[2023-06-13 05:35:01,130] [INFO] DFAST_QC pipeline started.
[2023-06-13 05:35:01,133] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 05:35:01,133] [INFO] DQC Reference Directory: /var/lib/cwl/stg47bcc23d-8f60-47b1-b163-36002c08dfe9/dqc_reference
[2023-06-13 05:35:02,719] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 05:35:02,720] [INFO] Task started: Prodigal
[2023-06-13 05:35:02,720] [INFO] Running command: gunzip -c /var/lib/cwl/stge61709f3-eb39-4345-a0d2-0fbf76f84234/GCA_022565155.1_ASM2256515v1_genomic.fna.gz | prodigal -d GCA_022565155.1_ASM2256515v1_genomic.fna/cds.fna -a GCA_022565155.1_ASM2256515v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 05:35:09,140] [INFO] Task succeeded: Prodigal
[2023-06-13 05:35:09,141] [INFO] Task started: HMMsearch
[2023-06-13 05:35:09,141] [INFO] Running command: hmmsearch --tblout GCA_022565155.1_ASM2256515v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg47bcc23d-8f60-47b1-b163-36002c08dfe9/dqc_reference/reference_markers.hmm GCA_022565155.1_ASM2256515v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 05:35:09,340] [INFO] Task succeeded: HMMsearch
[2023-06-13 05:35:09,341] [INFO] Found 6/6 markers.
[2023-06-13 05:35:09,366] [INFO] Query marker FASTA was written to GCA_022565155.1_ASM2256515v1_genomic.fna/markers.fasta
[2023-06-13 05:35:09,367] [INFO] Task started: Blastn
[2023-06-13 05:35:09,367] [INFO] Running command: blastn -query GCA_022565155.1_ASM2256515v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg47bcc23d-8f60-47b1-b163-36002c08dfe9/dqc_reference/reference_markers.fasta -out GCA_022565155.1_ASM2256515v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 05:35:09,968] [INFO] Task succeeded: Blastn
[2023-06-13 05:35:09,972] [INFO] Selected 22 target genomes.
[2023-06-13 05:35:09,972] [INFO] Target genome list was writen to GCA_022565155.1_ASM2256515v1_genomic.fna/target_genomes.txt
[2023-06-13 05:35:09,983] [INFO] Task started: fastANI
[2023-06-13 05:35:09,984] [INFO] Running command: fastANI --query /var/lib/cwl/stge61709f3-eb39-4345-a0d2-0fbf76f84234/GCA_022565155.1_ASM2256515v1_genomic.fna.gz --refList GCA_022565155.1_ASM2256515v1_genomic.fna/target_genomes.txt --output GCA_022565155.1_ASM2256515v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 05:35:28,221] [INFO] Task succeeded: fastANI
[2023-06-13 05:35:28,222] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg47bcc23d-8f60-47b1-b163-36002c08dfe9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 05:35:28,222] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg47bcc23d-8f60-47b1-b163-36002c08dfe9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 05:35:28,232] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 05:35:28,232] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 05:35:28,232] [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	75.5818	73	836	95	below_threshold
Conexibacter arvalis	strain=DSM 23288	GCA_014199525.1	912552	912552	type	True	75.1512	84	836	95	below_threshold
Dactylosporangium matsuzakiense	strain=NRRL B-16293	GCA_025264725.1	53360	53360	type	True	74.8867	75	836	95	below_threshold
Dactylosporangium vinaceum	strain=NRRL B-16297	GCA_019904175.1	53362	53362	type	True	74.8398	79	836	95	below_threshold
Amycolatopsis umgeniensis	strain=DSM 45272	GCA_014205155.1	336628	336628	type	True	74.7567	50	836	95	below_threshold
Amycolatopsis regifaucium	strain=DSM 45072	GCA_900113515.1	546365	546365	type	True	74.6663	51	836	95	below_threshold
Dactylosporangium siamense	strain=NBRC 106093	GCA_016862795.1	685454	685454	type	True	74.6614	100	836	95	below_threshold
Amycolatopsis regifaucium	strain=GY080	GCA_001558125.2	546365	546365	type	True	74.6602	53	836	95	below_threshold
Amycolatopsis regifaucium	strain=GY080	GCA_001613935.1	546365	546365	type	True	74.6602	53	836	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 05:35:28,234] [INFO] DFAST Taxonomy check result was written to GCA_022565155.1_ASM2256515v1_genomic.fna/tc_result.tsv
[2023-06-13 05:35:28,235] [INFO] ===== Taxonomy check completed =====
[2023-06-13 05:35:28,235] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 05:35:28,235] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg47bcc23d-8f60-47b1-b163-36002c08dfe9/dqc_reference/checkm_data
