[2024-01-24 12:25:20,517] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:25:20,519] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:25:20,519] [INFO] DQC Reference Directory: /var/lib/cwl/stg67335c55-44e4-49dc-9c44-3c9015822e5a/dqc_reference
[2024-01-24 12:25:21,762] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:25:21,763] [INFO] Task started: Prodigal
[2024-01-24 12:25:21,763] [INFO] Running command: gunzip -c /var/lib/cwl/stg83b5d19e-9c3c-4319-bf36-dd5af75abaf3/GCF_003268595.1_ASM326859v1_genomic.fna.gz | prodigal -d GCF_003268595.1_ASM326859v1_genomic.fna/cds.fna -a GCF_003268595.1_ASM326859v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:25:28,898] [INFO] Task succeeded: Prodigal
[2024-01-24 12:25:28,898] [INFO] Task started: HMMsearch
[2024-01-24 12:25:28,898] [INFO] Running command: hmmsearch --tblout GCF_003268595.1_ASM326859v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg67335c55-44e4-49dc-9c44-3c9015822e5a/dqc_reference/reference_markers.hmm GCF_003268595.1_ASM326859v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:25:29,162] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:25:29,163] [INFO] Found 6/6 markers.
[2024-01-24 12:25:29,197] [INFO] Query marker FASTA was written to GCF_003268595.1_ASM326859v1_genomic.fna/markers.fasta
[2024-01-24 12:25:29,198] [INFO] Task started: Blastn
[2024-01-24 12:25:29,198] [INFO] Running command: blastn -query GCF_003268595.1_ASM326859v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg67335c55-44e4-49dc-9c44-3c9015822e5a/dqc_reference/reference_markers.fasta -out GCF_003268595.1_ASM326859v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:25:29,788] [INFO] Task succeeded: Blastn
[2024-01-24 12:25:29,792] [INFO] Selected 20 target genomes.
[2024-01-24 12:25:29,793] [INFO] Target genome list was writen to GCF_003268595.1_ASM326859v1_genomic.fna/target_genomes.txt
[2024-01-24 12:25:29,807] [INFO] Task started: fastANI
[2024-01-24 12:25:29,808] [INFO] Running command: fastANI --query /var/lib/cwl/stg83b5d19e-9c3c-4319-bf36-dd5af75abaf3/GCF_003268595.1_ASM326859v1_genomic.fna.gz --refList GCF_003268595.1_ASM326859v1_genomic.fna/target_genomes.txt --output GCF_003268595.1_ASM326859v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:25:42,757] [INFO] Task succeeded: fastANI
[2024-01-24 12:25:42,758] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg67335c55-44e4-49dc-9c44-3c9015822e5a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:25:42,759] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg67335c55-44e4-49dc-9c44-3c9015822e5a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:25:42,774] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:25:42,774] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:25:42,774] [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
Paraliobacillus zengyii	strain=X-1125	GCA_003268595.1	2213194	2213194	type	True	100.0	1240	1242	95	conclusive
Paraliobacillus sediminis	strain=126C4	GCA_003426055.1	1885916	1885916	type	True	87.3541	815	1242	95	below_threshold
Paraliobacillus quinghaiensis	strain=YIM-C158	GCA_003426025.1	470815	470815	type	True	78.9548	391	1242	95	below_threshold
Paraliobacillus quinghaiensis	strain=CGMCC 1.6333	GCA_014645115.1	470815	470815	type	True	78.9353	399	1242	95	below_threshold
Oceanobacillus timonensis	strain=Marseille-P3532	GCA_900166635.1	1926285	1926285	type	True	78.1862	58	1242	95	below_threshold
Paraliobacillus salinarum	strain=G6-18	GCA_014083865.1	1158996	1158996	type	True	77.4608	187	1242	95	below_threshold
Aquibacillus koreensis	strain=JCM 12387	GCA_025154055.1	279446	279446	type	True	77.4059	174	1242	95	below_threshold
Aquibacillus sediminis	strain=BH258	GCA_005870085.1	2574734	2574734	type	True	77.2376	142	1242	95	below_threshold
Paraliobacillus ryukyuensis	strain=DSM 15140	GCA_003315295.1	200904	200904	type	True	77.1289	223	1242	95	below_threshold
Saliterribacillus persicus	strain=DSM 27696	GCA_003337485.1	930114	930114	type	True	77.1125	116	1242	95	below_threshold
Amphibacillus marinus	strain=CGMCC 1.10434	GCA_900110345.1	872970	872970	type	True	76.8166	101	1242	95	below_threshold
Salirhabdus euzebyi	strain=DSM 19612	GCA_014207435.1	394506	394506	type	True	76.5474	74	1242	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:25:42,776] [INFO] DFAST Taxonomy check result was written to GCF_003268595.1_ASM326859v1_genomic.fna/tc_result.tsv
[2024-01-24 12:25:42,777] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:25:42,778] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:25:42,778] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg67335c55-44e4-49dc-9c44-3c9015822e5a/dqc_reference/checkm_data
[2024-01-24 12:25:42,779] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:25:42,816] [INFO] Task started: CheckM
