[2024-01-25 17:35:50,551] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:35:50,553] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:35:50,553] [INFO] DQC Reference Directory: /var/lib/cwl/stg87693c37-6c77-46b6-9d76-fe5552c0d7f4/dqc_reference
[2024-01-25 17:35:51,704] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:35:51,705] [INFO] Task started: Prodigal
[2024-01-25 17:35:51,705] [INFO] Running command: gunzip -c /var/lib/cwl/stg21d04482-8b29-45ad-8ba7-71bfbc2ace10/GCF_016629665.1_ASM1662966v1_genomic.fna.gz | prodigal -d GCF_016629665.1_ASM1662966v1_genomic.fna/cds.fna -a GCF_016629665.1_ASM1662966v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:36:02,762] [INFO] Task succeeded: Prodigal
[2024-01-25 17:36:02,762] [INFO] Task started: HMMsearch
[2024-01-25 17:36:02,762] [INFO] Running command: hmmsearch --tblout GCF_016629665.1_ASM1662966v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg87693c37-6c77-46b6-9d76-fe5552c0d7f4/dqc_reference/reference_markers.hmm GCF_016629665.1_ASM1662966v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:36:03,000] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:36:03,001] [INFO] Found 6/6 markers.
[2024-01-25 17:36:03,038] [INFO] Query marker FASTA was written to GCF_016629665.1_ASM1662966v1_genomic.fna/markers.fasta
[2024-01-25 17:36:03,038] [INFO] Task started: Blastn
[2024-01-25 17:36:03,038] [INFO] Running command: blastn -query GCF_016629665.1_ASM1662966v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg87693c37-6c77-46b6-9d76-fe5552c0d7f4/dqc_reference/reference_markers.fasta -out GCF_016629665.1_ASM1662966v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:36:03,972] [INFO] Task succeeded: Blastn
[2024-01-25 17:36:03,975] [INFO] Selected 17 target genomes.
[2024-01-25 17:36:03,975] [INFO] Target genome list was writen to GCF_016629665.1_ASM1662966v1_genomic.fna/target_genomes.txt
[2024-01-25 17:36:03,981] [INFO] Task started: fastANI
[2024-01-25 17:36:03,981] [INFO] Running command: fastANI --query /var/lib/cwl/stg21d04482-8b29-45ad-8ba7-71bfbc2ace10/GCF_016629665.1_ASM1662966v1_genomic.fna.gz --refList GCF_016629665.1_ASM1662966v1_genomic.fna/target_genomes.txt --output GCF_016629665.1_ASM1662966v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:36:20,397] [INFO] Task succeeded: fastANI
[2024-01-25 17:36:20,397] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg87693c37-6c77-46b6-9d76-fe5552c0d7f4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:36:20,397] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg87693c37-6c77-46b6-9d76-fe5552c0d7f4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:36:20,410] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:36:20,411] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:36:20,411] [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 caeni	strain=MJ17	GCA_016629665.1	657651	657651	type	True	100.0	1386	1387	95	conclusive
Paracoccus siganidrum	strain=DSM 26381	GCA_003594835.1	1276757	1276757	type	True	81.4354	717	1387	95	below_threshold
Paracoccus siganidrum	strain=M26	GCA_003709565.1	1276757	1276757	type	True	81.3652	762	1387	95	below_threshold
Paracoccus alcaliphilus	strain=DSM 8512	GCA_900110285.1	34002	34002	type	True	81.343	700	1387	95	below_threshold
Paracoccus shandongensis	strain=wg2	GCA_017315735.1	2816048	2816048	type	True	80.8692	681	1387	95	below_threshold
Paracoccus homiensis	strain=DSM 17862	GCA_900111675.1	364199	364199	type	True	80.7729	613	1387	95	below_threshold
Paracoccus aerius	strain=KCTC 42845	GCA_016757275.1	1915382	1915382	type	True	80.6541	669	1387	95	below_threshold
Paracoccus lichenicola	strain=YIM 132242	GCA_009708075.1	2665644	2665644	type	True	80.6359	658	1387	95	below_threshold
Paracoccus aerius	strain=KCTC 42845	GCA_014656455.1	1915382	1915382	type	True	80.62	672	1387	95	below_threshold
Paracoccus zhejiangensis	strain=J6	GCA_002847445.1	1077935	1077935	type	True	80.5339	650	1387	95	below_threshold
Paracoccus everestensis	strain=S8-55	GCA_021491915.1	2903900	2903900	type	True	80.4174	620	1387	95	below_threshold
Paracoccus nototheniae	strain=I-41R45	GCA_004335005.1	2489002	2489002	type	True	80.4078	618	1387	95	below_threshold
Paracoccus aestuarii	strain=DSM 19484	GCA_003594815.1	453842	453842	type	True	80.29	566	1387	95	below_threshold
Paracoccus amoyensis	strain=11-3	GCA_014490725.1	2760093	2760093	type	True	80.2868	642	1387	95	below_threshold
Paracoccus salsus	strain=EGI L200073	GCA_021556615.1	2911061	2911061	type	True	80.1307	548	1387	95	below_threshold
