[2024-01-24 14:22:17,180] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:22:17,182] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:22:17,183] [INFO] DQC Reference Directory: /var/lib/cwl/stg6ea95441-7dac-4dd8-a5b2-25b3d589f86f/dqc_reference
[2024-01-24 14:22:18,464] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:22:18,465] [INFO] Task started: Prodigal
[2024-01-24 14:22:18,465] [INFO] Running command: gunzip -c /var/lib/cwl/stgb5141aeb-986c-42a7-bcee-e8720639c766/GCF_000622145.1_ASM62214v1_genomic.fna.gz | prodigal -d GCF_000622145.1_ASM62214v1_genomic.fna/cds.fna -a GCF_000622145.1_ASM62214v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:22:31,074] [INFO] Task succeeded: Prodigal
[2024-01-24 14:22:31,074] [INFO] Task started: HMMsearch
[2024-01-24 14:22:31,074] [INFO] Running command: hmmsearch --tblout GCF_000622145.1_ASM62214v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6ea95441-7dac-4dd8-a5b2-25b3d589f86f/dqc_reference/reference_markers.hmm GCF_000622145.1_ASM62214v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:22:31,350] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:22:31,352] [INFO] Found 6/6 markers.
[2024-01-24 14:22:31,395] [INFO] Query marker FASTA was written to GCF_000622145.1_ASM62214v1_genomic.fna/markers.fasta
[2024-01-24 14:22:31,395] [INFO] Task started: Blastn
[2024-01-24 14:22:31,395] [INFO] Running command: blastn -query GCF_000622145.1_ASM62214v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6ea95441-7dac-4dd8-a5b2-25b3d589f86f/dqc_reference/reference_markers.fasta -out GCF_000622145.1_ASM62214v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:22:32,426] [INFO] Task succeeded: Blastn
[2024-01-24 14:22:32,432] [INFO] Selected 15 target genomes.
[2024-01-24 14:22:32,432] [INFO] Target genome list was writen to GCF_000622145.1_ASM62214v1_genomic.fna/target_genomes.txt
[2024-01-24 14:22:32,444] [INFO] Task started: fastANI
[2024-01-24 14:22:32,444] [INFO] Running command: fastANI --query /var/lib/cwl/stgb5141aeb-986c-42a7-bcee-e8720639c766/GCF_000622145.1_ASM62214v1_genomic.fna.gz --refList GCF_000622145.1_ASM62214v1_genomic.fna/target_genomes.txt --output GCF_000622145.1_ASM62214v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:22:46,807] [INFO] Task succeeded: fastANI
[2024-01-24 14:22:46,807] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6ea95441-7dac-4dd8-a5b2-25b3d589f86f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:22:46,808] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6ea95441-7dac-4dd8-a5b2-25b3d589f86f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:22:46,826] [INFO] Found 15 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 14:22:46,826] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 14:22:46,826] [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 yeei	strain=ATCC BAA-599	GCA_000622145.1	147645	147645	type	True	100.0	1433	1439	95	inconclusive
Paracoccus yeei	strain=G1212	GCA_002196965.1	147645	147645	type	True	99.9344	1341	1439	95	inconclusive
Paracoccus mutanolyticus	strain=RSP-02	GCA_003285265.1	1499308	1499308	type	True	95.8134	1075	1439	95	inconclusive
Paracoccus binzhouensis	strain=wg1	GCA_016446475.1	2796149	2796149	type	True	85.2071	823	1439	95	below_threshold
Paracoccus aminovorans		GCA_900005615.1	34004	34004	type	True	85.1677	831	1439	95	below_threshold
Paracoccus aminovorans	strain=DSM 8537	GCA_900113565.1	34004	34004	type	True	85.0975	824	1439	95	below_threshold
Paracoccus pantotrophus	strain=DSM 2944	GCA_003633525.1	82367	82367	type	True	84.8626	849	1439	95	below_threshold
Paracoccus pantotrophus	strain=DSM 2944	GCA_008824185.1	82367	82367	type	True	84.8416	844	1439	95	below_threshold
Paracoccus limosus	strain=JCM 17370	GCA_009711185.1	913252	913252	type	True	84.7242	874	1439	95	below_threshold
Paracoccus denitrificans	strain=NBRC 102528	GCA_007989485.1	266	266	type	True	84.5414	857	1439	95	below_threshold
Paracoccus lutimaris	strain=CECT 8525	GCA_003337565.1	1490030	1490030	type	True	83.5328	796	1439	95	below_threshold
Paracoccus shandongensis	strain=wg2	GCA_017315735.1	2816048	2816048	type	True	81.8536	698	1439	95	below_threshold
Paracoccus everestensis	strain=S8-55	GCA_021491915.1	2903900	2903900	type	True	80.6271	583	1439	95	below_threshold
Paracoccus salsus	strain=EGI L200073	GCA_021556615.1	2911061	2911061	type	True	79.9529	522	1439	95	below_threshold
