[2024-01-24 12:22:37,523] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:22:37,525] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:22:37,526] [INFO] DQC Reference Directory: /var/lib/cwl/stgf29f3e7f-f525-4a87-a25c-a24419688f95/dqc_reference
[2024-01-24 12:22:38,896] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:22:38,897] [INFO] Task started: Prodigal
[2024-01-24 12:22:38,898] [INFO] Running command: gunzip -c /var/lib/cwl/stge7fc6af1-1ab9-4ef2-8f7e-9cb49e514aae/GCF_001598255.1_ASM159825v1_genomic.fna.gz | prodigal -d GCF_001598255.1_ASM159825v1_genomic.fna/cds.fna -a GCF_001598255.1_ASM159825v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:22:55,230] [INFO] Task succeeded: Prodigal
[2024-01-24 12:22:55,231] [INFO] Task started: HMMsearch
[2024-01-24 12:22:55,231] [INFO] Running command: hmmsearch --tblout GCF_001598255.1_ASM159825v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf29f3e7f-f525-4a87-a25c-a24419688f95/dqc_reference/reference_markers.hmm GCF_001598255.1_ASM159825v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:22:55,559] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:22:55,561] [INFO] Found 6/6 markers.
[2024-01-24 12:22:55,613] [INFO] Query marker FASTA was written to GCF_001598255.1_ASM159825v1_genomic.fna/markers.fasta
[2024-01-24 12:22:55,614] [INFO] Task started: Blastn
[2024-01-24 12:22:55,614] [INFO] Running command: blastn -query GCF_001598255.1_ASM159825v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf29f3e7f-f525-4a87-a25c-a24419688f95/dqc_reference/reference_markers.fasta -out GCF_001598255.1_ASM159825v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:22:56,634] [INFO] Task succeeded: Blastn
[2024-01-24 12:22:56,639] [INFO] Selected 16 target genomes.
[2024-01-24 12:22:56,640] [INFO] Target genome list was writen to GCF_001598255.1_ASM159825v1_genomic.fna/target_genomes.txt
[2024-01-24 12:22:56,646] [INFO] Task started: fastANI
[2024-01-24 12:22:56,647] [INFO] Running command: fastANI --query /var/lib/cwl/stge7fc6af1-1ab9-4ef2-8f7e-9cb49e514aae/GCF_001598255.1_ASM159825v1_genomic.fna.gz --refList GCF_001598255.1_ASM159825v1_genomic.fna/target_genomes.txt --output GCF_001598255.1_ASM159825v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:23:16,985] [INFO] Task succeeded: fastANI
[2024-01-24 12:23:16,986] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf29f3e7f-f525-4a87-a25c-a24419688f95/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:23:16,986] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf29f3e7f-f525-4a87-a25c-a24419688f95/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:23:16,999] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:23:16,999] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:23:16,999] [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
Mitsuaria chitinivorans	strain=HWN-4	GCA_002761755.1	2917965	2917965	type	True	87.1536	1379	1913	95	below_threshold
Roseateles depolymerans	strain=DSM 11813	GCA_003387155.1	76731	76731	type	True	82.6022	1145	1913	95	below_threshold
Roseateles terrae	strain=CECT 7247	GCA_014192155.1	431060	431060	type	True	82.149	1133	1913	95	below_threshold
Pelomonas saccharophila	strain=DSM 654	GCA_004342485.1	304	304	type	True	81.1938	886	1913	95	below_threshold
Pelomonas puraquae	strain=CCUG 52769	GCA_002205845.1	431059	431059	type	True	80.4971	854	1913	95	below_threshold
Schlegelella thermodepolymerans	strain=DSM 15344	GCA_002933415.1	215580	215580	type	True	80.477	680	1913	95	below_threshold
Schlegelella thermodepolymerans	strain=DSM 15344	GCA_015476235.1	215580	215580	type	True	80.4493	685	1913	95	below_threshold
Ideonella azotifigens	strain=DSM 21438	GCA_006519715.1	513160	513160	type	True	80.2787	596	1913	95	below_threshold
Ideonella dechloratans	strain=CCUG 30977	GCA_021049305.1	36863	36863	type	True	80.1385	660	1913	95	below_threshold
Paucibacter toxinivorans	strain=DSM 16998	GCA_004362525.1	270368	270368	type	True	80.0568	804	1913	95	below_threshold
Sphaerotilus sulfidivorans	strain=D-501	GCA_013426975.1	639200	639200	type	True	79.9367	695	1913	95	below_threshold
Azohydromonas caseinilytica	strain=G-1-1-14	GCA_012927045.1	2728836	2728836	type	True	79.5704	790	1913	95	below_threshold
Azohydromonas australica	strain=DSM 1124	GCA_000430725.1	364039	364039	type	True	79.5505	806	1913	95	below_threshold
