[2024-01-24 14:06:05,838] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:06:05,842] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:06:05,842] [INFO] DQC Reference Directory: /var/lib/cwl/stge0876800-a2a9-4671-9b13-3441c46136f8/dqc_reference
[2024-01-24 14:06:07,199] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:06:07,200] [INFO] Task started: Prodigal
[2024-01-24 14:06:07,200] [INFO] Running command: gunzip -c /var/lib/cwl/stg5f967c59-54b7-4393-884f-72f4a3fbb56d/GCF_026805325.1_ASM2680532v1_genomic.fna.gz | prodigal -d GCF_026805325.1_ASM2680532v1_genomic.fna/cds.fna -a GCF_026805325.1_ASM2680532v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:06:14,081] [INFO] Task succeeded: Prodigal
[2024-01-24 14:06:14,082] [INFO] Task started: HMMsearch
[2024-01-24 14:06:14,082] [INFO] Running command: hmmsearch --tblout GCF_026805325.1_ASM2680532v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge0876800-a2a9-4671-9b13-3441c46136f8/dqc_reference/reference_markers.hmm GCF_026805325.1_ASM2680532v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:06:14,397] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:06:14,399] [INFO] Found 6/6 markers.
[2024-01-24 14:06:14,435] [INFO] Query marker FASTA was written to GCF_026805325.1_ASM2680532v1_genomic.fna/markers.fasta
[2024-01-24 14:06:14,436] [INFO] Task started: Blastn
[2024-01-24 14:06:14,436] [INFO] Running command: blastn -query GCF_026805325.1_ASM2680532v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge0876800-a2a9-4671-9b13-3441c46136f8/dqc_reference/reference_markers.fasta -out GCF_026805325.1_ASM2680532v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:15,094] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:15,097] [INFO] Selected 31 target genomes.
[2024-01-24 14:06:15,097] [INFO] Target genome list was writen to GCF_026805325.1_ASM2680532v1_genomic.fna/target_genomes.txt
[2024-01-24 14:06:15,107] [INFO] Task started: fastANI
[2024-01-24 14:06:15,107] [INFO] Running command: fastANI --query /var/lib/cwl/stg5f967c59-54b7-4393-884f-72f4a3fbb56d/GCF_026805325.1_ASM2680532v1_genomic.fna.gz --refList GCF_026805325.1_ASM2680532v1_genomic.fna/target_genomes.txt --output GCF_026805325.1_ASM2680532v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:06:33,709] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:33,710] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge0876800-a2a9-4671-9b13-3441c46136f8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:06:33,710] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge0876800-a2a9-4671-9b13-3441c46136f8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:06:33,724] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:06:33,724] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:06:33,724] [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 cookii	strain=DSM 23721	GCA_016908375.1	767787	767787	type	True	78.1623	188	1120	95	below_threshold
Amphibacillus jilinensis	strain=Y1	GCA_000306965.1	1216008	1216008	type	True	78.1374	183	1120	95	below_threshold
Pelagirhabdus alkalitolerans	strain=S5	GCA_900096905.1	1612202	1612202	type	True	77.8164	124	1120	95	below_threshold
Paraliobacillus ryukyuensis	strain=DSM 15140	GCA_003315295.1	200904	200904	type	True	77.6402	131	1120	95	below_threshold
Halolactibacillus miurensis	strain=DSM 17074	GCA_900116255.1	306541	306541	type	True	77.6201	111	1120	95	below_threshold
Aquibacillus koreensis	strain=JCM 12387	GCA_025154055.1	279446	279446	type	True	77.5392	96	1120	95	below_threshold
Paraliobacillus quinghaiensis	strain=CGMCC 1.6333	GCA_014645115.1	470815	470815	type	True	77.5346	168	1120	95	below_threshold
Paraliobacillus salinarum	strain=G6-18	GCA_014083865.1	1158996	1158996	type	True	77.5232	140	1120	95	below_threshold
Paraliobacillus zengyii	strain=X-1125	GCA_003268595.1	2213194	2213194	type	True	77.5017	150	1120	95	below_threshold
Halolactibacillus miurensis	strain=NBRC 100873	GCA_007990305.1	306541	306541	type	True	77.4913	115	1120	95	below_threshold
Paraliobacillus quinghaiensis	strain=YIM-C158	GCA_003426025.1	470815	470815	type	True	77.4878	168	1120	95	below_threshold
Gracilibacillus dipsosauri	strain=DD1	GCA_003176895.1	178340	178340	type	True	77.3361	69	1120	95	below_threshold
Aquibacillus saliphilus	strain=KHM2	GCA_020404745.1	1909422	1909422	type	True	77.1956	82	1120	95	below_threshold
Aquibacillus kalidii	strain=HU2P27	GCA_014280935.1	2762597	2762597	type	True	77.0278	95	1120	95	below_threshold
Aquibacillus albus	strain=DSM 23711	GCA_016908325.1	1168171	1168171	type	True	76.9306	77	1120	95	below_threshold
Paraliobacillus sediminis	strain=126C4	GCA_003426055.1	1885916	1885916	type	True	76.7836	130	1120	95	below_threshold
Aquibacillus sediminis	strain=BH258	GCA_005870085.1	2574734	2574734	type	True	76.6963	97	1120	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:06:33,726] [INFO] DFAST Taxonomy check result was written to GCF_026805325.1_ASM2680532v1_genomic.fna/tc_result.tsv
