[2023-06-12 22:40:45,895] [INFO] DFAST_QC pipeline started.
[2023-06-12 22:40:45,912] [INFO] DFAST_QC version: 0.5.7
[2023-06-12 22:40:45,912] [INFO] DQC Reference Directory: /var/lib/cwl/stg90f53839-66ac-4c16-92c9-c2e4dab589fb/dqc_reference
[2023-06-12 22:40:49,311] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-12 22:40:49,313] [INFO] Task started: Prodigal
[2023-06-12 22:40:49,313] [INFO] Running command: gunzip -c /var/lib/cwl/stge06a8f21-4aaf-4325-aa82-60ab94ab9672/GCA_022776825.1_ASM2277682v1_genomic.fna.gz | prodigal -d GCA_022776825.1_ASM2277682v1_genomic.fna/cds.fna -a GCA_022776825.1_ASM2277682v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-12 22:40:54,836] [INFO] Task succeeded: Prodigal
[2023-06-12 22:40:54,836] [INFO] Task started: HMMsearch
[2023-06-12 22:40:54,837] [INFO] Running command: hmmsearch --tblout GCA_022776825.1_ASM2277682v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg90f53839-66ac-4c16-92c9-c2e4dab589fb/dqc_reference/reference_markers.hmm GCA_022776825.1_ASM2277682v1_genomic.fna/protein.faa > /dev/null
[2023-06-12 22:40:55,087] [INFO] Task succeeded: HMMsearch
[2023-06-12 22:40:55,089] [INFO] Found 6/6 markers.
[2023-06-12 22:40:55,117] [INFO] Query marker FASTA was written to GCA_022776825.1_ASM2277682v1_genomic.fna/markers.fasta
[2023-06-12 22:40:55,117] [INFO] Task started: Blastn
[2023-06-12 22:40:55,117] [INFO] Running command: blastn -query GCA_022776825.1_ASM2277682v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg90f53839-66ac-4c16-92c9-c2e4dab589fb/dqc_reference/reference_markers.fasta -out GCA_022776825.1_ASM2277682v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-12 22:40:57,876] [INFO] Task succeeded: Blastn
[2023-06-12 22:40:57,880] [INFO] Selected 31 target genomes.
[2023-06-12 22:40:57,881] [INFO] Target genome list was writen to GCA_022776825.1_ASM2277682v1_genomic.fna/target_genomes.txt
[2023-06-12 22:40:57,955] [INFO] Task started: fastANI
[2023-06-12 22:40:57,956] [INFO] Running command: fastANI --query /var/lib/cwl/stge06a8f21-4aaf-4325-aa82-60ab94ab9672/GCA_022776825.1_ASM2277682v1_genomic.fna.gz --refList GCA_022776825.1_ASM2277682v1_genomic.fna/target_genomes.txt --output GCA_022776825.1_ASM2277682v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-12 22:41:16,385] [INFO] Task succeeded: fastANI
[2023-06-12 22:41:16,385] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg90f53839-66ac-4c16-92c9-c2e4dab589fb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-12 22:41:16,386] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg90f53839-66ac-4c16-92c9-c2e4dab589fb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-12 22:41:16,398] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2023-06-12 22:41:16,398] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-12 22:41:16,398] [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
Anaerotruncus massiliensis	strain=AT3	GCA_900199635.1	1673720	1673720	type	True	76.1934	88	722	95	below_threshold
Agromyces mediolanus	strain=JCM 3346	GCA_014648575.1	41986	41986	type	True	75.0687	51	722	95	below_threshold
Methylosinus trichosporium	strain=OB3b	GCA_002752655.1	426	426	type	True	74.8704	55	722	95	below_threshold
Conexibacter arvalis	strain=DSM 23288	GCA_014199525.1	912552	912552	type	True	74.8437	83	722	95	below_threshold
Streptomyces parmotrematis	strain=Ptm05	GCA_019890615.1	2873249	2873249	type	True	74.8383	63	722	95	below_threshold
Methylosinus trichosporium	strain=OB3b	GCA_000178815.2	426	426	type	True	74.829	54	722	95	below_threshold
Actinomadura rudentiformis	strain=HMC1	GCA_008923185.1	359158	359158	type	True	74.7765	58	722	95	below_threshold
Streptomyces carpinensis	strain=NRRL B-16921	GCA_002154505.1	66369	66369	type	True	74.7277	58	722	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-12 22:41:16,406] [INFO] DFAST Taxonomy check result was written to GCA_022776825.1_ASM2277682v1_genomic.fna/tc_result.tsv
[2023-06-12 22:41:16,408] [INFO] ===== Taxonomy check completed =====
[2023-06-12 22:41:16,408] [INFO] ===== Start completeness check using CheckM =====
[2023-06-12 22:41:16,409] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg90f53839-66ac-4c16-92c9-c2e4dab589fb/dqc_reference/checkm_data
[2023-06-12 22:41:16,410] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-12 22:41:16,442] [INFO] Task started: CheckM
[2023-06-12 22:41:16,442] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022776825.1_ASM2277682v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022776825.1_ASM2277682v1_genomic.fna/checkm_input GCA_022776825.1_ASM2277682v1_genomic.fna/checkm_result
[2023-06-12 22:41:39,569] [INFO] Task succeeded: CheckM
[2023-06-12 22:41:39,571] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 2.08%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-12 22:41:39,594] [INFO] ===== Completeness check finished =====
[2023-06-12 22:41:39,594] [INFO] ===== Start GTDB Search =====
[2023-06-12 22:41:39,595] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022776825.1_ASM2277682v1_genomic.fna/markers.fasta)
[2023-06-12 22:41:39,595] [INFO] Task started: Blastn
[2023-06-12 22:41:39,595] [INFO] Running command: blastn -query GCA_022776825.1_ASM2277682v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg90f53839-66ac-4c16-92c9-c2e4dab589fb/dqc_reference/reference_markers_gtdb.fasta -out GCA_022776825.1_ASM2277682v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-12 22:41:40,861] [INFO] Task succeeded: Blastn
[2023-06-12 22:41:40,870] [INFO] Selected 25 target genomes.
