[2024-01-24 14:21:50,888] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:21:50,890] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:21:50,890] [INFO] DQC Reference Directory: /var/lib/cwl/stg8631f345-6b59-4836-be62-70022740f730/dqc_reference
[2024-01-24 14:21:52,274] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:21:52,275] [INFO] Task started: Prodigal
[2024-01-24 14:21:52,275] [INFO] Running command: gunzip -c /var/lib/cwl/stg688f440e-3890-49da-9020-dd0654dac830/GCF_003285265.1_ASM328526v1_genomic.fna.gz | prodigal -d GCF_003285265.1_ASM328526v1_genomic.fna/cds.fna -a GCF_003285265.1_ASM328526v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:22:03,763] [INFO] Task succeeded: Prodigal
[2024-01-24 14:22:03,763] [INFO] Task started: HMMsearch
[2024-01-24 14:22:03,763] [INFO] Running command: hmmsearch --tblout GCF_003285265.1_ASM328526v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8631f345-6b59-4836-be62-70022740f730/dqc_reference/reference_markers.hmm GCF_003285265.1_ASM328526v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:22:04,006] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:22:04,008] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg688f440e-3890-49da-9020-dd0654dac830/GCF_003285265.1_ASM328526v1_genomic.fna.gz]
[2024-01-24 14:22:04,043] [INFO] Query marker FASTA was written to GCF_003285265.1_ASM328526v1_genomic.fna/markers.fasta
[2024-01-24 14:22:04,043] [INFO] Task started: Blastn
[2024-01-24 14:22:04,043] [INFO] Running command: blastn -query GCF_003285265.1_ASM328526v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8631f345-6b59-4836-be62-70022740f730/dqc_reference/reference_markers.fasta -out GCF_003285265.1_ASM328526v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:22:05,067] [INFO] Task succeeded: Blastn
[2024-01-24 14:22:05,073] [INFO] Selected 14 target genomes.
[2024-01-24 14:22:05,074] [INFO] Target genome list was writen to GCF_003285265.1_ASM328526v1_genomic.fna/target_genomes.txt
[2024-01-24 14:22:05,084] [INFO] Task started: fastANI
[2024-01-24 14:22:05,084] [INFO] Running command: fastANI --query /var/lib/cwl/stg688f440e-3890-49da-9020-dd0654dac830/GCF_003285265.1_ASM328526v1_genomic.fna.gz --refList GCF_003285265.1_ASM328526v1_genomic.fna/target_genomes.txt --output GCF_003285265.1_ASM328526v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:22:18,516] [INFO] Task succeeded: fastANI
[2024-01-24 14:22:18,516] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8631f345-6b59-4836-be62-70022740f730/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:22:18,516] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8631f345-6b59-4836-be62-70022740f730/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:22:18,528] [INFO] Found 14 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 14:22:18,528] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 14:22:18,528] [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
Paracoccus mutanolyticus	strain=RSP-02	GCA_003285265.1	1499308	1499308	type	True	100.0	1196	1197	95	inconclusive
Paracoccus yeei	strain=ATCC BAA-599	GCA_000622145.1	147645	147645	type	True	95.9867	1062	1197	95	inconclusive
Paracoccus yeei	strain=G1212	GCA_002196965.1	147645	147645	type	True	95.8591	1028	1197	95	inconclusive
Paracoccus binzhouensis	strain=wg1	GCA_016446475.1	2796149	2796149	type	True	85.1063	734	1197	95	below_threshold
Paracoccus aminovorans	strain=DSM 8537	GCA_900113565.1	34004	34004	type	True	85.0356	740	1197	95	below_threshold
Paracoccus aminovorans		GCA_900005615.1	34004	34004	type	True	85.0295	756	1197	95	below_threshold
Paracoccus pantotrophus	strain=DSM 2944	GCA_003633525.1	82367	82367	type	True	84.8061	777	1197	95	below_threshold
Paracoccus pantotrophus	strain=DSM 2944	GCA_008824185.1	82367	82367	type	True	84.7622	781	1197	95	below_threshold
Paracoccus denitrificans	strain=NBRC 102528	GCA_007989485.1	266	266	type	True	84.4889	783	1197	95	below_threshold
Paracoccus limosus	strain=JCM 17370	GCA_009711185.1	913252	913252	type	True	84.4413	780	1197	95	below_threshold
Paracoccus shandongensis	strain=wg2	GCA_017315735.1	2816048	2816048	type	True	81.5181	631	1197	95	below_threshold
Paracoccus everestensis	strain=S8-55	GCA_021491915.1	2903900	2903900	type	True	80.4133	550	1197	95	below_threshold
