[2024-01-24 13:55:48,297] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:55:48,299] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:55:48,300] [INFO] DQC Reference Directory: /var/lib/cwl/stg59741690-654b-4078-986e-fb600fb48b89/dqc_reference
[2024-01-24 13:55:49,655] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:55:49,657] [INFO] Task started: Prodigal
[2024-01-24 13:55:49,657] [INFO] Running command: gunzip -c /var/lib/cwl/stg7b7bbd5f-0132-4957-846e-ff7521e336d6/GCF_012927265.1_ASM1292726v1_genomic.fna.gz | prodigal -d GCF_012927265.1_ASM1292726v1_genomic.fna/cds.fna -a GCF_012927265.1_ASM1292726v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:56:05,879] [INFO] Task succeeded: Prodigal
[2024-01-24 13:56:05,879] [INFO] Task started: HMMsearch
[2024-01-24 13:56:05,879] [INFO] Running command: hmmsearch --tblout GCF_012927265.1_ASM1292726v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg59741690-654b-4078-986e-fb600fb48b89/dqc_reference/reference_markers.hmm GCF_012927265.1_ASM1292726v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:56:06,157] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:56:06,159] [INFO] Found 6/6 markers.
[2024-01-24 13:56:06,208] [INFO] Query marker FASTA was written to GCF_012927265.1_ASM1292726v1_genomic.fna/markers.fasta
[2024-01-24 13:56:06,208] [INFO] Task started: Blastn
[2024-01-24 13:56:06,208] [INFO] Running command: blastn -query GCF_012927265.1_ASM1292726v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg59741690-654b-4078-986e-fb600fb48b89/dqc_reference/reference_markers.fasta -out GCF_012927265.1_ASM1292726v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:56:06,857] [INFO] Task succeeded: Blastn
[2024-01-24 13:56:06,860] [INFO] Selected 11 target genomes.
[2024-01-24 13:56:06,861] [INFO] Target genome list was writen to GCF_012927265.1_ASM1292726v1_genomic.fna/target_genomes.txt
[2024-01-24 13:56:06,877] [INFO] Task started: fastANI
[2024-01-24 13:56:06,877] [INFO] Running command: fastANI --query /var/lib/cwl/stg7b7bbd5f-0132-4957-846e-ff7521e336d6/GCF_012927265.1_ASM1292726v1_genomic.fna.gz --refList GCF_012927265.1_ASM1292726v1_genomic.fna/target_genomes.txt --output GCF_012927265.1_ASM1292726v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:56:17,454] [INFO] Task succeeded: fastANI
[2024-01-24 13:56:17,455] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg59741690-654b-4078-986e-fb600fb48b89/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:56:17,456] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg59741690-654b-4078-986e-fb600fb48b89/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:56:17,470] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:56:17,471] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:56:17,471] [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
Chryseobacterium cheonjiense	strain=RJ-7-14	GCA_012927265.1	2728845	2728845	type	True	100.0	1421	1421	95	conclusive
Chryseobacterium hispalense	strain=DSM 25574	GCA_000708615.2	1453492	1453492	type	True	86.0633	1121	1421	95	below_threshold
Chryseobacterium takakiae	strain=DSM 26898	GCA_900129385.1	1302685	1302685	type	True	85.8368	1083	1421	95	below_threshold
Chryseobacterium taichungense	strain=DSM 17453	GCA_900109935.1	295069	295069	type	True	83.1802	946	1421	95	below_threshold
Chryseobacterium taeanense	strain=DSM 17071	GCA_900099685.1	311334	311334	type	True	82.6183	894	1421	95	below_threshold
Chryseobacterium ginsenosidimutans	strain=THG 15	GCA_024807225.1	687846	687846	type	True	80.8235	843	1421	95	below_threshold
Chryseobacterium gwangjuense	strain=THG-A18	GCA_021311115.1	1069980	1069980	type	True	80.5642	650	1421	95	below_threshold
Chryseobacterium tagetis	strain=RG1	GCA_016735585.2	2801334	2801334	type	True	80.3297	742	1421	95	below_threshold
Chryseobacterium carnipullorum	strain=DSM 25581	GCA_900142785.1	1124835	1124835	type	True	79.7186	598	1421	95	below_threshold
