[2024-01-24 11:43:53,500] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:43:53,503] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:43:53,503] [INFO] DQC Reference Directory: /var/lib/cwl/stgab30fd96-e55f-4042-82ee-5c3392ce343c/dqc_reference
[2024-01-24 11:43:54,684] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:43:54,684] [INFO] Task started: Prodigal
[2024-01-24 11:43:54,685] [INFO] Running command: gunzip -c /var/lib/cwl/stgeffd1b24-cf91-456e-8f10-81e97d9a06df/GCF_003324675.1_ASM332467v1_genomic.fna.gz | prodigal -d GCF_003324675.1_ASM332467v1_genomic.fna/cds.fna -a GCF_003324675.1_ASM332467v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:44:04,113] [INFO] Task succeeded: Prodigal
[2024-01-24 11:44:04,114] [INFO] Task started: HMMsearch
[2024-01-24 11:44:04,114] [INFO] Running command: hmmsearch --tblout GCF_003324675.1_ASM332467v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgab30fd96-e55f-4042-82ee-5c3392ce343c/dqc_reference/reference_markers.hmm GCF_003324675.1_ASM332467v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:44:04,302] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:44:04,303] [INFO] Found 6/6 markers.
[2024-01-24 11:44:04,331] [INFO] Query marker FASTA was written to GCF_003324675.1_ASM332467v1_genomic.fna/markers.fasta
[2024-01-24 11:44:04,331] [INFO] Task started: Blastn
[2024-01-24 11:44:04,331] [INFO] Running command: blastn -query GCF_003324675.1_ASM332467v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgab30fd96-e55f-4042-82ee-5c3392ce343c/dqc_reference/reference_markers.fasta -out GCF_003324675.1_ASM332467v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:44:05,273] [INFO] Task succeeded: Blastn
[2024-01-24 11:44:05,276] [INFO] Selected 18 target genomes.
[2024-01-24 11:44:05,276] [INFO] Target genome list was writen to GCF_003324675.1_ASM332467v1_genomic.fna/target_genomes.txt
[2024-01-24 11:44:05,297] [INFO] Task started: fastANI
[2024-01-24 11:44:05,298] [INFO] Running command: fastANI --query /var/lib/cwl/stgeffd1b24-cf91-456e-8f10-81e97d9a06df/GCF_003324675.1_ASM332467v1_genomic.fna.gz --refList GCF_003324675.1_ASM332467v1_genomic.fna/target_genomes.txt --output GCF_003324675.1_ASM332467v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:44:17,819] [INFO] Task succeeded: fastANI
[2024-01-24 11:44:17,820] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgab30fd96-e55f-4042-82ee-5c3392ce343c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:44:17,820] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgab30fd96-e55f-4042-82ee-5c3392ce343c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:44:17,833] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:44:17,834] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:44:17,834] [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 suum	strain=SC2-6	GCA_003324675.1	2259340	2259340	type	True	100.0	1082	1083	95	conclusive
Paracoccus luteus	strain=CFH 10530	GCA_004522155.1	2508543	2508543	type	True	79.8876	523	1083	95	below_threshold
Paracoccus sanguinis	strain=DSM 29303	GCA_900106665.1	1545044	1545044	type	True	79.7599	514	1083	95	below_threshold
Paracoccus binzhouensis	strain=wg1	GCA_016446475.1	2796149	2796149	type	True	79.7383	515	1083	95	below_threshold
Paracoccus aminovorans	strain=DSM 8537	GCA_900113565.1	34004	34004	type	True	79.6565	486	1083	95	below_threshold
Paracoccus aeridis	strain=JC501	GCA_004923205.2	1966466	1966466	type	True	79.6021	462	1083	95	below_threshold
Paracoccus endophyticus	strain=SYSUP0003	GCA_003286075.1	2233774	2233774	type	True	79.4721	479	1083	95	below_threshold
Paracoccus solventivorans	strain=DSM 6637	GCA_900142875.1	53463	53463	type	True	79.3294	443	1083	95	below_threshold
Paracoccus limosus	strain=JCM 17370	GCA_009711185.1	913252	913252	type	True	79.1121	473	1083	95	below_threshold
Paracoccus siganidrum	strain=M26	GCA_003709565.1	1276757	1276757	type	True	79.099	516	1083	95	below_threshold
Paracoccus mutanolyticus	strain=RSP-02	GCA_003285265.1	1499308	1499308	type	True	79.0456	465	1083	95	below_threshold
Paracoccus siganidrum	strain=DSM 26381	GCA_003594835.1	1276757	1276757	type	True	79.0417	498	1083	95	below_threshold
Paracoccus shandongensis	strain=wg2	GCA_017315735.1	2816048	2816048	type	True	79.009	450	1083	95	below_threshold
Paracoccus fontiphilus	strain=MVW-1	GCA_017356265.1	1815556	1815556	type	True	78.7734	441	1083	95	below_threshold
Paracoccus zeaxanthinifaciens	strain=ATCC 21588	GCA_000420145.1	187400	187400	type	True	78.7114	395	1083	95	below_threshold
Paracoccus everestensis	strain=S8-55	GCA_021491915.1	2903900	2903900	type	True	78.552	355	1083	95	below_threshold
Paracoccus nototheniae	strain=I-41R45	GCA_004335005.1	2489002	2489002	type	True	78.2874	424	1083	95	below_threshold
Paracoccus tegillarcae	strain=BM15	GCA_002847305.1	1529068	1529068	type	True	77.8823	361	1083	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:44:17,835] [INFO] DFAST Taxonomy check result was written to GCF_003324675.1_ASM332467v1_genomic.fna/tc_result.tsv