Paracoccus salsus	strain=EGI L200073	GCA_021556615.1	2911061	2911061	type	True	79.7913	492	1197	95	below_threshold
Paracoccus tegillarcae	strain=BM15	GCA_002847305.1	1529068	1529068	type	True	78.6527	448	1197	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:22:18,534] [INFO] DFAST Taxonomy check result was written to GCF_003285265.1_ASM328526v1_genomic.fna/tc_result.tsv
[2024-01-24 14:22:18,535] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:22:18,535] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:22:18,535] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8631f345-6b59-4836-be62-70022740f730/dqc_reference/checkm_data
[2024-01-24 14:22:18,537] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:22:18,579] [INFO] Task started: CheckM
[2024-01-24 14:22:18,579] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003285265.1_ASM328526v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003285265.1_ASM328526v1_genomic.fna/checkm_input GCF_003285265.1_ASM328526v1_genomic.fna/checkm_result
[2024-01-24 14:22:55,357] [INFO] Task succeeded: CheckM
[2024-01-24 14:22:55,358] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 30.71%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:22:55,375] [INFO] ===== Completeness check finished =====
[2024-01-24 14:22:55,375] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:22:55,376] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003285265.1_ASM328526v1_genomic.fna/markers.fasta)
[2024-01-24 14:22:55,376] [INFO] Task started: Blastn
[2024-01-24 14:22:55,376] [INFO] Running command: blastn -query GCF_003285265.1_ASM328526v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8631f345-6b59-4836-be62-70022740f730/dqc_reference/reference_markers_gtdb.fasta -out GCF_003285265.1_ASM328526v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:22:57,171] [INFO] Task succeeded: Blastn
[2024-01-24 14:22:57,175] [INFO] Selected 10 target genomes.
[2024-01-24 14:22:57,175] [INFO] Target genome list was writen to GCF_003285265.1_ASM328526v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:22:57,183] [INFO] Task started: fastANI
[2024-01-24 14:22:57,183] [INFO] Running command: fastANI --query /var/lib/cwl/stg688f440e-3890-49da-9020-dd0654dac830/GCF_003285265.1_ASM328526v1_genomic.fna.gz --refList GCF_003285265.1_ASM328526v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003285265.1_ASM328526v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:23:08,007] [INFO] Task succeeded: fastANI
[2024-01-24 14:23:08,018] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:23:08,019] [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_003285265.1	s__Paracoccus mutanolyticus	100.0	1194	1197	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	96.0533	N/A	N/A	N/A	N/A	1	conclusive
GCF_000622145.1	s__Paracoccus yeei	95.9763	1063	1197	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	96.0533	98.39	97.89	0.87	0.83	7	-
GCF_001546115.1	s__Paracoccus aminovorans_B	85.3741	817	1197	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	95.35	95.35	0.81	0.81	2	-
GCF_016446475.1	s__Paracoccus binzhouensis	85.0929	736	1197	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900005615.1	s__Paracoccus aminovorans	85.0477	760	1197	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	99.98	99.98	1.00	1.00	2	-
GCF_008824185.1	s__Paracoccus pantotrophus	84.7394	782	1197	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	99.22	98.98	0.90	0.84	8	-
GCF_000518925.1	s__Paracoccus sp000518925	84.7349	789	1197	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	99.13	98.71	0.90	0.89	3	-
GCF_000763885.1	s__Paracoccus versutus	84.7206	800	1197	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	98.67	98.17	0.87	0.76	7	-
GCF_009711185.1	s__Paracoccus limosus	84.4669	778	1197	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001447385.1	s__Paracoccus sp001447385	84.4542	788	1197	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:23:08,020] [INFO] GTDB search result was written to GCF_003285265.1_ASM328526v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:23:08,021] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:23:08,024] [INFO] DFAST_QC result json was written to GCF_003285265.1_ASM328526v1_genomic.fna/dqc_result.json
[2024-01-24 14:23:08,025] [INFO] DFAST_QC completed!
[2024-01-24 14:23:08,025] [INFO] Total running time: 0h1m17s