[2024-01-24 13:55:40,470] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:55:40,472] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:55:40,472] [INFO] DQC Reference Directory: /var/lib/cwl/stge1b0b542-6d7d-4d21-bc4d-88223a490f64/dqc_reference
[2024-01-24 13:55:41,682] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:55:41,683] [INFO] Task started: Prodigal
[2024-01-24 13:55:41,683] [INFO] Running command: gunzip -c /var/lib/cwl/stg845b964e-1f2c-4eb4-bb43-ad94fe99d89b/GCF_021311115.1_ASM2131111v1_genomic.fna.gz | prodigal -d GCF_021311115.1_ASM2131111v1_genomic.fna/cds.fna -a GCF_021311115.1_ASM2131111v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:55:54,182] [INFO] Task succeeded: Prodigal
[2024-01-24 13:55:54,183] [INFO] Task started: HMMsearch
[2024-01-24 13:55:54,183] [INFO] Running command: hmmsearch --tblout GCF_021311115.1_ASM2131111v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge1b0b542-6d7d-4d21-bc4d-88223a490f64/dqc_reference/reference_markers.hmm GCF_021311115.1_ASM2131111v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:55:54,487] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:55:54,489] [INFO] Found 6/6 markers.
[2024-01-24 13:55:54,528] [INFO] Query marker FASTA was written to GCF_021311115.1_ASM2131111v1_genomic.fna/markers.fasta
[2024-01-24 13:55:54,528] [INFO] Task started: Blastn
[2024-01-24 13:55:54,528] [INFO] Running command: blastn -query GCF_021311115.1_ASM2131111v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge1b0b542-6d7d-4d21-bc4d-88223a490f64/dqc_reference/reference_markers.fasta -out GCF_021311115.1_ASM2131111v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:55:55,176] [INFO] Task succeeded: Blastn
[2024-01-24 13:55:55,180] [INFO] Selected 14 target genomes.
[2024-01-24 13:55:55,181] [INFO] Target genome list was writen to GCF_021311115.1_ASM2131111v1_genomic.fna/target_genomes.txt
[2024-01-24 13:55:55,242] [INFO] Task started: fastANI
[2024-01-24 13:55:55,242] [INFO] Running command: fastANI --query /var/lib/cwl/stg845b964e-1f2c-4eb4-bb43-ad94fe99d89b/GCF_021311115.1_ASM2131111v1_genomic.fna.gz --refList GCF_021311115.1_ASM2131111v1_genomic.fna/target_genomes.txt --output GCF_021311115.1_ASM2131111v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:56:09,031] [INFO] Task succeeded: fastANI
[2024-01-24 13:56:09,031] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge1b0b542-6d7d-4d21-bc4d-88223a490f64/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:56:09,032] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge1b0b542-6d7d-4d21-bc4d-88223a490f64/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:56:09,047] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:56:09,047] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:56:09,047] [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 gwangjuense	strain=THG-A18	GCA_021311115.1	1069980	1069980	type	True	100.0	1157	1158	95	conclusive
Chryseobacterium tagetis	strain=RG1	GCA_016735585.2	2801334	2801334	type	True	86.4412	944	1158	95	below_threshold
Chryseobacterium geocarposphaerae	strain=DSM 27617	GCA_002797535.1	1416776	1416776	type	True	85.758	909	1158	95	below_threshold
Chryseobacterium ginsenosidimutans	strain=THG 15	GCA_024807225.1	687846	687846	type	True	82.6016	799	1158	95	below_threshold
Chryseobacterium wanjuense	strain=DSM 17724	GCA_900111495.1	356305	356305	type	True	82.4989	770	1158	95	below_threshold
Chryseobacterium limigenitum	strain=SUR2	GCA_900114875.1	1612149	1612149	type	True	81.7608	740	1158	95	below_threshold
Chryseobacterium gambrini	strain=DSM 18014	GCA_900156825.1	373672	373672	type	True	81.6909	734	1158	95	below_threshold
Chryseobacterium taeanense	strain=DSM 17071	GCA_900099685.1	311334	311334	type	True	80.9329	647	1158	95	below_threshold
Chryseobacterium ureilyticum	strain=DSM 18017	GCA_900156735.1	373668	373668	type	True	80.8599	713	1158	95	below_threshold
Chryseobacterium jejuense	strain=DSM 19299	GCA_900100075.1	445960	445960	type	True	80.7744	685	1158	95	below_threshold
Chryseobacterium schmidteae	strain=Marseille-P9602	GCA_903166575.1	2730404	2730404	type	True	80.6284	695	1158	95	below_threshold
Chryseobacterium oleae	strain=DSM 25575	GCA_900115055.1	491207	491207	type	True	80.5535	649	1158	95	below_threshold
Chryseobacterium pennae	strain=1_F178	GCA_003385515.1	2258962	2258962	type	True	80.4328	689	1158	95	below_threshold
Chryseobacterium fistulae	strain=CECT 9393	GCA_902729325.1	2675058	2675058	type	True	79.4967	542	1158	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:56:09,049] [INFO] DFAST Taxonomy check result was written to GCF_021311115.1_ASM2131111v1_genomic.fna/tc_result.tsv
