[2024-01-24 14:38:45,557] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:38:45,567] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:38:45,567] [INFO] DQC Reference Directory: /var/lib/cwl/stg567cfbba-d901-4f42-807a-502ce18af209/dqc_reference
[2024-01-24 14:38:48,278] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:38:48,280] [INFO] Task started: Prodigal
[2024-01-24 14:38:48,280] [INFO] Running command: gunzip -c /var/lib/cwl/stg4f0a1829-723c-4b86-a280-357d5c679d42/GCF_014642735.1_ASM1464273v1_genomic.fna.gz | prodigal -d GCF_014642735.1_ASM1464273v1_genomic.fna/cds.fna -a GCF_014642735.1_ASM1464273v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:39:00,296] [INFO] Task succeeded: Prodigal
[2024-01-24 14:39:00,296] [INFO] Task started: HMMsearch
[2024-01-24 14:39:00,297] [INFO] Running command: hmmsearch --tblout GCF_014642735.1_ASM1464273v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg567cfbba-d901-4f42-807a-502ce18af209/dqc_reference/reference_markers.hmm GCF_014642735.1_ASM1464273v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:39:00,616] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:39:00,621] [INFO] Found 6/6 markers.
[2024-01-24 14:39:00,664] [INFO] Query marker FASTA was written to GCF_014642735.1_ASM1464273v1_genomic.fna/markers.fasta
[2024-01-24 14:39:00,665] [INFO] Task started: Blastn
[2024-01-24 14:39:00,665] [INFO] Running command: blastn -query GCF_014642735.1_ASM1464273v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg567cfbba-d901-4f42-807a-502ce18af209/dqc_reference/reference_markers.fasta -out GCF_014642735.1_ASM1464273v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:39:01,643] [INFO] Task succeeded: Blastn
[2024-01-24 14:39:01,648] [INFO] Selected 13 target genomes.
[2024-01-24 14:39:01,648] [INFO] Target genome list was writen to GCF_014642735.1_ASM1464273v1_genomic.fna/target_genomes.txt
[2024-01-24 14:39:01,694] [INFO] Task started: fastANI
[2024-01-24 14:39:01,695] [INFO] Running command: fastANI --query /var/lib/cwl/stg4f0a1829-723c-4b86-a280-357d5c679d42/GCF_014642735.1_ASM1464273v1_genomic.fna.gz --refList GCF_014642735.1_ASM1464273v1_genomic.fna/target_genomes.txt --output GCF_014642735.1_ASM1464273v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:39:13,448] [INFO] Task succeeded: fastANI
[2024-01-24 14:39:13,449] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg567cfbba-d901-4f42-807a-502ce18af209/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:39:13,449] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg567cfbba-d901-4f42-807a-502ce18af209/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:39:13,463] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:39:13,463] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:39:13,463] [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 acridae	strain=CGMCC 1.15419	GCA_014642735.1	1795310	1795310	type	True	100.0	1281	1283	95	conclusive
Paracoccus aerius	strain=KCTC 42845	GCA_014656455.1	1915382	1915382	type	True	88.8667	957	1283	95	below_threshold
Paracoccus aerius	strain=KCTC 42845	GCA_016757275.1	1915382	1915382	type	True	88.8514	977	1283	95	below_threshold
Paracoccus shandongensis	strain=wg2	GCA_017315735.1	2816048	2816048	type	True	88.0776	917	1283	95	below_threshold
Paracoccus lichenicola	strain=YIM 132242	GCA_009708075.1	2665644	2665644	type	True	87.7615	870	1283	95	below_threshold
Paracoccus everestensis	strain=S8-55	GCA_021491915.1	2903900	2903900	type	True	87.7088	825	1283	95	below_threshold
Paracoccus fontiphilus	strain=MVW-1	GCA_017356265.1	1815556	1815556	type	True	87.3763	882	1283	95	below_threshold
Paracoccus sediminis	strain=DSM 26170	GCA_900188295.1	1214787	1214787	type	True	86.1766	808	1283	95	below_threshold
Paracoccus sediminis	strain=CMB17	GCA_004310385.1	1214787	1214787	type	True	86.1505	803	1283	95	below_threshold
Paracoccus nototheniae	strain=I-41R45	GCA_004335005.1	2489002	2489002	type	True	81.4755	681	1283	95	below_threshold
Paracoccus salipaludis	strain=WN007	GCA_002287065.1	2032623	2032623	type	True	81.0034	577	1283	95	below_threshold
