[2024-01-24 13:09:51,820] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:09:51,822] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:09:51,822] [INFO] DQC Reference Directory: /var/lib/cwl/stgfa5cb82f-a73e-4dbc-8dcf-228b5d0473ba/dqc_reference
[2024-01-24 13:09:53,381] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:09:53,382] [INFO] Task started: Prodigal
[2024-01-24 13:09:53,382] [INFO] Running command: gunzip -c /var/lib/cwl/stg54aa876d-fea6-4d40-8895-849485cd87af/GCF_003290185.1_ASM329018v1_genomic.fna.gz | prodigal -d GCF_003290185.1_ASM329018v1_genomic.fna/cds.fna -a GCF_003290185.1_ASM329018v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:10:11,065] [INFO] Task succeeded: Prodigal
[2024-01-24 13:10:11,065] [INFO] Task started: HMMsearch
[2024-01-24 13:10:11,066] [INFO] Running command: hmmsearch --tblout GCF_003290185.1_ASM329018v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfa5cb82f-a73e-4dbc-8dcf-228b5d0473ba/dqc_reference/reference_markers.hmm GCF_003290185.1_ASM329018v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:10:11,388] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:10:11,390] [INFO] Found 6/6 markers.
[2024-01-24 13:10:11,432] [INFO] Query marker FASTA was written to GCF_003290185.1_ASM329018v1_genomic.fna/markers.fasta
[2024-01-24 13:10:11,433] [INFO] Task started: Blastn
[2024-01-24 13:10:11,433] [INFO] Running command: blastn -query GCF_003290185.1_ASM329018v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfa5cb82f-a73e-4dbc-8dcf-228b5d0473ba/dqc_reference/reference_markers.fasta -out GCF_003290185.1_ASM329018v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:10:12,105] [INFO] Task succeeded: Blastn
[2024-01-24 13:10:12,108] [INFO] Selected 16 target genomes.
[2024-01-24 13:10:12,109] [INFO] Target genome list was writen to GCF_003290185.1_ASM329018v1_genomic.fna/target_genomes.txt
[2024-01-24 13:10:12,114] [INFO] Task started: fastANI
[2024-01-24 13:10:12,114] [INFO] Running command: fastANI --query /var/lib/cwl/stg54aa876d-fea6-4d40-8895-849485cd87af/GCF_003290185.1_ASM329018v1_genomic.fna.gz --refList GCF_003290185.1_ASM329018v1_genomic.fna/target_genomes.txt --output GCF_003290185.1_ASM329018v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:10:28,891] [INFO] Task succeeded: fastANI
[2024-01-24 13:10:28,892] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfa5cb82f-a73e-4dbc-8dcf-228b5d0473ba/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:10:28,892] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfa5cb82f-a73e-4dbc-8dcf-228b5d0473ba/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:10:28,906] [INFO] Found 15 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:10:28,906] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:10:28,906] [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 lathyri	strain=KCTC 22544	GCA_003290185.1	395933	395933	type	True	100.0	1590	1593	95	conclusive
Chryseobacterium lathyri	strain=NBRC 105250	GCA_007991435.1	395933	395933	type	True	99.9832	1566	1593	95	conclusive
Chryseobacterium elymi	strain=KCTC 22547	GCA_003385495.1	395936	395936	type	True	91.4314	1236	1593	95	below_threshold
Chryseobacterium luteum	strain=DSM 18605	GCA_000737785.1	421531	421531	type	True	86.6352	1097	1593	95	below_threshold
Chryseobacterium oranimense	strain=DSM 19055	GCA_900129755.1	421058	421058	type	True	85.9225	1145	1593	95	below_threshold
Chryseobacterium antibioticum	strain=RP-3-3	GCA_012927325.1	2728847	2728847	type	True	85.8819	1131	1593	95	below_threshold
Chryseobacterium oleae	strain=DSM 25575	GCA_900115055.1	491207	491207	type	True	85.4427	1131	1593	95	below_threshold
Chryseobacterium shigense	strain=DSM 17126	GCA_002943655.1	297244	297244	type	True	84.8525	1108	1593	95	below_threshold
Chryseobacterium shigense	strain=DSM 17126	GCA_900156575.1	297244	297244	type	True	84.8326	1094	1593	95	below_threshold
Chryseobacterium endalhagicum	strain=L7	GCA_016745235.1	2797638	2797638	type	True	84.7637	1113	1593	95	below_threshold
Chryseobacterium vrystaatense	strain=LMG 22846	GCA_000737765.1	307480	307480	type	True	84.5705	1080	1593	95	below_threshold
Chryseobacterium ginsenosidimutans	strain=THG 15	GCA_024807225.1	687846	687846	type	True	80.5466	786	1593	95	below_threshold
Chryseobacterium tagetis	strain=RG1	GCA_016735585.2	2801334	2801334	type	True	80.2606	705	1593	95	below_threshold
Chryseobacterium schmidteae	strain=Marseille-P9602	GCA_903166575.1	2730404	2730404	type	True	79.3586	578	1593	95	below_threshold
