[2024-01-24 13:56:27,490] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:56:27,492] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:56:27,492] [INFO] DQC Reference Directory: /var/lib/cwl/stgb146a6ba-9ea5-473e-a451-8ff3e8e8a0c9/dqc_reference
[2024-01-24 13:56:28,766] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:56:28,767] [INFO] Task started: Prodigal
[2024-01-24 13:56:28,767] [INFO] Running command: gunzip -c /var/lib/cwl/stg53b63f12-d624-4df5-82a0-eef96b7eabc9/GCF_008838325.1_ASM883832v1_genomic.fna.gz | prodigal -d GCF_008838325.1_ASM883832v1_genomic.fna/cds.fna -a GCF_008838325.1_ASM883832v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:56:36,191] [INFO] Task succeeded: Prodigal
[2024-01-24 13:56:36,192] [INFO] Task started: HMMsearch
[2024-01-24 13:56:36,192] [INFO] Running command: hmmsearch --tblout GCF_008838325.1_ASM883832v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb146a6ba-9ea5-473e-a451-8ff3e8e8a0c9/dqc_reference/reference_markers.hmm GCF_008838325.1_ASM883832v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:56:36,400] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:56:36,401] [INFO] Found 6/6 markers.
[2024-01-24 13:56:36,425] [INFO] Query marker FASTA was written to GCF_008838325.1_ASM883832v1_genomic.fna/markers.fasta
[2024-01-24 13:56:36,426] [INFO] Task started: Blastn
[2024-01-24 13:56:36,426] [INFO] Running command: blastn -query GCF_008838325.1_ASM883832v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb146a6ba-9ea5-473e-a451-8ff3e8e8a0c9/dqc_reference/reference_markers.fasta -out GCF_008838325.1_ASM883832v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:56:37,075] [INFO] Task succeeded: Blastn
[2024-01-24 13:56:37,079] [INFO] Selected 20 target genomes.
[2024-01-24 13:56:37,080] [INFO] Target genome list was writen to GCF_008838325.1_ASM883832v1_genomic.fna/target_genomes.txt
[2024-01-24 13:56:37,116] [INFO] Task started: fastANI
[2024-01-24 13:56:37,117] [INFO] Running command: fastANI --query /var/lib/cwl/stg53b63f12-d624-4df5-82a0-eef96b7eabc9/GCF_008838325.1_ASM883832v1_genomic.fna.gz --refList GCF_008838325.1_ASM883832v1_genomic.fna/target_genomes.txt --output GCF_008838325.1_ASM883832v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:56:49,307] [INFO] Task succeeded: fastANI
[2024-01-24 13:56:49,307] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb146a6ba-9ea5-473e-a451-8ff3e8e8a0c9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:56:49,308] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb146a6ba-9ea5-473e-a451-8ff3e8e8a0c9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:56:49,321] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:56:49,322] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:56:49,322] [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
Tepidiforma bonchosmolovskayae	strain=3753O	GCA_008838325.1	2601677	2601677	type	True	100.0	915	915	95	conclusive
Vulcaniibacterium gelatinicum	strain=R-5-52-3	GCA_008033445.1	2598725	2598725	type	True	75.0604	62	915	95	below_threshold
Brachybacterium squillarum	strain=M-6-3	GCA_000225825.2	661979	661979	type	True	75.0546	75	915	95	below_threshold
Euzebya pacifica	strain=DY32-46	GCA_003344865.1	1608957	1608957	type	True	74.9304	80	915	95	below_threshold
Arenimonas metalli	strain=CF5-1	GCA_000747155.1	948077	948077	type	True	74.8849	64	915	95	below_threshold
Paroceanicella profunda	strain=D4M1	GCA_005887635.2	2579971	2579971	type	True	74.8319	83	915	95	below_threshold
Actinomadura roseirufa		GCA_900659635.1	2094049	2094049	type	True	74.8149	126	915	95	below_threshold
Actinomadura macrotermitis	strain=RB68	GCA_009604375.1	2585200	2585200	type	True	74.7185	175	915	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:56:49,323] [INFO] DFAST Taxonomy check result was written to GCF_008838325.1_ASM883832v1_genomic.fna/tc_result.tsv
[2024-01-24 13:56:49,324] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:56:49,324] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:56:49,324] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb146a6ba-9ea5-473e-a451-8ff3e8e8a0c9/dqc_reference/checkm_data
[2024-01-24 13:56:49,325] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:56:49,357] [INFO] Task started: CheckM
[2024-01-24 13:56:49,357] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008838325.1_ASM883832v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008838325.1_ASM883832v1_genomic.fna/checkm_input GCF_008838325.1_ASM883832v1_genomic.fna/checkm_result
[2024-01-24 13:57:15,827] [INFO] Task succeeded: CheckM
[2024-01-24 13:57:15,828] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:57:15,866] [INFO] ===== Completeness check finished =====
[2024-01-24 13:57:15,866] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:57:15,866] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008838325.1_ASM883832v1_genomic.fna/markers.fasta)
[2024-01-24 13:57:15,867] [INFO] Task started: Blastn
[2024-01-24 13:57:15,867] [INFO] Running command: blastn -query GCF_008838325.1_ASM883832v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb146a6ba-9ea5-473e-a451-8ff3e8e8a0c9/dqc_reference/reference_markers_gtdb.fasta -out GCF_008838325.1_ASM883832v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:57:16,952] [INFO] Task succeeded: Blastn
[2024-01-24 13:57:16,957] [INFO] Selected 14 target genomes.
