[2023-06-28 19:03:52,595] [INFO] DFAST_QC pipeline started.
[2023-06-28 19:03:52,623] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 19:03:52,624] [INFO] DQC Reference Directory: /var/lib/cwl/stgabfcd5f2-4ea5-4f68-81d0-12c169f35094/dqc_reference
[2023-06-28 19:03:53,856] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 19:03:53,857] [INFO] Task started: Prodigal
[2023-06-28 19:03:53,857] [INFO] Running command: gunzip -c /var/lib/cwl/stg779e0c95-52de-4e01-a246-e281524e8fb6/GCA_002708795.1_ASM270879v1_genomic.fna.gz | prodigal -d GCA_002708795.1_ASM270879v1_genomic.fna/cds.fna -a GCA_002708795.1_ASM270879v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 19:04:03,350] [INFO] Task succeeded: Prodigal
[2023-06-28 19:04:03,351] [INFO] Task started: HMMsearch
[2023-06-28 19:04:03,351] [INFO] Running command: hmmsearch --tblout GCA_002708795.1_ASM270879v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgabfcd5f2-4ea5-4f68-81d0-12c169f35094/dqc_reference/reference_markers.hmm GCA_002708795.1_ASM270879v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 19:04:03,625] [INFO] Task succeeded: HMMsearch
[2023-06-28 19:04:03,626] [INFO] Found 6/6 markers.
[2023-06-28 19:04:03,669] [INFO] Query marker FASTA was written to GCA_002708795.1_ASM270879v1_genomic.fna/markers.fasta
[2023-06-28 19:04:03,670] [INFO] Task started: Blastn
[2023-06-28 19:04:03,670] [INFO] Running command: blastn -query GCA_002708795.1_ASM270879v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgabfcd5f2-4ea5-4f68-81d0-12c169f35094/dqc_reference/reference_markers.fasta -out GCA_002708795.1_ASM270879v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 19:04:04,575] [INFO] Task succeeded: Blastn
[2023-06-28 19:04:04,600] [INFO] Selected 18 target genomes.
[2023-06-28 19:04:04,601] [INFO] Target genome list was writen to GCA_002708795.1_ASM270879v1_genomic.fna/target_genomes.txt
[2023-06-28 19:04:04,609] [INFO] Task started: fastANI
[2023-06-28 19:04:04,609] [INFO] Running command: fastANI --query /var/lib/cwl/stg779e0c95-52de-4e01-a246-e281524e8fb6/GCA_002708795.1_ASM270879v1_genomic.fna.gz --refList GCA_002708795.1_ASM270879v1_genomic.fna/target_genomes.txt --output GCA_002708795.1_ASM270879v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 19:04:18,837] [INFO] Task succeeded: fastANI
[2023-06-28 19:04:18,837] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgabfcd5f2-4ea5-4f68-81d0-12c169f35094/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 19:04:18,838] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgabfcd5f2-4ea5-4f68-81d0-12c169f35094/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 19:04:18,853] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 19:04:18,854] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 19:04:18,854] [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 siganidrum	strain=DSM 26381	GCA_003594835.1	1276757	1276757	type	True	82.5146	638	1068	95	below_threshold
Paracoccus siganidrum	strain=M26	GCA_003709565.1	1276757	1276757	type	True	82.4296	673	1068	95	below_threshold
Paracoccus shandongensis	strain=wg2	GCA_017315735.1	2816048	2816048	type	True	81.7212	612	1068	95	below_threshold
Paracoccus salsus	strain=EGI L200073	GCA_021556615.1	2911061	2911061	type	True	81.6462	636	1068	95	below_threshold
Paracoccus fontiphilus	strain=MVW-1	GCA_017356265.1	1815556	1815556	type	True	81.5729	602	1068	95	below_threshold
Paracoccus aestuarii	strain=DSM 19484	GCA_003594815.1	453842	453842	type	True	81.5332	580	1068	95	below_threshold
Paracoccus acridae	strain=CGMCC 1.15419	GCA_014642735.1	1795310	1795310	type	True	81.4826	605	1068	95	below_threshold
Paracoccus alcaliphilus	strain=DSM 8512	GCA_900110285.1	34002	34002	type	True	81.4143	590	1068	95	below_threshold
Paracoccus homiensis	strain=DSM 17862	GCA_900111675.1	364199	364199	type	True	81.3979	635	1068	95	below_threshold
Paracoccus lichenicola	strain=YIM 132242	GCA_009708075.1	2665644	2665644	type	True	81.3456	629	1068	95	below_threshold
Paracoccus aerius	strain=KCTC 42845	GCA_016757275.1	1915382	1915382	type	True	81.275	605	1068	95	below_threshold
Paracoccus aerius	strain=KCTC 42845	GCA_014656455.1	1915382	1915382	type	True	81.1976	619	1068	95	below_threshold
Paracoccus nototheniae	strain=I-41R45	GCA_004335005.1	2489002	2489002	type	True	81.0833	609	1068	95	below_threshold
Paracoccus sediminis	strain=DSM 26170	GCA_900188295.1	1214787	1214787	type	True	80.9961	617	1068	95	below_threshold
Paracoccus sediminis	strain=CMB17	GCA_004310385.1	1214787	1214787	type	True	80.9308	608	1068	95	below_threshold
Paracoccus everestensis	strain=S8-55	GCA_021491915.1	2903900	2903900	type	True	80.7572	573	1068	95	below_threshold
