[2024-01-24 12:21:57,404] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:21:57,406] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:21:57,406] [INFO] DQC Reference Directory: /var/lib/cwl/stg4198ea63-03c4-4a3a-994c-1b69ed07a444/dqc_reference
[2024-01-24 12:21:58,968] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:21:58,970] [INFO] Task started: Prodigal
[2024-01-24 12:21:58,970] [INFO] Running command: gunzip -c /var/lib/cwl/stg978de21a-f98c-4b7b-b0a2-62dc3a847876/GCF_000306965.1_ASM30696v1_genomic.fna.gz | prodigal -d GCF_000306965.1_ASM30696v1_genomic.fna/cds.fna -a GCF_000306965.1_ASM30696v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:22:06,872] [INFO] Task succeeded: Prodigal
[2024-01-24 12:22:06,872] [INFO] Task started: HMMsearch
[2024-01-24 12:22:06,872] [INFO] Running command: hmmsearch --tblout GCF_000306965.1_ASM30696v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4198ea63-03c4-4a3a-994c-1b69ed07a444/dqc_reference/reference_markers.hmm GCF_000306965.1_ASM30696v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:22:07,164] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:22:07,166] [INFO] Found 6/6 markers.
[2024-01-24 12:22:07,200] [INFO] Query marker FASTA was written to GCF_000306965.1_ASM30696v1_genomic.fna/markers.fasta
[2024-01-24 12:22:07,200] [INFO] Task started: Blastn
[2024-01-24 12:22:07,200] [INFO] Running command: blastn -query GCF_000306965.1_ASM30696v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4198ea63-03c4-4a3a-994c-1b69ed07a444/dqc_reference/reference_markers.fasta -out GCF_000306965.1_ASM30696v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:22:07,829] [INFO] Task succeeded: Blastn
[2024-01-24 12:22:07,833] [INFO] Selected 22 target genomes.
[2024-01-24 12:22:07,834] [INFO] Target genome list was writen to GCF_000306965.1_ASM30696v1_genomic.fna/target_genomes.txt
[2024-01-24 12:22:07,842] [INFO] Task started: fastANI
[2024-01-24 12:22:07,843] [INFO] Running command: fastANI --query /var/lib/cwl/stg978de21a-f98c-4b7b-b0a2-62dc3a847876/GCF_000306965.1_ASM30696v1_genomic.fna.gz --refList GCF_000306965.1_ASM30696v1_genomic.fna/target_genomes.txt --output GCF_000306965.1_ASM30696v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:22:22,570] [INFO] Task succeeded: fastANI
[2024-01-24 12:22:22,570] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4198ea63-03c4-4a3a-994c-1b69ed07a444/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:22:22,571] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4198ea63-03c4-4a3a-994c-1b69ed07a444/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:22:22,585] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:22:22,585] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:22:22,586] [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
Amphibacillus jilinensis	strain=Y1	GCA_000306965.1	1216008	1216008	type	True	100.0	1264	1265	95	conclusive
Amphibacillus cookii	strain=DSM 23721	GCA_016908375.1	767787	767787	type	True	91.2421	1049	1265	95	below_threshold
Amphibacillus marinus	strain=CGMCC 1.10434	GCA_900110345.1	872970	872970	type	True	77.7682	206	1265	95	below_threshold
Streptohalobacillus salinus	strain=DSM 22440	GCA_003201605.1	621096	621096	type	True	77.7232	114	1265	95	below_threshold
Amphibacillus sediminis	strain=NBRC 103570	GCA_001552275.1	360185	360185	type	True	77.6719	221	1265	95	below_threshold
Halolactibacillus alkaliphilus	strain=CGMCC 1.6843	GCA_014645215.1	442899	442899	type	True	77.5963	99	1265	95	below_threshold
Halolactibacillus alkaliphilus	strain=NBRC 103919	GCA_007991355.1	442899	442899	type	True	77.5352	100	1265	95	below_threshold
Paraliobacillus zengyii	strain=X-1125	GCA_003268595.1	2213194	2213194	type	True	77.4383	110	1265	95	below_threshold
Paraliobacillus ryukyuensis	strain=DSM 15140	GCA_003315295.1	200904	200904	type	True	77.2199	115	1265	95	below_threshold
Amphibacillus xylanus	strain=NBRC 15112	GCA_000307165.1	1449	1449	type	True	77.0629	117	1265	95	below_threshold
Ornithinibacillus contaminans	strain=DSM 22953	GCA_001038425.2	694055	694055	type	True	76.9727	51	1265	95	below_threshold
Aquibacillus saliphilus	strain=KHM2	GCA_020404745.1	1909422	1909422	type	True	76.9303	65	1265	95	below_threshold
Aquibacillus albus	strain=DSM 23711	GCA_016908325.1	1168171	1168171	type	True	76.8627	70	1265	95	below_threshold
Aquibacillus kalidii	strain=HU2P27	GCA_014280935.1	2762597	2762597	type	True	76.8298	70	1265	95	below_threshold
Gracilibacillus orientalis	strain=CGMCC 1.4250	GCA_900114645.1	334253	334253	type	True	76.7617	73	1265	95	below_threshold
Paraliobacillus sediminis	strain=126C4	GCA_003426055.1	1885916	1885916	type	True	76.1639	103	1265	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:22:22,595] [INFO] DFAST Taxonomy check result was written to GCF_000306965.1_ASM30696v1_genomic.fna/tc_result.tsv