[2024-01-24 13:57:16,957] [INFO] Target genome list was writen to GCF_008838325.1_ASM883832v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:57:16,989] [INFO] Task started: fastANI
[2024-01-24 13:57:16,989] [INFO] Running command: fastANI --query /var/lib/cwl/stg53b63f12-d624-4df5-82a0-eef96b7eabc9/GCF_008838325.1_ASM883832v1_genomic.fna.gz --refList GCF_008838325.1_ASM883832v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008838325.1_ASM883832v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:57:26,392] [INFO] Task succeeded: fastANI
[2024-01-24 13:57:26,406] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:57:26,406] [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_008838325.1	s__Tepidiforma bonchosmolovskayae	100.0	915	915	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__Tepidiformales;f__Tepidiformaceae;g__Tepidiforma	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002563855.1	s__Tepidiforma sp002563855	91.9369	857	915	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__Tepidiformales;f__Tepidiformaceae;g__Tepidiforma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003104995.1	s__FeB-14 sp003104995	78.425	365	915	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__Tepidiformales;f__Tepidiformaceae;g__FeB-14	95.0	99.84	99.84	0.86	0.86	2	-
GCA_016234445.1	s__JACRBT01 sp016234445	78.0169	321	915	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__Tepidiformales;f__Tepidiformaceae;g__JACRBT01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016703545.1	s__JACPOQ01 sp016703545	77.8398	288	915	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__Tepidiformales;f__Tepidiformaceae;g__JACPOQ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015075555.1	s__UCB2 sp015075555	77.7658	209	915	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__Tepidiformales;f__Tepidiformaceae;g__UCB2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016719395.1	s__FeB-14 sp016719395	77.73	269	915	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__Tepidiformales;f__Tepidiformaceae;g__FeB-14	95.0	98.39	98.17	0.95	0.93	9	-
GCA_003577245.1	s__UCB2 sp003577245	77.7148	145	915	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__Tepidiformales;f__Tepidiformaceae;g__UCB2	95.0	99.02	98.75	0.69	0.69	3	-
GCA_011055725.1	s__FeB-14 sp011055725	77.6626	258	915	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__Tepidiformales;f__Tepidiformaceae;g__FeB-14	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009838385.1	s__UBA2991 sp009838385	77.5995	114	915	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__Tepidiformales;f__Tepidiformaceae;g__UBA2991	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011048275.1	s__HRBIN29 sp011048275	77.1819	225	915	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__Tepidiformales;f__Tepidiformaceae;g__HRBIN29	95.0	99.99	99.99	0.99	0.99	3	-
GCA_013822275.1	s__PNKC01 sp013822275	77.1311	195	915	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__Tepidiformales;f__Tepidiformaceae;g__PNKC01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009840965.1	s__VXMT01 sp009840965	75.6545	80	915	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA2979;f__UBA2979;g__VXMT01	95.0	96.91	96.91	0.81	0.81	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:57:26,408] [INFO] GTDB search result was written to GCF_008838325.1_ASM883832v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:57:26,409] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:57:26,412] [INFO] DFAST_QC result json was written to GCF_008838325.1_ASM883832v1_genomic.fna/dqc_result.json
[2024-01-24 13:57:26,412] [INFO] DFAST_QC completed!
[2024-01-24 13:57:26,412] [INFO] Total running time: 0h0m59s