Paracoccus lutimaris	strain=CECT 8525	GCA_003337565.1	1490030	1490030	type	True	79.8633	519	1068	95	below_threshold
Paracoccus tegillarcae	strain=BM15	GCA_002847305.1	1529068	1529068	type	True	79.6437	530	1068	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 19:04:18,856] [INFO] DFAST Taxonomy check result was written to GCA_002708795.1_ASM270879v1_genomic.fna/tc_result.tsv
[2023-06-28 19:04:18,857] [INFO] ===== Taxonomy check completed =====
[2023-06-28 19:04:18,857] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 19:04:18,857] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgabfcd5f2-4ea5-4f68-81d0-12c169f35094/dqc_reference/checkm_data
[2023-06-28 19:04:18,859] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 19:04:18,901] [INFO] Task started: CheckM
[2023-06-28 19:04:18,902] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_002708795.1_ASM270879v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_002708795.1_ASM270879v1_genomic.fna/checkm_input GCA_002708795.1_ASM270879v1_genomic.fna/checkm_result
[2023-06-28 19:04:51,823] [INFO] Task succeeded: CheckM
[2023-06-28 19:04:51,825] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 19:04:51,846] [INFO] ===== Completeness check finished =====
[2023-06-28 19:04:51,846] [INFO] ===== Start GTDB Search =====
[2023-06-28 19:04:51,847] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_002708795.1_ASM270879v1_genomic.fna/markers.fasta)
[2023-06-28 19:04:51,847] [INFO] Task started: Blastn
[2023-06-28 19:04:51,847] [INFO] Running command: blastn -query GCA_002708795.1_ASM270879v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgabfcd5f2-4ea5-4f68-81d0-12c169f35094/dqc_reference/reference_markers_gtdb.fasta -out GCA_002708795.1_ASM270879v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 19:04:53,235] [INFO] Task succeeded: Blastn
[2023-06-28 19:04:53,239] [INFO] Selected 14 target genomes.
[2023-06-28 19:04:53,239] [INFO] Target genome list was writen to GCA_002708795.1_ASM270879v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 19:04:53,253] [INFO] Task started: fastANI
[2023-06-28 19:04:53,253] [INFO] Running command: fastANI --query /var/lib/cwl/stg779e0c95-52de-4e01-a246-e281524e8fb6/GCA_002708795.1_ASM270879v1_genomic.fna.gz --refList GCA_002708795.1_ASM270879v1_genomic.fna/target_genomes_gtdb.txt --output GCA_002708795.1_ASM270879v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 19:05:04,660] [INFO] Task succeeded: fastANI
[2023-06-28 19:05:04,675] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 19:05:04,676] [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
GCA_002294185.1	s__Paracoccus sp002294185	99.7574	973	1068	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	99.77	99.74	0.93	0.89	5	conclusive
GCF_018860165.1	s__Paracoccus sp018860165	82.5767	653	1068	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003709565.1	s__Paracoccus siganidrum	82.4287	673	1068	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	99.99	99.99	0.98	0.98	2	-
GCF_900631945.1	s__Paracoccus haematequi	81.8079	634	1068	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	81.779	672	1068	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	99.29	98.58	0.98	0.95	3	-
GCF_017315735.1	s__Paracoccus sp017315735	81.7183	613	1068	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014642735.1	s__Paracoccus acridae	81.4754	606	1068	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	97.80	97.80	0.86	0.86	2	-
GCF_900110285.1	s__Paracoccus alcaliphilus	81.4141	590	1068	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	81.3981	635	1068	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	81.1733	622	1068	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	99.01	98.03	0.91	0.84	3	-
GCF_900188295.1	s__Paracoccus sediminis	80.9974	616	1068	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	99.99	99.99	0.99	0.99	2	-
GCF_003337565.1	s__Paracoccus lutimaris	79.9045	515	1068	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002847305.1	s__Paracoccus sp002847305	79.6435	530	1068	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	79.4343	353	1068	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 19:05:04,678] [INFO] GTDB search result was written to GCA_002708795.1_ASM270879v1_genomic.fna/result_gtdb.tsv
[2023-06-28 19:05:04,678] [INFO] ===== GTDB Search completed =====
[2023-06-28 19:05:04,682] [INFO] DFAST_QC result json was written to GCA_002708795.1_ASM270879v1_genomic.fna/dqc_result.json
[2023-06-28 19:05:04,682] [INFO] DFAST_QC completed!
[2023-06-28 19:05:04,682] [INFO] Total running time: 0h1m12s