[2024-01-24 12:22:26,669] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:22:26,671] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:22:26,671] [INFO] DQC Reference Directory: /var/lib/cwl/stg9ffdb2a8-c1a1-4a8d-9be2-1535e72ddecb/dqc_reference
[2024-01-24 12:22:27,968] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:22:27,969] [INFO] Task started: Prodigal
[2024-01-24 12:22:27,970] [INFO] Running command: gunzip -c /var/lib/cwl/stg32cb2c90-1afd-4609-8c1d-c2323bddeb2e/GCF_007993065.1_ASM799306v1_genomic.fna.gz | prodigal -d GCF_007993065.1_ASM799306v1_genomic.fna/cds.fna -a GCF_007993065.1_ASM799306v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:22:39,226] [INFO] Task succeeded: Prodigal
[2024-01-24 12:22:39,226] [INFO] Task started: HMMsearch
[2024-01-24 12:22:39,227] [INFO] Running command: hmmsearch --tblout GCF_007993065.1_ASM799306v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9ffdb2a8-c1a1-4a8d-9be2-1535e72ddecb/dqc_reference/reference_markers.hmm GCF_007993065.1_ASM799306v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:22:39,503] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:22:39,504] [INFO] Found 6/6 markers.
[2024-01-24 12:22:39,546] [INFO] Query marker FASTA was written to GCF_007993065.1_ASM799306v1_genomic.fna/markers.fasta
[2024-01-24 12:22:39,547] [INFO] Task started: Blastn
[2024-01-24 12:22:39,547] [INFO] Running command: blastn -query GCF_007993065.1_ASM799306v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9ffdb2a8-c1a1-4a8d-9be2-1535e72ddecb/dqc_reference/reference_markers.fasta -out GCF_007993065.1_ASM799306v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:22:40,405] [INFO] Task succeeded: Blastn
[2024-01-24 12:22:40,408] [INFO] Selected 17 target genomes.
[2024-01-24 12:22:40,409] [INFO] Target genome list was writen to GCF_007993065.1_ASM799306v1_genomic.fna/target_genomes.txt
[2024-01-24 12:22:40,416] [INFO] Task started: fastANI
[2024-01-24 12:22:40,416] [INFO] Running command: fastANI --query /var/lib/cwl/stg32cb2c90-1afd-4609-8c1d-c2323bddeb2e/GCF_007993065.1_ASM799306v1_genomic.fna.gz --refList GCF_007993065.1_ASM799306v1_genomic.fna/target_genomes.txt --output GCF_007993065.1_ASM799306v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:22:53,294] [INFO] Task succeeded: fastANI
[2024-01-24 12:22:53,295] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9ffdb2a8-c1a1-4a8d-9be2-1535e72ddecb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:22:53,295] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9ffdb2a8-c1a1-4a8d-9be2-1535e72ddecb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:22:53,314] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:22:53,314] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:22:53,315] [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 aurantiacus	strain=TK008	GCA_007993065.1	2599412	2599412	type	True	100.0	1245	1246	95	conclusive
Paracoccus xiamenensis	strain=12-3	GCA_011308835.1	2714901	2714901	type	True	82.548	756	1246	95	below_threshold
Paracoccus isoporae	strain=DSM 22220	GCA_900101865.1	591205	591205	type	True	81.3543	643	1246	95	below_threshold
Paracoccus jeotgali	strain=CBA4604	GCA_002865605.1	2065379	2065379	type	True	81.2269	602	1246	95	below_threshold
Paracoccus lutimaris	strain=CECT 8525	GCA_003337565.1	1490030	1490030	type	True	79.8252	478	1246	95	below_threshold
Paracoccus siganidrum	strain=M26	GCA_003709565.1	1276757	1276757	type	True	79.4083	500	1246	95	below_threshold
Paracoccus pantotrophus	strain=DSM 2944	GCA_003633525.1	82367	82367	type	True	79.251	441	1246	95	below_threshold
Paracoccus zeaxanthinifaciens	strain=ATCC 21588	GCA_000420145.1	187400	187400	type	True	79.1971	391	1246	95	below_threshold
Paracoccus caeni	strain=MJ17	GCA_016629665.1	657651	657651	type	True	79.1497	444	1246	95	below_threshold
Paracoccus mutanolyticus	strain=RSP-02	GCA_003285265.1	1499308	1499308	type	True	79.0435	408	1246	95	below_threshold
Paracoccus shandongensis	strain=wg2	GCA_017315735.1	2816048	2816048	type	True	78.9773	418	1246	95	below_threshold
Paracoccus salsus	strain=EGI L200073	GCA_021556615.1	2911061	2911061	type	True	78.8673	398	1246	95	below_threshold
Paracoccus lichenicola	strain=YIM 132242	GCA_009708075.1	2665644	2665644	type	True	78.7989	402	1246	95	below_threshold
Phaeovulum vinaykumarii	strain=JA123	GCA_900217755.1	407234	407234	type	True	78.6735	298	1246	95	below_threshold