[2023-06-12 22:41:40,870] [INFO] Target genome list was writen to GCA_022776825.1_ASM2277682v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-12 22:41:40,883] [INFO] Task started: fastANI
[2023-06-12 22:41:40,883] [INFO] Running command: fastANI --query /var/lib/cwl/stge06a8f21-4aaf-4325-aa82-60ab94ab9672/GCA_022776825.1_ASM2277682v1_genomic.fna.gz --refList GCA_022776825.1_ASM2277682v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022776825.1_ASM2277682v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-12 22:41:49,856] [INFO] Task succeeded: fastANI
[2023-06-12 22:41:49,882] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-12 22:41:49,883] [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
GCA_016297585.1	s__JAAZKA01 sp016297585	98.7882	579	722	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Butyricicoccaceae;g__JAAZKA01	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_012800055.1	s__JAAZKA01 sp012800055	78.4474	213	722	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Butyricicoccaceae;g__JAAZKA01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900546415.1	s__Faecousia sp900546415	77.2686	59	722	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	98.49	97.72	0.83	0.81	4	-
GCA_000432375.1	s__CAG-103 sp000432375	76.9659	60	722	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-103	95.0	98.15	97.87	0.87	0.82	10	-
GCA_900319935.1	s__Limivicinus sp900319935	76.8363	71	722	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	99.02	98.62	0.86	0.80	6	-
GCA_017991935.1	s__UMGS1668 sp017991935	76.6636	52	722	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__UMGS1668	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900546615.1	s__Scatomorpha pullistercoris	76.6135	52	722	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Scatomorpha	95.0	99.45	98.95	0.93	0.93	3	-
GCA_015067675.1	s__SIG502 sp015067675	76.5871	140	722	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Butyricicoccaceae;g__SIG502	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902795195.1	s__Faecousia sp902795195	76.5486	55	722	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900552375.1	s__ER4 sp900552375	76.4865	65	722	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__ER4	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900199635.1	s__Anaerotruncus massiliensis	76.1934	88	722	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Anaerotruncus	95.0	98.56	98.01	0.95	0.93	6	-
GCA_017447645.1	s__Limivicinus sp017447645	76.1125	58	722	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017541825.1	s__UBA738 sp017541825	76.0508	51	722	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__UBA738	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017463865.1	s__SIG693 sp017463865	75.9814	59	722	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-272;g__SIG693	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017430985.1	s__Limivicinus sp017430985	75.9726	54	722	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002404605.1	s__UBA738 sp002404605	75.9357	52	722	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__UBA738	95.0	99.68	99.62	0.91	0.89	3	-
GCA_019114345.1	s__Agathobaculum pullistercoris	75.6818	50	722	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Butyricicoccaceae;g__Agathobaculum	95.0	98.72	98.13	0.86	0.78	4	-
--------------------------------------------------------------------------------
[2023-06-12 22:41:49,885] [INFO] GTDB search result was written to GCA_022776825.1_ASM2277682v1_genomic.fna/result_gtdb.tsv
[2023-06-12 22:41:49,885] [INFO] ===== GTDB Search completed =====
[2023-06-12 22:41:49,889] [INFO] DFAST_QC result json was written to GCA_022776825.1_ASM2277682v1_genomic.fna/dqc_result.json
[2023-06-12 22:41:49,889] [INFO] DFAST_QC completed!
[2023-06-12 22:41:49,889] [INFO] Total running time: 0h1m4s