[2024-01-25 19:38:05,868] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:38:05,874] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:38:05,874] [INFO] DQC Reference Directory: /var/lib/cwl/stg3fd5cce1-4b01-4336-895c-a79d3190cd59/dqc_reference
[2024-01-25 19:38:07,009] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:38:07,010] [INFO] Task started: Prodigal
[2024-01-25 19:38:07,010] [INFO] Running command: gunzip -c /var/lib/cwl/stge1735815-7065-4ac2-8af8-f3afb0cbe50d/GCF_003149085.1_ASM314908v1_genomic.fna.gz | prodigal -d GCF_003149085.1_ASM314908v1_genomic.fna/cds.fna -a GCF_003149085.1_ASM314908v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:38:29,004] [INFO] Task succeeded: Prodigal
[2024-01-25 19:38:29,005] [INFO] Task started: HMMsearch
[2024-01-25 19:38:29,005] [INFO] Running command: hmmsearch --tblout GCF_003149085.1_ASM314908v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3fd5cce1-4b01-4336-895c-a79d3190cd59/dqc_reference/reference_markers.hmm GCF_003149085.1_ASM314908v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:38:29,269] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:38:29,270] [INFO] Found 6/6 markers.
[2024-01-25 19:38:29,313] [INFO] Query marker FASTA was written to GCF_003149085.1_ASM314908v1_genomic.fna/markers.fasta
[2024-01-25 19:38:29,314] [INFO] Task started: Blastn
[2024-01-25 19:38:29,314] [INFO] Running command: blastn -query GCF_003149085.1_ASM314908v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3fd5cce1-4b01-4336-895c-a79d3190cd59/dqc_reference/reference_markers.fasta -out GCF_003149085.1_ASM314908v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:38:29,853] [INFO] Task succeeded: Blastn
[2024-01-25 19:38:29,856] [INFO] Selected 17 target genomes.
[2024-01-25 19:38:29,856] [INFO] Target genome list was writen to GCF_003149085.1_ASM314908v1_genomic.fna/target_genomes.txt
[2024-01-25 19:38:29,866] [INFO] Task started: fastANI
[2024-01-25 19:38:29,866] [INFO] Running command: fastANI --query /var/lib/cwl/stge1735815-7065-4ac2-8af8-f3afb0cbe50d/GCF_003149085.1_ASM314908v1_genomic.fna.gz --refList GCF_003149085.1_ASM314908v1_genomic.fna/target_genomes.txt --output GCF_003149085.1_ASM314908v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:38:48,067] [INFO] Task succeeded: fastANI
[2024-01-25 19:38:48,067] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3fd5cce1-4b01-4336-895c-a79d3190cd59/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:38:48,068] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3fd5cce1-4b01-4336-895c-a79d3190cd59/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:38:48,077] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:38:48,077] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:38:48,077] [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
Dyadobacter jejuensis	strain=DSM 100346	GCA_003149085.1	1082580	1082580	type	True	100.0	1884	1885	95	conclusive
Dyadobacter tibetensis	strain=Y620-1	GCA_000566685.1	1211851	1211851	type	True	79.3459	448	1885	95	below_threshold
Dyadobacter luteus	strain=RS19	GCA_003383615.1	2259619	2259619	type	True	77.6047	129	1885	95	below_threshold
Dyadobacter alkalitolerans	strain=DSM 23607	GCA_000428845.1	492736	492736	type	True	77.387	109	1885	95	below_threshold
Dyadobacter subterraneus	strain=UP-52	GCA_015221875.1	2773304	2773304	type	True	77.3435	119	1885	95	below_threshold
Dyadobacter sediminis	strain=CGMCC 1.12895	GCA_014640015.1	1493691	1493691	type	True	77.2281	110	1885	95	below_threshold
Dyadobacter flavalbus	strain=NS28	GCA_006149045.1	2579942	2579942	type	True	77.195	113	1885	95	below_threshold
Dyadobacter sediminis	strain=Z12	GCA_005860765.1	1493691	1493691	type	True	77.1797	112	1885	95	below_threshold
Dyadobacter bucti	strain=QTA69	GCA_005869225.1	2572203	2572203	type	True	77.0695	137	1885	95	below_threshold
Dyadobacter psychrotolerans	strain=AR-3-6	GCA_004349265.1	2541721	2541721	type	True	77.0334	145	1885	95	below_threshold
Dyadobacter beijingensis	strain=CGMCC 1.6375	GCA_014645155.1	365489	365489	type	True	76.9305	141	1885	95	below_threshold
Dyadobacter beijingensis	strain=DSM 21582	GCA_000382205.1	365489	365489	type	True	76.9114	141	1885	95	below_threshold
Dyadobacter fermentans	strain=DSM 18053	GCA_000023125.1	94254	94254	type	True	76.8121	137	1885	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:38:48,079] [INFO] DFAST Taxonomy check result was written to GCF_003149085.1_ASM314908v1_genomic.fna/tc_result.tsv
[2024-01-25 19:38:48,079] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:38:48,079] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:38:48,079] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3fd5cce1-4b01-4336-895c-a79d3190cd59/dqc_reference/checkm_data