Paracoccus bogoriensis	strain=BOG6	GCA_019431455.1	242065	242065	type	True	80.0855	528	1387	95	below_threshold
Paracoccus tegillarcae	strain=BM15	GCA_002847305.1	1529068	1529068	type	True	79.3282	518	1387	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:36:20,412] [INFO] DFAST Taxonomy check result was written to GCF_016629665.1_ASM1662966v1_genomic.fna/tc_result.tsv
[2024-01-25 17:36:20,414] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:36:20,414] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:36:20,415] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg87693c37-6c77-46b6-9d76-fe5552c0d7f4/dqc_reference/checkm_data
[2024-01-25 17:36:20,416] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:36:20,460] [INFO] Task started: CheckM
[2024-01-25 17:36:20,460] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016629665.1_ASM1662966v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016629665.1_ASM1662966v1_genomic.fna/checkm_input GCF_016629665.1_ASM1662966v1_genomic.fna/checkm_result
[2024-01-25 17:36:56,115] [INFO] Task succeeded: CheckM
[2024-01-25 17:36:56,116] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:36:56,134] [INFO] ===== Completeness check finished =====
[2024-01-25 17:36:56,135] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:36:56,135] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016629665.1_ASM1662966v1_genomic.fna/markers.fasta)
[2024-01-25 17:36:56,135] [INFO] Task started: Blastn
[2024-01-25 17:36:56,135] [INFO] Running command: blastn -query GCF_016629665.1_ASM1662966v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg87693c37-6c77-46b6-9d76-fe5552c0d7f4/dqc_reference/reference_markers_gtdb.fasta -out GCF_016629665.1_ASM1662966v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:36:57,911] [INFO] Task succeeded: Blastn
[2024-01-25 17:36:57,914] [INFO] Selected 13 target genomes.
[2024-01-25 17:36:57,914] [INFO] Target genome list was writen to GCF_016629665.1_ASM1662966v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:36:57,921] [INFO] Task started: fastANI
[2024-01-25 17:36:57,921] [INFO] Running command: fastANI --query /var/lib/cwl/stg21d04482-8b29-45ad-8ba7-71bfbc2ace10/GCF_016629665.1_ASM1662966v1_genomic.fna.gz --refList GCF_016629665.1_ASM1662966v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016629665.1_ASM1662966v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:37:10,014] [INFO] Task succeeded: fastANI
[2024-01-25 17:37:10,029] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:37:10,029] [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_016629665.1	s__Paracoccus caeni	100.0	1386	1387	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_003709565.1	s__Paracoccus siganidrum	81.3612	763	1387	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	99.99	99.99	0.98	0.98	2	-
GCF_900110285.1	s__Paracoccus alcaliphilus	81.3482	699	1387	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	81.274	690	1387	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018860165.1	s__Paracoccus sp018860165	81.255	662	1387	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	80.8385	685	1387	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900111675.1	s__Paracoccus homiensis	80.7563	615	1387	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014656455.1	s__Paracoccus aerius	80.62	672	1387	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	99.01	98.03	0.91	0.84	3	-
GCF_009708075.1	s__Paracoccus lichenicola	80.6118	661	1387	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002847445.1	s__Paracoccus zhejiangensis	80.5084	652	1387	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017744015.1	s__Paracoccus sp002732665	80.4023	620	1387	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	99.29	98.58	0.98	0.95	3	-
GCF_014490725.1	s__Paracoccus amoyensis	80.2787	644	1387	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003594815.1	s__Paracoccus aestuarii	80.2646	569	1387	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:37:10,030] [INFO] GTDB search result was written to GCF_016629665.1_ASM1662966v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:37:10,031] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:37:10,034] [INFO] DFAST_QC result json was written to GCF_016629665.1_ASM1662966v1_genomic.fna/dqc_result.json
[2024-01-25 17:37:10,034] [INFO] DFAST_QC completed!
[2024-01-25 17:37:10,034] [INFO] Total running time: 0h1m19s