[2024-01-24 12:22:22,598] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:22:22,598] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:22:22,598] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4198ea63-03c4-4a3a-994c-1b69ed07a444/dqc_reference/checkm_data
[2024-01-24 12:22:22,599] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:22:22,666] [INFO] Task started: CheckM
[2024-01-24 12:22:22,667] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000306965.1_ASM30696v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000306965.1_ASM30696v1_genomic.fna/checkm_input GCF_000306965.1_ASM30696v1_genomic.fna/checkm_result
[2024-01-24 12:22:51,738] [INFO] Task succeeded: CheckM
[2024-01-24 12:22:51,740] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:22:51,761] [INFO] ===== Completeness check finished =====
[2024-01-24 12:22:51,761] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:22:51,762] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000306965.1_ASM30696v1_genomic.fna/markers.fasta)
[2024-01-24 12:22:51,762] [INFO] Task started: Blastn
[2024-01-24 12:22:51,762] [INFO] Running command: blastn -query GCF_000306965.1_ASM30696v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4198ea63-03c4-4a3a-994c-1b69ed07a444/dqc_reference/reference_markers_gtdb.fasta -out GCF_000306965.1_ASM30696v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:22:52,554] [INFO] Task succeeded: Blastn
[2024-01-24 12:22:52,557] [INFO] Selected 18 target genomes.
[2024-01-24 12:22:52,557] [INFO] Target genome list was writen to GCF_000306965.1_ASM30696v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:22:52,569] [INFO] Task started: fastANI
[2024-01-24 12:22:52,569] [INFO] Running command: fastANI --query /var/lib/cwl/stg978de21a-f98c-4b7b-b0a2-62dc3a847876/GCF_000306965.1_ASM30696v1_genomic.fna.gz --refList GCF_000306965.1_ASM30696v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000306965.1_ASM30696v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:23:03,361] [INFO] Task succeeded: fastANI
[2024-01-24 12:23:03,375] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:23:03,377] [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_000306965.1	s__Amphibacillus_C jilinensis	100.0	1264	1265	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Amphibacillus_C	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_016908375.1	s__Amphibacillus_C cookii	91.2421	1049	1265	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Amphibacillus_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110345.1	s__Amphibacillus_D marinus	77.7796	206	1265	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_003201605.1	s__Streptohalobacillus salinus	77.7158	115	1265	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Streptohalobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001552275.1	s__Amphibacillus_B sediminis	77.6719	221	1265	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Amphibacillus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900115465.1	s__Halolactibacillus alkaliphilus	77.474	102	1265	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Halolactibacillus	95.0	99.99	99.98	0.99	0.99	3	-
GCF_003268595.1	s__Paraliobacillus_A zengyii	77.4106	111	1265	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	-
GCF_001368815.1	s__Paraliobacillus sp001368815	77.3969	114	1265	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_003315295.1	s__Paraliobacillus ryukyuensis	77.1986	115	1265	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_018919165.1	s__Amphibacillus sp018919165	77.0717	140	1265	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_000307165.1	s__Amphibacillus xylanus	77.0606	118	1265	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_001038425.2	s__Ornithinibacillus contaminans	76.9769	53	1265	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_900129485.1	s__Ornithinibacillus halophilus	76.6122	51	1265	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Ornithinibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012838505.1	s__Amphibacillus sp012838505	76.5314	118	1265	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_005870085.1	s__BH258 sp005870085	76.2918	90	1265	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__BH258	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:23:03,379] [INFO] GTDB search result was written to GCF_000306965.1_ASM30696v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:23:03,380] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:23:03,384] [INFO] DFAST_QC result json was written to GCF_000306965.1_ASM30696v1_genomic.fna/dqc_result.json
[2024-01-24 12:23:03,385] [INFO] DFAST_QC completed!
[2024-01-24 12:23:03,389] [INFO] Total running time: 0h1m6s