[2024-01-24 12:25:42,816] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003268595.1_ASM326859v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003268595.1_ASM326859v1_genomic.fna/checkm_input GCF_003268595.1_ASM326859v1_genomic.fna/checkm_result
[2024-01-24 12:26:10,115] [INFO] Task succeeded: CheckM
[2024-01-24 12:26:10,117] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:26:10,138] [INFO] ===== Completeness check finished =====
[2024-01-24 12:26:10,138] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:26:10,139] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003268595.1_ASM326859v1_genomic.fna/markers.fasta)
[2024-01-24 12:26:10,139] [INFO] Task started: Blastn
[2024-01-24 12:26:10,139] [INFO] Running command: blastn -query GCF_003268595.1_ASM326859v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg67335c55-44e4-49dc-9c44-3c9015822e5a/dqc_reference/reference_markers_gtdb.fasta -out GCF_003268595.1_ASM326859v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:26:10,884] [INFO] Task succeeded: Blastn
[2024-01-24 12:26:10,888] [INFO] Selected 22 target genomes.
[2024-01-24 12:26:10,888] [INFO] Target genome list was writen to GCF_003268595.1_ASM326859v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:26:10,901] [INFO] Task started: fastANI
[2024-01-24 12:26:10,901] [INFO] Running command: fastANI --query /var/lib/cwl/stg83b5d19e-9c3c-4319-bf36-dd5af75abaf3/GCF_003268595.1_ASM326859v1_genomic.fna.gz --refList GCF_003268595.1_ASM326859v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003268595.1_ASM326859v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:26:24,504] [INFO] Task succeeded: fastANI
[2024-01-24 12:26:24,531] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:26:24,532] [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_003268595.1	s__Paraliobacillus_A zengyii	100.0	1241	1242	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Paraliobacillus_A	95.0	99.46	99.36	0.95	0.93	3	conclusive
GCF_003426025.1	s__Paraliobacillus_A quinghaiensis	79.0255	389	1242	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Paraliobacillus_A	95.0	99.99	99.99	0.99	0.99	2	-
GCF_900166635.1	s__Oceanobacillus timonensis	78.1771	61	1242	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	78.1243	87	1242	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_000307165.1	s__Amphibacillus xylanus	78.1195	76	1242	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Amphibacillus	95.0	97.98	97.98	0.94	0.94	2	-
GCF_001368815.1	s__Paraliobacillus sp001368815	77.9548	196	1242	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Paraliobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014083865.1	s__Paraliobacillus salinarum	77.4604	188	1242	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Paraliobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900096905.1	s__Pelagirhabdus alkalitolerans	77.2639	100	1242	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Pelagirhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005870085.1	s__BH258 sp005870085	77.2506	144	1242	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__BH258	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014280935.1	s__HU2P27 sp014280935	77.1807	154	1242	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__HU2P27	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003315295.1	s__Paraliobacillus ryukyuensis	77.129	225	1242	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Paraliobacillus	95.0	98.18	98.18	0.92	0.92	2	-
GCF_003337485.1	s__Saliterribacillus persicus	77.0922	116	1242	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Saliterribacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900115465.1	s__Halolactibacillus alkaliphilus	77.0563	88	1242	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Halolactibacillus	95.0	99.99	99.98	0.99	0.99	3	-
GCA_012838505.1	s__Amphibacillus sp012838505	76.8532	65	1242	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Amphibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110345.1	s__Amphibacillus_D marinus	76.8166	101	1242	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Amphibacillus_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014207435.1	s__Salirhabdus euzebyi	76.577	73	1242	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Alkalibacillaceae;g__Salirhabdus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_010993955.1	s__YIM-98839 sp010993955	76.5356	76	1242	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__YIM-98839	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:26:24,533] [INFO] GTDB search result was written to GCF_003268595.1_ASM326859v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:26:24,534] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:26:24,538] [INFO] DFAST_QC result json was written to GCF_003268595.1_ASM326859v1_genomic.fna/dqc_result.json
[2024-01-24 12:26:24,538] [INFO] DFAST_QC completed!
[2024-01-24 12:26:24,538] [INFO] Total running time: 0h1m4s