[2024-01-24 13:56:09,049] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:56:09,049] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:56:09,050] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge1b0b542-6d7d-4d21-bc4d-88223a490f64/dqc_reference/checkm_data
[2024-01-24 13:56:09,050] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:56:09,084] [INFO] Task started: CheckM
[2024-01-24 13:56:09,085] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_021311115.1_ASM2131111v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_021311115.1_ASM2131111v1_genomic.fna/checkm_input GCF_021311115.1_ASM2131111v1_genomic.fna/checkm_result
[2024-01-24 13:56:49,844] [INFO] Task succeeded: CheckM
[2024-01-24 13:56:49,846] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:56:49,919] [INFO] ===== Completeness check finished =====
[2024-01-24 13:56:49,919] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:56:49,920] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_021311115.1_ASM2131111v1_genomic.fna/markers.fasta)
[2024-01-24 13:56:49,920] [INFO] Task started: Blastn
[2024-01-24 13:56:49,921] [INFO] Running command: blastn -query GCF_021311115.1_ASM2131111v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge1b0b542-6d7d-4d21-bc4d-88223a490f64/dqc_reference/reference_markers_gtdb.fasta -out GCF_021311115.1_ASM2131111v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:56:50,778] [INFO] Task succeeded: Blastn
[2024-01-24 13:56:50,782] [INFO] Selected 17 target genomes.
[2024-01-24 13:56:50,782] [INFO] Target genome list was writen to GCF_021311115.1_ASM2131111v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:56:50,840] [INFO] Task started: fastANI
[2024-01-24 13:56:50,840] [INFO] Running command: fastANI --query /var/lib/cwl/stg845b964e-1f2c-4eb4-bb43-ad94fe99d89b/GCF_021311115.1_ASM2131111v1_genomic.fna.gz --refList GCF_021311115.1_ASM2131111v1_genomic.fna/target_genomes_gtdb.txt --output GCF_021311115.1_ASM2131111v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:57:07,498] [INFO] Task succeeded: fastANI
[2024-01-24 13:57:07,512] [INFO] Found 17 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:57:07,513] [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_000813825.1	s__Chryseobacterium taiwanense	86.857	978	1158	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000799455.1	s__Chryseobacterium sp000799455	86.6461	970	1158	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002797535.1	s__Chryseobacterium geocarposphaerae	85.7773	907	1158	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	95.65	95.65	0.87	0.87	2	-
GCF_000799195.1	s__Chryseobacterium sp000799195	82.7593	801	1158	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900111495.1	s__Chryseobacterium wanjuense	82.4767	773	1158	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002455915.1	s__Chryseobacterium sp002455915	82.2718	608	1158	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001045455.1	s__Chryseobacterium sp001045455	82.1609	727	1158	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114875.1	s__Chryseobacterium limigenitum	81.7511	741	1158	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900156825.1	s__Chryseobacterium gambrini	81.7009	733	1158	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.1494	96.49	96.36	0.87	0.82	3	-
GCF_000799515.1	s__Chryseobacterium sp000799515	81.1432	658	1158	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900156735.1	s__Chryseobacterium ureilyticum	80.8658	712	1158	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900100075.1	s__Chryseobacterium jejuense	80.774	685	1158	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	99.99	99.99	0.98	0.98	2	-
GCF_004119455.1	s__Chryseobacterium sp004119455	80.7553	688	1158	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	99.99	99.99	1.00	1.00	2	-
GCF_900115055.1	s__Chryseobacterium oleae	80.5354	650	1158	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900128945.1	s__Chryseobacterium sp900128945	80.4754	652	1158	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	97.14	97.03	0.94	0.94	3	-
GCF_003385515.1	s__Chryseobacterium sp003385515	80.4217	690	1158	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	97.92	97.92	0.86	0.86	2	-
GCF_003815975.1	s__Chryseobacterium bernardetii_A	80.2643	666	1158	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	98.62	98.62	0.90	0.90	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:57:07,518] [INFO] GTDB search result was written to GCF_021311115.1_ASM2131111v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:57:07,519] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:57:07,524] [INFO] DFAST_QC result json was written to GCF_021311115.1_ASM2131111v1_genomic.fna/dqc_result.json
[2024-01-24 13:57:07,524] [INFO] DFAST_QC completed!
[2024-01-24 13:57:07,524] [INFO] Total running time: 0h1m27s