[2024-01-24 12:31:56,767] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:31:56,772] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:31:56,772] [INFO] DQC Reference Directory: /var/lib/cwl/stg88012336-ba79-4afa-a086-cd90fa23104e/dqc_reference
[2024-01-24 12:31:58,214] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:31:58,215] [INFO] Task started: Prodigal
[2024-01-24 12:31:58,215] [INFO] Running command: gunzip -c /var/lib/cwl/stgd5f49624-157c-4453-833f-189cb034e89a/GCF_000285495.1_ASM28549v1_genomic.fna.gz | prodigal -d GCF_000285495.1_ASM28549v1_genomic.fna/cds.fna -a GCF_000285495.1_ASM28549v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:32:06,669] [INFO] Task succeeded: Prodigal
[2024-01-24 12:32:06,670] [INFO] Task started: HMMsearch
[2024-01-24 12:32:06,670] [INFO] Running command: hmmsearch --tblout GCF_000285495.1_ASM28549v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg88012336-ba79-4afa-a086-cd90fa23104e/dqc_reference/reference_markers.hmm GCF_000285495.1_ASM28549v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:32:06,940] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:32:06,941] [INFO] Found 6/6 markers.
[2024-01-24 12:32:06,987] [INFO] Query marker FASTA was written to GCF_000285495.1_ASM28549v1_genomic.fna/markers.fasta
[2024-01-24 12:32:06,988] [INFO] Task started: Blastn
[2024-01-24 12:32:06,988] [INFO] Running command: blastn -query GCF_000285495.1_ASM28549v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg88012336-ba79-4afa-a086-cd90fa23104e/dqc_reference/reference_markers.fasta -out GCF_000285495.1_ASM28549v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:32:07,638] [INFO] Task succeeded: Blastn
[2024-01-24 12:32:07,642] [INFO] Selected 17 target genomes.
[2024-01-24 12:32:07,642] [INFO] Target genome list was writen to GCF_000285495.1_ASM28549v1_genomic.fna/target_genomes.txt
[2024-01-24 12:32:07,654] [INFO] Task started: fastANI
[2024-01-24 12:32:07,654] [INFO] Running command: fastANI --query /var/lib/cwl/stgd5f49624-157c-4453-833f-189cb034e89a/GCF_000285495.1_ASM28549v1_genomic.fna.gz --refList GCF_000285495.1_ASM28549v1_genomic.fna/target_genomes.txt --output GCF_000285495.1_ASM28549v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:32:22,125] [INFO] Task succeeded: fastANI
[2024-01-24 12:32:22,125] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg88012336-ba79-4afa-a086-cd90fa23104e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:32:22,126] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg88012336-ba79-4afa-a086-cd90fa23104e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:32:22,135] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:32:22,136] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:32:22,136] [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 massiliensis	strain=Ndiop	GCA_000285495.1	1465765	1465765	type	True	99.9998	1183	1186	95	conclusive
Oceanobacillus damuensis	strain=PT-20	GCA_001618145.1	937928	937928	type	True	78.8843	390	1186	95	below_threshold
Oceanobacillus rekensis	strain=PT-11	GCA_002153375.1	937927	937927	type	True	78.6085	344	1186	95	below_threshold
Oceanobacillus polygoni	strain=SA9	GCA_008304605.1	1235259	1235259	type	True	77.9237	279	1186	95	below_threshold
Virgibacillus dakarensis	strain=Marseille-P3469	GCA_900155625.1	1917889	1917889	type	True	77.7985	142	1186	95	below_threshold
Oceanobacillus chungangensis	strain=CAU 1051	GCA_003369565.1	1229152	1229152	type	True	77.7244	156	1186	95	below_threshold
Oceanobacillus neutriphilus	strain=CGMCC 1.7693	GCA_014645515.1	531815	531815	type	True	77.2587	128	1186	95	below_threshold
Virgibacillus profundi	strain=P3-H5	GCA_002287375.1	2024555	2024555	type	True	77.1807	190	1186	95	below_threshold
Oceanobacillus salinisoli	strain=YIM B00359	GCA_009733865.1	2678611	2678611	type	True	77.1331	159	1186	95	below_threshold
Gracilibacillus orientalis	strain=CGMCC 1.4250	GCA_900114645.1	334253	334253	type	True	76.6333	54	1186	95	below_threshold
Compostibacillus humi	strain=CGMCC 1.12360	GCA_014637175.1	1245525	1245525	type	True	76.4506	74	1186	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:32:22,138] [INFO] DFAST Taxonomy check result was written to GCF_000285495.1_ASM28549v1_genomic.fna/tc_result.tsv
[2024-01-24 12:32:22,139] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:32:22,139] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:32:22,139] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg88012336-ba79-4afa-a086-cd90fa23104e/dqc_reference/checkm_data