Ramlibacter humi	strain=18x22-1	GCA_004681975.1	2530451	2530451	type	True	79.1896	620	1913	95	below_threshold
Ramlibacter pinisoli	strain=MAH-25	GCA_009758015.1	2682844	2682844	type	True	78.9844	660	1913	95	below_threshold
Diaphorobacter caeni	strain=NR2-3-3-1	GCA_015354245.1	2784387	2784387	type	True	77.9921	486	1913	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:23:17,001] [INFO] DFAST Taxonomy check result was written to GCF_001598255.1_ASM159825v1_genomic.fna/tc_result.tsv
[2024-01-24 12:23:17,002] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:23:17,002] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:23:17,002] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf29f3e7f-f525-4a87-a25c-a24419688f95/dqc_reference/checkm_data
[2024-01-24 12:23:17,003] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:23:17,066] [INFO] Task started: CheckM
[2024-01-24 12:23:17,067] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001598255.1_ASM159825v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001598255.1_ASM159825v1_genomic.fna/checkm_input GCF_001598255.1_ASM159825v1_genomic.fna/checkm_result
[2024-01-24 12:24:29,111] [INFO] Task succeeded: CheckM
[2024-01-24 12:24:29,113] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:24:29,137] [INFO] ===== Completeness check finished =====
[2024-01-24 12:24:29,137] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:24:29,138] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001598255.1_ASM159825v1_genomic.fna/markers.fasta)
[2024-01-24 12:24:29,138] [INFO] Task started: Blastn
[2024-01-24 12:24:29,138] [INFO] Running command: blastn -query GCF_001598255.1_ASM159825v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf29f3e7f-f525-4a87-a25c-a24419688f95/dqc_reference/reference_markers_gtdb.fasta -out GCF_001598255.1_ASM159825v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:24:31,191] [INFO] Task succeeded: Blastn
[2024-01-24 12:24:31,196] [INFO] Selected 7 target genomes.
[2024-01-24 12:24:31,196] [INFO] Target genome list was writen to GCF_001598255.1_ASM159825v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:24:31,203] [INFO] Task started: fastANI
[2024-01-24 12:24:31,203] [INFO] Running command: fastANI --query /var/lib/cwl/stge7fc6af1-1ab9-4ef2-8f7e-9cb49e514aae/GCF_001598255.1_ASM159825v1_genomic.fna.gz --refList GCF_001598255.1_ASM159825v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001598255.1_ASM159825v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:24:43,215] [INFO] Task succeeded: fastANI
[2024-01-24 12:24:43,222] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:24:43,223] [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_001598255.1	s__Mitsuaria chitosanitabida	100.0	1911	1913	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Mitsuaria	95.0	99.05	99.05	0.96	0.96	2	conclusive
GCF_900113225.1	s__Mitsuaria sp900113225	87.4275	1441	1913	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Mitsuaria	95.0	98.36	98.28	0.95	0.95	4	-
GCF_002205645.1	s__Mitsuaria aquatilis	87.2435	1424	1913	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Mitsuaria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002761755.1	s__Mitsuaria sp002761755	87.1172	1383	1913	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Mitsuaria	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002205125.1	s__Mitsuaria noduli	86.7935	1486	1913	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Mitsuaria	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004210455.1	s__Mitsuaria sp004210455	86.6047	1379	1913	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Mitsuaria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001653795.1	s__Mitsuaria sp001653795	86.5513	1329	1913	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Mitsuaria	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:24:43,225] [INFO] GTDB search result was written to GCF_001598255.1_ASM159825v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:24:43,226] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:24:43,229] [INFO] DFAST_QC result json was written to GCF_001598255.1_ASM159825v1_genomic.fna/dqc_result.json
[2024-01-24 12:24:43,230] [INFO] DFAST_QC completed!
[2024-01-24 12:24:43,230] [INFO] Total running time: 0h2m6s