[2024-01-25 19:38:48,080] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:38:48,137] [INFO] Task started: CheckM
[2024-01-25 19:38:48,138] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003149085.1_ASM314908v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003149085.1_ASM314908v1_genomic.fna/checkm_input GCF_003149085.1_ASM314908v1_genomic.fna/checkm_result
[2024-01-25 19:39:47,579] [INFO] Task succeeded: CheckM
[2024-01-25 19:39:47,581] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:39:47,599] [INFO] ===== Completeness check finished =====
[2024-01-25 19:39:47,599] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:39:47,599] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003149085.1_ASM314908v1_genomic.fna/markers.fasta)
[2024-01-25 19:39:47,599] [INFO] Task started: Blastn
[2024-01-25 19:39:47,600] [INFO] Running command: blastn -query GCF_003149085.1_ASM314908v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3fd5cce1-4b01-4336-895c-a79d3190cd59/dqc_reference/reference_markers_gtdb.fasta -out GCF_003149085.1_ASM314908v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:39:48,311] [INFO] Task succeeded: Blastn
[2024-01-25 19:39:48,314] [INFO] Selected 22 target genomes.
[2024-01-25 19:39:48,314] [INFO] Target genome list was writen to GCF_003149085.1_ASM314908v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:39:48,354] [INFO] Task started: fastANI
[2024-01-25 19:39:48,355] [INFO] Running command: fastANI --query /var/lib/cwl/stge1735815-7065-4ac2-8af8-f3afb0cbe50d/GCF_003149085.1_ASM314908v1_genomic.fna.gz --refList GCF_003149085.1_ASM314908v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003149085.1_ASM314908v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:40:14,733] [INFO] Task succeeded: fastANI
[2024-01-25 19:40:14,744] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:40:14,745] [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_003149085.1	s__Dyadobacter jejuensis	100.0	1884	1885	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Dyadobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000566685.1	s__Dyadobacter tibetensis	79.3438	447	1885	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Dyadobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003383615.1	s__Dyadobacter luteus	77.6047	129	1885	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Dyadobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008369915.1	s__Dyadobacter sp008369915	77.4329	113	1885	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Dyadobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000428845.1	s__Dyadobacter alkalitolerans	77.4129	108	1885	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Dyadobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015221875.1	s__Dyadobacter sp015221875	77.3435	119	1885	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Dyadobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001424405.1	s__Dyadobacter sp001424405	77.2212	109	1885	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Dyadobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006149045.1	s__Dyadobacter flavalbus	77.195	113	1885	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Dyadobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005860765.1	s__Dyadobacter sediminis	77.1797	112	1885	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Dyadobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_005869225.1	s__Dyadobacter bucti	77.0695	137	1885	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Dyadobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004349265.1	s__Dyadobacter psychrotolerans	77.0334	145	1885	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Dyadobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017744695.1	s__Dyadobacter sp017744695	76.9914	132	1885	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Dyadobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000382205.1	s__Dyadobacter beijingensis	76.9114	141	1885	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Dyadobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000023125.1	s__Dyadobacter fermentans	76.8121	137	1885	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Dyadobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:40:14,748] [INFO] GTDB search result was written to GCF_003149085.1_ASM314908v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:40:14,748] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:40:14,752] [INFO] DFAST_QC result json was written to GCF_003149085.1_ASM314908v1_genomic.fna/dqc_result.json
[2024-01-25 19:40:14,752] [INFO] DFAST_QC completed!
[2024-01-25 19:40:14,752] [INFO] Total running time: 0h2m9s