[2024-01-24 12:32:22,141] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:32:22,178] [INFO] Task started: CheckM
[2024-01-24 12:32:22,178] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000285495.1_ASM28549v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000285495.1_ASM28549v1_genomic.fna/checkm_input GCF_000285495.1_ASM28549v1_genomic.fna/checkm_result
[2024-01-24 12:32:53,542] [INFO] Task succeeded: CheckM
[2024-01-24 12:32:53,543] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:32:53,568] [INFO] ===== Completeness check finished =====
[2024-01-24 12:32:53,568] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:32:53,568] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000285495.1_ASM28549v1_genomic.fna/markers.fasta)
[2024-01-24 12:32:53,569] [INFO] Task started: Blastn
[2024-01-24 12:32:53,569] [INFO] Running command: blastn -query GCF_000285495.1_ASM28549v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg88012336-ba79-4afa-a086-cd90fa23104e/dqc_reference/reference_markers_gtdb.fasta -out GCF_000285495.1_ASM28549v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:32:54,355] [INFO] Task succeeded: Blastn
[2024-01-24 12:32:54,358] [INFO] Selected 20 target genomes.
[2024-01-24 12:32:54,358] [INFO] Target genome list was writen to GCF_000285495.1_ASM28549v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:32:54,370] [INFO] Task started: fastANI
[2024-01-24 12:32:54,371] [INFO] Running command: fastANI --query /var/lib/cwl/stgd5f49624-157c-4453-833f-189cb034e89a/GCF_000285495.1_ASM28549v1_genomic.fna.gz --refList GCF_000285495.1_ASM28549v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000285495.1_ASM28549v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:33:08,520] [INFO] Task succeeded: fastANI
[2024-01-24 12:33:08,534] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:33:08,535] [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_000285495.1	s__Oceanobacillus massiliensis	99.9998	1183	1186	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Oceanobacillus	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_001618145.1	s__Oceanobacillus damuensis	78.9089	388	1186	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_002153375.1	s__Oceanobacillus rekensis	78.6039	345	1186	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_018333215.1	s__Oceanobacillus sp018333215	77.909	139	1186	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_000724085.1	s__Virgibacillus manasiensis	77.7983	126	1186	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_003628445.1	s__Oceanobacillus bengalensis	77.6804	136	1186	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_016919725.1	s__Virgibacillus sp016919725	77.3557	109	1186	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_014645515.1	s__Oceanobacillus neutriphilus	77.2723	128	1186	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Oceanobacillus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001659985.1	s__Oceanobacillus sp001659985	77.2566	114	1186	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	77.1417	160	1186	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_002287375.1	s__Virgibacillus_G profundi	77.1207	193	1186	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_900162695.1	s__Lentibacillus siamensis	76.9561	105	1186	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_018333235.1	s__Ornithinibacillus bavariensis	76.9474	95	1186	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_900162615.1	s__Virgibacillus proomii_A	76.9176	96	1186	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_018916875.1	s__Virgibacillus proomii_B	76.8856	86	1186	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_013373365.1	s__Lentibacillus sp013373365	76.7993	85	1186	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_010994035.1	s__Virgibacillus sp010994035	76.6604	94	1186	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_900114645.1	s__Gracilibacillus orientalis	76.6333	54	1186	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Gracilibacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:33:08,537] [INFO] GTDB search result was written to GCF_000285495.1_ASM28549v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:33:08,538] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:33:08,541] [INFO] DFAST_QC result json was written to GCF_000285495.1_ASM28549v1_genomic.fna/dqc_result.json
[2024-01-24 12:33:08,542] [INFO] DFAST_QC completed!
[2024-01-24 12:33:08,542] [INFO] Total running time: 0h1m12s