Chryseobacterium fistulae	strain=CECT 9393	GCA_902729325.1	2675058	2675058	type	True	79.299	464	1593	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:10:28,908] [INFO] DFAST Taxonomy check result was written to GCF_003290185.1_ASM329018v1_genomic.fna/tc_result.tsv
[2024-01-24 13:10:28,908] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:10:28,909] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:10:28,909] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfa5cb82f-a73e-4dbc-8dcf-228b5d0473ba/dqc_reference/checkm_data
[2024-01-24 13:10:28,910] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:10:28,957] [INFO] Task started: CheckM
[2024-01-24 13:10:28,957] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003290185.1_ASM329018v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003290185.1_ASM329018v1_genomic.fna/checkm_input GCF_003290185.1_ASM329018v1_genomic.fna/checkm_result
[2024-01-24 13:11:21,548] [INFO] Task succeeded: CheckM
[2024-01-24 13:11:21,549] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:11:21,572] [INFO] ===== Completeness check finished =====
[2024-01-24 13:11:21,572] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:11:21,573] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003290185.1_ASM329018v1_genomic.fna/markers.fasta)
[2024-01-24 13:11:21,573] [INFO] Task started: Blastn
[2024-01-24 13:11:21,573] [INFO] Running command: blastn -query GCF_003290185.1_ASM329018v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfa5cb82f-a73e-4dbc-8dcf-228b5d0473ba/dqc_reference/reference_markers_gtdb.fasta -out GCF_003290185.1_ASM329018v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:11:22,522] [INFO] Task succeeded: Blastn
[2024-01-24 13:11:22,526] [INFO] Selected 12 target genomes.
[2024-01-24 13:11:22,526] [INFO] Target genome list was writen to GCF_003290185.1_ASM329018v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:11:22,535] [INFO] Task started: fastANI
[2024-01-24 13:11:22,536] [INFO] Running command: fastANI --query /var/lib/cwl/stg54aa876d-fea6-4d40-8895-849485cd87af/GCF_003290185.1_ASM329018v1_genomic.fna.gz --refList GCF_003290185.1_ASM329018v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003290185.1_ASM329018v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:11:35,706] [INFO] Task succeeded: fastANI
[2024-01-24 13:11:35,724] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:11:35,724] [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_003290185.1	s__Chryseobacterium lathyri	100.0	1590	1593	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	99.99	99.99	1.00	1.00	2	conclusive
GCF_003385495.1	s__Chryseobacterium elymi	91.4018	1238	1593	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000737785.1	s__Chryseobacterium luteum	86.624	1098	1593	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001045445.1	s__Chryseobacterium sp001045445	85.9814	1136	1593	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129755.1	s__Chryseobacterium oranimense	85.9225	1145	1593	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	97.88	97.88	0.91	0.91	3	-
GCF_012927325.1	s__Chryseobacterium antibioticum	85.8819	1131	1593	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000737715.1	s__Chryseobacterium sp000737715	85.5208	1094	1593	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014207845.1	s__Chryseobacterium shigense_A	85.4817	1040	1593	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900115055.1	s__Chryseobacterium oleae	85.4489	1130	1593	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142785.1	s__Chryseobacterium carnipullorum	84.9482	1094	1593	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	98.36	98.32	0.90	0.88	5	-
GCF_900156575.1	s__Chryseobacterium shigense	84.8216	1095	1593	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	99.99	99.99	1.00	1.00	2	-
GCF_000737765.1	s__Chryseobacterium vrystaatense	84.5633	1081	1593	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	98.86	98.86	0.93	0.93	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:11:35,725] [INFO] GTDB search result was written to GCF_003290185.1_ASM329018v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:11:35,732] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:11:35,736] [INFO] DFAST_QC result json was written to GCF_003290185.1_ASM329018v1_genomic.fna/dqc_result.json
[2024-01-24 13:11:35,736] [INFO] DFAST_QC completed!
[2024-01-24 13:11:35,736] [INFO] Total running time: 0h1m44s