Chryseobacterium schmidteae	strain=Marseille-P9602	GCA_903166575.1	2730404	2730404	type	True	79.2497	574	1421	95	below_threshold
Chryseobacterium fistulae	strain=CECT 9393	GCA_902729325.1	2675058	2675058	type	True	78.759	447	1421	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:56:17,473] [INFO] DFAST Taxonomy check result was written to GCF_012927265.1_ASM1292726v1_genomic.fna/tc_result.tsv
[2024-01-24 13:56:17,473] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:56:17,473] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:56:17,474] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg59741690-654b-4078-986e-fb600fb48b89/dqc_reference/checkm_data
[2024-01-24 13:56:17,475] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:56:17,519] [INFO] Task started: CheckM
[2024-01-24 13:56:17,519] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_012927265.1_ASM1292726v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_012927265.1_ASM1292726v1_genomic.fna/checkm_input GCF_012927265.1_ASM1292726v1_genomic.fna/checkm_result
[2024-01-24 13:57:06,039] [INFO] Task succeeded: CheckM
[2024-01-24 13:57:06,041] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:57:06,062] [INFO] ===== Completeness check finished =====
[2024-01-24 13:57:06,063] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:57:06,063] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_012927265.1_ASM1292726v1_genomic.fna/markers.fasta)
[2024-01-24 13:57:06,064] [INFO] Task started: Blastn
[2024-01-24 13:57:06,064] [INFO] Running command: blastn -query GCF_012927265.1_ASM1292726v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg59741690-654b-4078-986e-fb600fb48b89/dqc_reference/reference_markers_gtdb.fasta -out GCF_012927265.1_ASM1292726v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:57:06,951] [INFO] Task succeeded: Blastn
[2024-01-24 13:57:06,955] [INFO] Selected 7 target genomes.
[2024-01-24 13:57:06,956] [INFO] Target genome list was writen to GCF_012927265.1_ASM1292726v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:57:06,971] [INFO] Task started: fastANI
[2024-01-24 13:57:06,972] [INFO] Running command: fastANI --query /var/lib/cwl/stg7b7bbd5f-0132-4957-846e-ff7521e336d6/GCF_012927265.1_ASM1292726v1_genomic.fna.gz --refList GCF_012927265.1_ASM1292726v1_genomic.fna/target_genomes_gtdb.txt --output GCF_012927265.1_ASM1292726v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:57:14,097] [INFO] Task succeeded: fastANI
[2024-01-24 13:57:14,104] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:57:14,104] [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_012927265.1	s__Chryseobacterium cheonjiense	100.0	1421	1421	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002434285.1	s__Chryseobacterium sp002434285	87.4547	937	1421	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000708615.2	s__Chryseobacterium hispalense	86.0575	1122	1421	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	98.96	98.96	0.90	0.90	2	-
GCF_900129385.1	s__Chryseobacterium takakiae	85.8368	1083	1421	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003815835.1	s__Chryseobacterium shandongense	85.3411	1057	1421	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	98.85	98.22	0.93	0.90	4	-
GCF_900109935.1	s__Chryseobacterium taichungense	83.1666	948	1421	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900099685.1	s__Chryseobacterium taeanense	82.6139	894	1421	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:57:14,106] [INFO] GTDB search result was written to GCF_012927265.1_ASM1292726v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:57:14,106] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:57:14,109] [INFO] DFAST_QC result json was written to GCF_012927265.1_ASM1292726v1_genomic.fna/dqc_result.json
[2024-01-24 13:57:14,110] [INFO] DFAST_QC completed!
[2024-01-24 13:57:14,110] [INFO] Total running time: 0h1m26s