,721] [INFO] Selected 18 target genomes.
[2024-01-24 13:31:47,722] [INFO] Target genome list was writen to GCF_017874935.1_ASM1787493v1_genomic.fna/target_genomes.txt
[2024-01-24 13:31:47,729] [INFO] Task started: fastANI
[2024-01-24 13:31:47,729] [INFO] Running command: fastANI --query /var/lib/cwl/stgd416677f-55f7-4c9f-add5-856cb111185a/GCF_017874935.1_ASM1787493v1_genomic.fna.gz --refList GCF_017874935.1_ASM1787493v1_genomic.fna/target_genomes.txt --output GCF_017874935.1_ASM1787493v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:32:02,564] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:02,564] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd94a845b-64ef-42d0-9f41-53c0a505b750/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:32:02,565] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd94a845b-64ef-42d0-9f41-53c0a505b750/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:32:02,576] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:32:02,576] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:32:02,576] [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 polygoni	strain=SA9	GCA_008304605.1	1235259	1235259	type	True	99.9899	1471	1493	95	conclusive
Oceanobacillus profundus	strain=DSM 18246	GCA_003515705.1	372463	372463	type	True	87.992	1162	1493	95	below_threshold
Oceanobacillus profundus	strain=CL-MP28	GCA_008087205.1	372463	372463	type	True	87.9651	1175	1493	95	below_threshold
Oceanobacillus kimchii	strain=X50	GCA_000340475.1	746691	746691	type	True	78.6942	199	1493	95	below_threshold
Oceanobacillus rekensis	strain=PT-11	GCA_002153375.1	937927	937927	type	True	78.6794	345	1493	95	below_threshold
Oceanobacillus zhaokaii	strain=160	GCA_003352005.1	2052660	2052660	type	True	78.583	223	1493	95	below_threshold
Oceanobacillus damuensis	strain=PT-20	GCA_001618145.1	937928	937928	type	True	78.5099	332	1493	95	below_threshold
Lentibacillus amyloliquefaciens	strain=LAM0015	GCA_001307805.2	1472767	1472767	type	True	78.046	65	1493	95	below_threshold
Oceanobacillus jordanicus	strain=GSFE11	GCA_022095695.1	2867266	2867266	type	True	77.8095	174	1493	95	below_threshold
Virgibacillus profundi	strain=P3-H5	GCA_002287375.1	2024555	2024555	type	True	77.6285	213	1493	95	below_threshold
Oceanobacillus senegalensis	strain=Marseille-P3587	GCA_900176885.1	1936063	1936063	type	True	77.3469	180	1493	95	below_threshold
Oceanobacillus bengalensis	strain=MCCC 1K00260	GCA_003628445.1	1435466	1435466	type	True	77.3009	214	1493	95	below_threshold
Virgibacillus ihumii	strain=Marseille-Q1233	GCA_902726655.1	2686091	2686091	type	True	77.1963	111	1493	95	below_threshold
Sutcliffiella halmapala	strain=DSM 8723	GCA_002019665.1	79882	79882	type	True	77.1064	61	1493	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:32:02,578] [INFO] DFAST Taxonomy check result was written to GCF_017874935.1_ASM1787493v1_genomic.fna/tc_result.tsv
[2024-01-24 13:32:02,578] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:32:02,578] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:32:02,579] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd94a845b-64ef-42d0-9f41-53c0a505b750/dqc_reference/checkm_data
[2024-01-24 13:32:02,580] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:32:02,634] [INFO] Task started: CheckM
[2024-01-24 13:32:02,635] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017874935.1_ASM1787493v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017874935.1_ASM1787493v1_genomic.fna/checkm_input GCF_017874935.1_ASM1787493v1_genomic.fna/checkm_result
[2024-01-24 13:32:36,407] [INFO] Task succeeded: CheckM
[2024-01-24 13:32:36,409] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:32:36,427] [INFO] ===== Completeness check finished =====
[2024-01-24 13:32:36,427] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:32:36,427] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017874935.1_ASM1787493v1_genomic.fna/markers.fasta)
[2024-01-24 13:32:36,428] [INFO] Task started: Blastn
[2024-01-24 13:32:36,428] [INFO] Running command: blastn -query GCF_017874935.1_ASM1787493v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd94a845b-64ef-42d0-9f41-53c0a505b750/dqc_reference/reference_markers_gtdb.fasta -out GCF_017874935.1_ASM1787493v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:37,232] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:37,236] [INFO] Selected 19 target genomes.
[2024-01-24 13:32:37,237] [INFO] Target genome list was writen to GCF_017874935.1_ASM1787493v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:32:37,261] [INFO] Task started: fastANI
[2024-01-24 13:32:37,262] [INFO] Running command: fastANI --query /var/lib/cwl/stgd416677f-55f7-4c9f-add5-856cb111185a/GCF_017874935.1_ASM1787493v1_genomic.fna.gz --refList GCF_017874935.1_ASM1787493v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017874935.1_ASM1787493v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:32:51,646] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:51,660] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:32:51,660] [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_008304605.1	s__Oceanobacillus polygoni	99.9899	1471	1493	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Oceanobacillus	95.0	99.99	99.99	1.00	1.00	2	conclusive
GCF_003515705.1	s__Oceanobacillus profundus	87.9825	1163	1493	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_000340475.1	s__Oceanobacillus kimchii	78.7573	196	1493	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Oceanobacillus	95.0	99.20	99.13	0.93	0.91	5	-
GCF_002153375.1	s__Oceanobacillus rekensis	78.6307	347	1493	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_003352005.1	s__Oceanobacillus zhaokaii	78.5139	225	1493	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	78.4933	334	1493	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_016908155.1	s__Oceanobacillus caeni	78.3848	190	1493	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Oceanobacillus	95.0	98.65	98.42	0.88	0.86	14	-
GCF_001307805.1	s__Lentibacillus amyloliquefaciens	78.0364	67	1493	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_003369565.1	s__Oceanobacillus chungangensis	77.9331	236	1493	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_900111445.1	s__Ornithinibacillus limi	77.5711	138	1493	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_001659985.1	s__Oceanobacillus sp001659985	77.4181	198	1493	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_900176885.1	s__Oceanobacillus senegalensis	77.3425	180	1493	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	77.2578	216	1493	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_902726655.1	s__Lentibacillus ihumii	77.2197	110	1493	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_014637405.1	s__Ornithinibacillus halotolerans	77.2064	130	1493	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_009389585.1	s__Oceanobacillus sp009389585	77.1015	156	1493	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_900110695.1	s__Lentibacillus subterraneus	76.9575	126	1493	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Lentibacillus	95.0	98.85	98.85	0.91	0.91	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:32:51,662] [INFO] GTDB search result was written to GCF_017874935.1_ASM1787493v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:32:51,663] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:32:51,666] [INFO] DFAST_QC result json was written to GCF_017874935.1_ASM1787493v1_genomic.fna/dqc_result.json
[2024-01-24 13:32:51,666] [INFO] DFAST_QC completed!
[2024-01-24 13:32:51,666] [INFO] Total running time: 0h1m16s