Paracoccus salipaludis	strain=WN007	GCA_002287065.1	2032623	2032623	type	True	78.6648	367	1246	95	below_threshold
Paracoccus everestensis	strain=S8-55	GCA_021491915.1	2903900	2903900	type	True	78.4784	360	1246	95	below_threshold
Pseudogemmobacter bohemicus	strain=Cd-10	GCA_003290025.1	2250708	2250708	type	True	77.455	256	1246	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:22:53,318] [INFO] DFAST Taxonomy check result was written to GCF_007993065.1_ASM799306v1_genomic.fna/tc_result.tsv
[2024-01-24 12:22:53,320] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:22:53,321] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:22:53,321] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9ffdb2a8-c1a1-4a8d-9be2-1535e72ddecb/dqc_reference/checkm_data
[2024-01-24 12:22:53,323] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:22:53,372] [INFO] Task started: CheckM
[2024-01-24 12:22:53,373] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007993065.1_ASM799306v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007993065.1_ASM799306v1_genomic.fna/checkm_input GCF_007993065.1_ASM799306v1_genomic.fna/checkm_result
[2024-01-24 12:23:30,207] [INFO] Task succeeded: CheckM
[2024-01-24 12:23:30,208] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:23:30,229] [INFO] ===== Completeness check finished =====
[2024-01-24 12:23:30,229] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:23:30,230] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007993065.1_ASM799306v1_genomic.fna/markers.fasta)
[2024-01-24 12:23:30,230] [INFO] Task started: Blastn
[2024-01-24 12:23:30,230] [INFO] Running command: blastn -query GCF_007993065.1_ASM799306v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9ffdb2a8-c1a1-4a8d-9be2-1535e72ddecb/dqc_reference/reference_markers_gtdb.fasta -out GCF_007993065.1_ASM799306v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:23:31,724] [INFO] Task succeeded: Blastn
[2024-01-24 12:23:31,728] [INFO] Selected 12 target genomes.
[2024-01-24 12:23:31,728] [INFO] Target genome list was writen to GCF_007993065.1_ASM799306v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:23:31,747] [INFO] Task started: fastANI
[2024-01-24 12:23:31,748] [INFO] Running command: fastANI --query /var/lib/cwl/stg32cb2c90-1afd-4609-8c1d-c2323bddeb2e/GCF_007993065.1_ASM799306v1_genomic.fna.gz --refList GCF_007993065.1_ASM799306v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007993065.1_ASM799306v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:23:41,552] [INFO] Task succeeded: fastANI
[2024-01-24 12:23:41,567] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:23:41,567] [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_007993065.1	s__Paracoccus aurantiacus	100.0	1245	1246	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_011308835.1	s__Paracoccus xiamenensis	82.5481	756	1246	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005768755.1	s__Paracoccus denitrificans_B	81.9183	687	1246	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013868135.1	s__Paracoccus sp013868135	81.8007	755	1246	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900101865.1	s__Paracoccus isoporae	81.3436	644	1246	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002865605.1	s__Paracoccus jeotgali	81.1934	605	1246	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	96.34	96.34	0.97	0.97	2	-
GCF_003709565.1	s__Paracoccus siganidrum	79.3661	505	1246	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	99.99	99.99	0.98	0.98	2	-
GCF_000763885.1	s__Paracoccus versutus	79.3558	460	1246	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	98.67	98.17	0.87	0.76	7	-
GCF_000420145.1	s__Paracoccus zeaxanthinifaciens	79.1968	391	1246	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900631945.1	s__Paracoccus haematequi	79.1674	436	1246	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016629665.1	s__Paracoccus caeni	79.1282	446	1246	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017315735.1	s__Paracoccus sp017315735	78.9882	417	1246	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 12:23:41,569] [INFO] GTDB search result was written to GCF_007993065.1_ASM799306v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:23:41,569] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:23:41,573] [INFO] DFAST_QC result json was written to GCF_007993065.1_ASM799306v1_genomic.fna/dqc_result.json
[2024-01-24 12:23:41,573] [INFO] DFAST_QC completed!
[2024-01-24 12:23:41,573] [INFO] Total running time: 0h1m15s