[2023-06-13 05:35:28,237] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 05:35:28,271] [INFO] Task started: CheckM
[2023-06-13 05:35:28,271] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022565155.1_ASM2256515v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022565155.1_ASM2256515v1_genomic.fna/checkm_input GCA_022565155.1_ASM2256515v1_genomic.fna/checkm_result
[2023-06-13 05:35:53,216] [INFO] Task succeeded: CheckM
[2023-06-13 05:35:53,217] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.62%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 05:35:53,232] [INFO] ===== Completeness check finished =====
[2023-06-13 05:35:53,233] [INFO] ===== Start GTDB Search =====
[2023-06-13 05:35:53,233] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022565155.1_ASM2256515v1_genomic.fna/markers.fasta)
[2023-06-13 05:35:53,233] [INFO] Task started: Blastn
[2023-06-13 05:35:53,233] [INFO] Running command: blastn -query GCA_022565155.1_ASM2256515v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg47bcc23d-8f60-47b1-b163-36002c08dfe9/dqc_reference/reference_markers_gtdb.fasta -out GCA_022565155.1_ASM2256515v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 05:35:54,120] [INFO] Task succeeded: Blastn
[2023-06-13 05:35:54,124] [INFO] Selected 24 target genomes.
[2023-06-13 05:35:54,124] [INFO] Target genome list was writen to GCA_022565155.1_ASM2256515v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 05:35:54,168] [INFO] Task started: fastANI
[2023-06-13 05:35:54,168] [INFO] Running command: fastANI --query /var/lib/cwl/stge61709f3-eb39-4345-a0d2-0fbf76f84234/GCA_022565155.1_ASM2256515v1_genomic.fna.gz --refList GCA_022565155.1_ASM2256515v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022565155.1_ASM2256515v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 05:36:04,641] [INFO] Task succeeded: fastANI
[2023-06-13 05:36:04,650] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-13 05:36:04,651] [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_001796995.1	s__RBG-16-68-14 sp001796995	78.6865	284	836	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__DSTF01;f__RBG-16-68-14;g__RBG-16-68-14	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003228685.1	s__SZUA-185 sp003228685	78.209	306	836	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__DSTF01;f__RBG-16-68-14;g__SZUA-185	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009840945.1	s__VXMT01 sp009840945	76.2746	77	836	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA2979;f__UBA2979;g__VXMT01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009841435.1	s__UBA2991 sp009841435	76.1998	70	836	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__Tepidiformales;f__Tepidiformaceae;g__UBA2991	95.0	97.17	95.58	0.93	0.85	4	-
GCA_016178045.1	s__JACOUE01 sp016178045	76.1529	95	836	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__SM23-28-2;f__RBG-16-64-32;g__JACOUE01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011330885.1	s__WHTK01 sp011330885	76.0206	66	836	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__DSTF01;f__WHTK01;g__WHTK01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009839925.1	s__VXMT01 sp009839925	75.9111	96	836	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA2979;f__UBA2979;g__VXMT01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009837285.1	s__VXMT01 sp009837285	75.7674	76	836	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA2979;f__UBA2979;g__VXMT01	95.0	95.62	95.50	0.87	0.82	3	-
GCA_016191435.1	s__JACPOQ01 sp016191435	75.3827	64	836	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__Tepidiformales;f__Tepidiformaceae;g__JACPOQ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902806345.1	s__CADCWF01 sp902806345	75.1652	62	836	d__Bacteria;p__Chloroflexota;c__Chloroflexia;o__Thermomicrobiales;f__UBA6265;g__CADCWF01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 05:36:04,653] [INFO] GTDB search result was written to GCA_022565155.1_ASM2256515v1_genomic.fna/result_gtdb.tsv
[2023-06-13 05:36:04,653] [INFO] ===== GTDB Search completed =====
[2023-06-13 05:36:04,656] [INFO] DFAST_QC result json was written to GCA_022565155.1_ASM2256515v1_genomic.fna/dqc_result.json
[2023-06-13 05:36:04,656] [INFO] DFAST_QC completed!
[2023-06-13 05:36:04,656] [INFO] Total running time: 0h1m4s