Paracoccus tegillarcae	strain=BM15	GCA_002847305.1	1529068	1529068	type	True	78.6141	506	1439	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:22:46,828] [INFO] DFAST Taxonomy check result was written to GCF_000622145.1_ASM62214v1_genomic.fna/tc_result.tsv
[2024-01-24 14:22:46,828] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:22:46,829] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:22:46,829] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6ea95441-7dac-4dd8-a5b2-25b3d589f86f/dqc_reference/checkm_data
[2024-01-24 14:22:46,830] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:22:46,871] [INFO] Task started: CheckM
[2024-01-24 14:22:46,871] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000622145.1_ASM62214v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000622145.1_ASM62214v1_genomic.fna/checkm_input GCF_000622145.1_ASM62214v1_genomic.fna/checkm_result
[2024-01-24 14:23:30,178] [INFO] Task succeeded: CheckM
[2024-01-24 14:23:30,180] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:23:30,208] [INFO] ===== Completeness check finished =====
[2024-01-24 14:23:30,208] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:23:30,209] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000622145.1_ASM62214v1_genomic.fna/markers.fasta)
[2024-01-24 14:23:30,209] [INFO] Task started: Blastn
[2024-01-24 14:23:30,209] [INFO] Running command: blastn -query GCF_000622145.1_ASM62214v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6ea95441-7dac-4dd8-a5b2-25b3d589f86f/dqc_reference/reference_markers_gtdb.fasta -out GCF_000622145.1_ASM62214v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:23:32,311] [INFO] Task succeeded: Blastn
[2024-01-24 14:23:32,316] [INFO] Selected 13 target genomes.
[2024-01-24 14:23:32,317] [INFO] Target genome list was writen to GCF_000622145.1_ASM62214v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:23:32,331] [INFO] Task started: fastANI
[2024-01-24 14:23:32,331] [INFO] Running command: fastANI --query /var/lib/cwl/stgb5141aeb-986c-42a7-bcee-e8720639c766/GCF_000622145.1_ASM62214v1_genomic.fna.gz --refList GCF_000622145.1_ASM62214v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000622145.1_ASM62214v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:23:46,031] [INFO] Task succeeded: fastANI
[2024-01-24 14:23:46,047] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:23:46,048] [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_000622145.1	s__Paracoccus yeei	100.0	1435	1439	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	96.0533	98.39	97.89	0.87	0.83	7	conclusive
GCF_003285265.1	s__Paracoccus mutanolyticus	95.8656	1070	1439	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	96.0533	N/A	N/A	N/A	N/A	1	-
GCF_001546115.1	s__Paracoccus aminovorans_B	85.6855	891	1439	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	85.1509	828	1439	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	85.1037	835	1439	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	99.98	99.98	1.00	1.00	2	-
GCF_000763885.1	s__Paracoccus versutus	84.9412	862	1439	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	98.67	98.17	0.87	0.76	7	-
GCF_008824185.1	s__Paracoccus pantotrophus	84.8317	845	1439	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	99.22	98.98	0.90	0.84	8	-
GCF_009711185.1	s__Paracoccus limosus	84.7246	874	1439	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900100045.1	s__Paracoccus denitrificans	84.6346	871	1439	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	99.78	98.70	0.97	0.88	7	-
GCF_000518925.1	s__Paracoccus sp000518925	84.6315	893	1439	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	99.13	98.71	0.90	0.89	3	-
GCF_001447385.1	s__Paracoccus sp001447385	84.5417	852	1439	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003337565.1	s__Paracoccus lutimaris	83.579	793	1439	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018056045.1	s__Paracoccus sp018056045	82.5063	488	1439	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 14:23:46,050] [INFO] GTDB search result was written to GCF_000622145.1_ASM62214v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:23:46,050] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:23:46,054] [INFO] DFAST_QC result json was written to GCF_000622145.1_ASM62214v1_genomic.fna/dqc_result.json
[2024-01-24 14:23:46,054] [INFO] DFAST_QC completed!
[2024-01-24 14:23:46,054] [INFO] Total running time: 0h1m29s