[2024-01-24 11:44:17,836] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:44:17,836] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:44:17,836] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgab30fd96-e55f-4042-82ee-5c3392ce343c/dqc_reference/checkm_data
[2024-01-24 11:44:17,837] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:44:17,869] [INFO] Task started: CheckM
[2024-01-24 11:44:17,869] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003324675.1_ASM332467v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003324675.1_ASM332467v1_genomic.fna/checkm_input GCF_003324675.1_ASM332467v1_genomic.fna/checkm_result
[2024-01-24 11:44:49,569] [INFO] Task succeeded: CheckM
[2024-01-24 11:44:49,570] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:44:49,589] [INFO] ===== Completeness check finished =====
[2024-01-24 11:44:49,590] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:44:49,590] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003324675.1_ASM332467v1_genomic.fna/markers.fasta)
[2024-01-24 11:44:49,590] [INFO] Task started: Blastn
[2024-01-24 11:44:49,590] [INFO] Running command: blastn -query GCF_003324675.1_ASM332467v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgab30fd96-e55f-4042-82ee-5c3392ce343c/dqc_reference/reference_markers_gtdb.fasta -out GCF_003324675.1_ASM332467v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:44:51,474] [INFO] Task succeeded: Blastn
[2024-01-24 11:44:51,478] [INFO] Selected 19 target genomes.
[2024-01-24 11:44:51,478] [INFO] Target genome list was writen to GCF_003324675.1_ASM332467v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:44:51,491] [INFO] Task started: fastANI
[2024-01-24 11:44:51,492] [INFO] Running command: fastANI --query /var/lib/cwl/stgeffd1b24-cf91-456e-8f10-81e97d9a06df/GCF_003324675.1_ASM332467v1_genomic.fna.gz --refList GCF_003324675.1_ASM332467v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003324675.1_ASM332467v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:45:05,038] [INFO] Task succeeded: fastANI
[2024-01-24 11:45:05,053] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:45:05,053] [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_003324675.1	s__Paracoccus suum	100.0	1083	1083	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_004522155.1	s__Paracoccus luteus	79.9309	520	1083	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009674885.1	s__Paracoccus sp009674885	79.8573	532	1083	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900106665.1	s__Paracoccus sanguinis	79.7479	516	1083	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	97.10	96.00	0.89	0.81	6	-
GCF_016446475.1	s__Paracoccus binzhouensis	79.7434	513	1083	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007018965.1	s__Paracoccus marinus	79.7	487	1083	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004923205.2	s__Paracoccus aeridis	79.6239	460	1083	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003286075.1	s__Paracoccus endophyticus	79.446	483	1083	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001447385.1	s__Paracoccus sp001447385	79.2879	496	1083	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142875.1	s__Paracoccus solventivorans	79.265	449	1083	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	96.61	95.99	0.87	0.87	3	-
GCF_000518925.1	s__Paracoccus sp000518925	79.2512	513	1083	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	99.13	98.71	0.90	0.89	3	-
GCF_019061185.1	s__Paracoccus sp019061185	79.2002	464	1083	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016617715.1	s__Paracoccus sp014164625	79.194	452	1083	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	99.50	99.01	0.95	0.90	3	-
GCF_009711185.1	s__Paracoccus limosus	79.1459	469	1083	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102885.1	s__Paracoccus chinensis	79.1255	444	1083	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	79.0938	518	1083	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	99.99	99.99	0.98	0.98	2	-
GCF_018860165.1	s__Paracoccus sp018860165	79.0747	458	1083	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006151785.1	s__Paracoccus marcusii	79.0473	424	1083	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	97.50	96.78	0.86	0.75	9	-
GCF_000420145.1	s__Paracoccus zeaxanthinifaciens	78.732	394	1083	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 11:45:05,054] [INFO] GTDB search result was written to GCF_003324675.1_ASM332467v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:45:05,055] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:45:05,059] [INFO] DFAST_QC result json was written to GCF_003324675.1_ASM332467v1_genomic.fna/dqc_result.json
[2024-01-24 11:45:05,059] [INFO] DFAST_QC completed!
[2024-01-24 11:45:05,059] [INFO] Total running time: 0h1m12s