Paracoccus salsus	strain=EGI L200073	GCA_021556615.1	2911061	2911061	type	True	80.8887	620	1283	95	below_threshold
Paracoccus tegillarcae	strain=BM15	GCA_002847305.1	1529068	1529068	type	True	79.2186	495	1283	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:39:13,466] [INFO] DFAST Taxonomy check result was written to GCF_014642735.1_ASM1464273v1_genomic.fna/tc_result.tsv
[2024-01-24 14:39:13,467] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:39:13,467] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:39:13,467] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg567cfbba-d901-4f42-807a-502ce18af209/dqc_reference/checkm_data
[2024-01-24 14:39:13,468] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:39:13,512] [INFO] Task started: CheckM
[2024-01-24 14:39:13,512] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014642735.1_ASM1464273v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014642735.1_ASM1464273v1_genomic.fna/checkm_input GCF_014642735.1_ASM1464273v1_genomic.fna/checkm_result
[2024-01-24 14:39:57,459] [INFO] Task succeeded: CheckM
[2024-01-24 14:39:57,461] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:39:57,477] [INFO] ===== Completeness check finished =====
[2024-01-24 14:39:57,477] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:39:57,478] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014642735.1_ASM1464273v1_genomic.fna/markers.fasta)
[2024-01-24 14:39:57,478] [INFO] Task started: Blastn
[2024-01-24 14:39:57,478] [INFO] Running command: blastn -query GCF_014642735.1_ASM1464273v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg567cfbba-d901-4f42-807a-502ce18af209/dqc_reference/reference_markers_gtdb.fasta -out GCF_014642735.1_ASM1464273v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:39:59,296] [INFO] Task succeeded: Blastn
[2024-01-24 14:39:59,300] [INFO] Selected 8 target genomes.
[2024-01-24 14:39:59,300] [INFO] Target genome list was writen to GCF_014642735.1_ASM1464273v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:39:59,307] [INFO] Task started: fastANI
[2024-01-24 14:39:59,307] [INFO] Running command: fastANI --query /var/lib/cwl/stg4f0a1829-723c-4b86-a280-357d5c679d42/GCF_014642735.1_ASM1464273v1_genomic.fna.gz --refList GCF_014642735.1_ASM1464273v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014642735.1_ASM1464273v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:40:07,221] [INFO] Task succeeded: fastANI
[2024-01-24 14:40:07,232] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:40:07,233] [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_014642735.1	s__Paracoccus acridae	100.0	1281	1283	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	97.80	97.80	0.86	0.86	2	conclusive
GCF_014656455.1	s__Paracoccus aerius	88.8372	959	1283	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	99.01	98.03	0.91	0.84	3	-
GCF_017315735.1	s__Paracoccus sp017315735	88.0558	919	1283	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	87.8567	880	1283	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009708075.1	s__Paracoccus lichenicola	87.7615	870	1283	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017356265.1	s__Paracoccus fontiphilus	87.3822	881	1283	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900188295.1	s__Paracoccus sediminis	86.1911	807	1283	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	99.99	99.99	0.99	0.99	2	-
GCF_006151785.1	s__Paracoccus marcusii	82.243	629	1283	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	97.50	96.78	0.86	0.75	9	-
--------------------------------------------------------------------------------
[2024-01-24 14:40:07,234] [INFO] GTDB search result was written to GCF_014642735.1_ASM1464273v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:40:07,235] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:40:07,238] [INFO] DFAST_QC result json was written to GCF_014642735.1_ASM1464273v1_genomic.fna/dqc_result.json
[2024-01-24 14:40:07,239] [INFO] DFAST_QC completed!
[2024-01-24 14:40:07,239] [INFO] Total running time: 0h1m22s