[2024-01-24 14:06:33,727] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:06:33,727] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:06:33,727] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge0876800-a2a9-4671-9b13-3441c46136f8/dqc_reference/checkm_data
[2024-01-24 14:06:33,728] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:06:33,766] [INFO] Task started: CheckM
[2024-01-24 14:06:33,766] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_026805325.1_ASM2680532v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_026805325.1_ASM2680532v1_genomic.fna/checkm_input GCF_026805325.1_ASM2680532v1_genomic.fna/checkm_result
[2024-01-24 14:07:01,195] [INFO] Task succeeded: CheckM
[2024-01-24 14:07:01,196] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:07:01,218] [INFO] ===== Completeness check finished =====
[2024-01-24 14:07:01,218] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:07:01,219] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_026805325.1_ASM2680532v1_genomic.fna/markers.fasta)
[2024-01-24 14:07:01,219] [INFO] Task started: Blastn
[2024-01-24 14:07:01,219] [INFO] Running command: blastn -query GCF_026805325.1_ASM2680532v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge0876800-a2a9-4671-9b13-3441c46136f8/dqc_reference/reference_markers_gtdb.fasta -out GCF_026805325.1_ASM2680532v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:07:02,093] [INFO] Task succeeded: Blastn
[2024-01-24 14:07:02,098] [INFO] Selected 27 target genomes.
[2024-01-24 14:07:02,098] [INFO] Target genome list was writen to GCF_026805325.1_ASM2680532v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:07:02,145] [INFO] Task started: fastANI
[2024-01-24 14:07:02,145] [INFO] Running command: fastANI --query /var/lib/cwl/stg5f967c59-54b7-4393-884f-72f4a3fbb56d/GCF_026805325.1_ASM2680532v1_genomic.fna.gz --refList GCF_026805325.1_ASM2680532v1_genomic.fna/target_genomes_gtdb.txt --output GCF_026805325.1_ASM2680532v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:07:16,451] [INFO] Task succeeded: fastANI
[2024-01-24 14:07:16,467] [INFO] Found 19 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 14:07:16,468] [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	78.1777	181	1120	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_016908375.1	s__Amphibacillus_C cookii	78.1623	188	1120	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_900096905.1	s__Pelagirhabdus alkalitolerans	77.8164	124	1120	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_001368815.1	s__Paraliobacillus sp001368815	77.7014	126	1120	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	77.6402	131	1120	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_900116255.1	s__Halolactibacillus miurensis	77.6201	111	1120	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Halolactibacillus	95.0	99.76	99.51	0.98	0.95	3	-
GCF_014083865.1	s__Paraliobacillus salinarum	77.5206	141	1120	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_003268595.1	s__Paraliobacillus_A zengyii	77.5199	149	1120	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_003426025.1	s__Paraliobacillus_A quinghaiensis	77.5026	167	1120	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_003176895.1	s__Gracilibacillus dipsosauri	77.3736	68	1120	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Gracilibacillus	95.0	99.23	99.13	0.93	0.92	3	-
GCF_900111195.1	s__Gracilibacillus ureilyticus	77.1845	69	1120	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Gracilibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012838505.1	s__Amphibacillus sp012838505	77.177	81	1120	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_014280935.1	s__HU2P27 sp014280935	77.0266	95	1120	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_018919165.1	s__Amphibacillus sp018919165	76.9362	108	1120	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_016908325.1	s__Aquibacillus albus	76.9306	77	1120	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Aquibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900143085.1	s__Gracilibacillus kekensis	76.8861	81	1120	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Gracilibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016908155.1	s__Oceanobacillus caeni	76.6783	58	1120	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_005870085.1	s__BH258 sp005870085	76.6768	98	1120	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_900129485.1	s__Ornithinibacillus halophilus	76.5677	72	1120	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Ornithinibacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:07:16,470] [INFO] GTDB search result was written to GCF_026805325.1_ASM2680532v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:07:16,470] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:07:16,475] [INFO] DFAST_QC result json was written to GCF_026805325.1_ASM2680532v1_genomic.fna/dqc_result.json
[2024-01-24 14:07:16,475] [INFO] DFAST_QC completed!
[2024-01-24 14:07:16,475] [INFO] Total running time: 0h1m11s