[2024-01-24 13:42:56,447] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:42:56,449] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:42:56,449] [INFO] DQC Reference Directory: /var/lib/cwl/stg61b3e329-1f37-4ded-b9e9-3a2dc625a8fd/dqc_reference
[2024-01-24 13:42:57,784] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:42:57,785] [INFO] Task started: Prodigal
[2024-01-24 13:42:57,786] [INFO] Running command: gunzip -c /var/lib/cwl/stgb6f08ad5-e638-4d2c-bcf3-2185f7270e5c/GCF_005048265.1_ASM504826v1_genomic.fna.gz | prodigal -d GCF_005048265.1_ASM504826v1_genomic.fna/cds.fna -a GCF_005048265.1_ASM504826v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:43:09,302] [INFO] Task succeeded: Prodigal
[2024-01-24 13:43:09,303] [INFO] Task started: HMMsearch
[2024-01-24 13:43:09,303] [INFO] Running command: hmmsearch --tblout GCF_005048265.1_ASM504826v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg61b3e329-1f37-4ded-b9e9-3a2dc625a8fd/dqc_reference/reference_markers.hmm GCF_005048265.1_ASM504826v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:43:09,574] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:43:09,576] [INFO] Found 6/6 markers.
[2024-01-24 13:43:09,617] [INFO] Query marker FASTA was written to GCF_005048265.1_ASM504826v1_genomic.fna/markers.fasta
[2024-01-24 13:43:09,617] [INFO] Task started: Blastn
[2024-01-24 13:43:09,617] [INFO] Running command: blastn -query GCF_005048265.1_ASM504826v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg61b3e329-1f37-4ded-b9e9-3a2dc625a8fd/dqc_reference/reference_markers.fasta -out GCF_005048265.1_ASM504826v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:43:10,635] [INFO] Task succeeded: Blastn
[2024-01-24 13:43:10,639] [INFO] Selected 11 target genomes.
[2024-01-24 13:43:10,639] [INFO] Target genome list was writen to GCF_005048265.1_ASM504826v1_genomic.fna/target_genomes.txt
[2024-01-24 13:43:10,643] [INFO] Task started: fastANI
[2024-01-24 13:43:10,644] [INFO] Running command: fastANI --query /var/lib/cwl/stgb6f08ad5-e638-4d2c-bcf3-2185f7270e5c/GCF_005048265.1_ASM504826v1_genomic.fna.gz --refList GCF_005048265.1_ASM504826v1_genomic.fna/target_genomes.txt --output GCF_005048265.1_ASM504826v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:43:20,740] [INFO] Task succeeded: fastANI
[2024-01-24 13:43:20,741] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg61b3e329-1f37-4ded-b9e9-3a2dc625a8fd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:43:20,741] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg61b3e329-1f37-4ded-b9e9-3a2dc625a8fd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:43:20,754] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:43:20,754] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:43:20,755] [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 hibiscisoli	strain=CCTCC AB2016182	GCA_005048265.1	2023261	2023261	type	True	100.0	1263	1267	95	conclusive
Paracoccus aestuarii	strain=DSM 19484	GCA_003594815.1	453842	453842	type	True	87.1644	806	1267	95	below_threshold
Paracoccus gahaiensis	strain=KCTC 42687	GCA_005048225.1	1706839	1706839	type	True	86.3735	911	1267	95	below_threshold
Paracoccus liaowanqingii	strain=2251	GCA_004683865.2	2560053	2560053	type	True	86.23	947	1267	95	below_threshold
Paracoccus nototheniae	strain=I-41R45	GCA_004335005.1	2489002	2489002	type	True	85.5955	883	1267	95	below_threshold
Paracoccus sediminilitoris	strain=DSL-16	GCA_003259195.1	2202419	2202419	type	True	83.9426	804	1267	95	below_threshold
Paracoccus indicus	strain=IO390502	GCA_003056335.1	2079229	2079229	type	True	83.7324	778	1267	95	below_threshold
Paracoccus shandongensis	strain=wg2	GCA_017315735.1	2816048	2816048	type	True	82.4923	714	1267	95	below_threshold
Paracoccus everestensis	strain=S8-55	GCA_021491915.1	2903900	2903900	type	True	81.905	619	1267	95	below_threshold
Paracoccus salsus	strain=EGI L200073	GCA_021556615.1	2911061	2911061	type	True	80.9623	636	1267	95	below_threshold
Paracoccus tegillarcae	strain=BM15	GCA_002847305.1	1529068	1529068	type	True	79.3864	537	1267	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:43:20,756] [INFO] DFAST Taxonomy check result was written to GCF_005048265.1_ASM504826v1_genomic.fna/tc_result.tsv
[2024-01-24 13:43:20,757] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:43:20,757] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:43:20,757] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg61b3e329-1f37-4ded-b9e9-3a2dc625a8fd/dqc_reference/checkm_data
[2024-01-24 13:43:20,758] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:43:20,796] [INFO] Task started: CheckM
[2024-01-24 13:43:20,797] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_005048265.1_ASM504826v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_005048265.1_ASM504826v1_genomic.fna/checkm_input GCF_005048265.1_ASM504826v1_genomic.fna/checkm_result
[2024-01-24 13:44:01,180] [INFO] Task succeeded: CheckM
[2024-01-24 13:44:01,181] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:44:01,202] [INFO] ===== Completeness check finished =====
[2024-01-24 13:44:01,203] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:44:01,203] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_005048265.1_ASM504826v1_genomic.fna/markers.fasta)
[2024-01-24 13:44:01,204] [INFO] Task started: Blastn
[2024-01-24 13:44:01,204] [INFO] Running command: blastn -query GCF_005048265.1_ASM504826v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg61b3e329-1f37-4ded-b9e9-3a2dc625a8fd/dqc_reference/reference_markers_gtdb.fasta -out GCF_005048265.1_ASM504826v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:44:03,095] [INFO] Task succeeded: Blastn
[2024-01-24 13:44:03,098] [INFO] Selected 8 target genomes.
[2024-01-24 13:44:03,099] [INFO] Target genome list was writen to GCF_005048265.1_ASM504826v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:44:03,114] [INFO] Task started: fastANI
[2024-01-24 13:44:03,115] [INFO] Running command: fastANI --query /var/lib/cwl/stgb6f08ad5-e638-4d2c-bcf3-2185f7270e5c/GCF_005048265.1_ASM504826v1_genomic.fna.gz --refList GCF_005048265.1_ASM504826v1_genomic.fna/target_genomes_gtdb.txt --output GCF_005048265.1_ASM504826v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:44:11,277] [INFO] Task succeeded: fastANI
[2024-01-24 13:44:11,292] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:44:11,293] [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_005048265.1	s__Paracoccus hibiscisoli	100.0	1260	1267	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	96.40	96.40	0.91	0.91	2	conclusive
GCF_000787695.1	s__Paracoccus sp000787695	88.7715	849	1267	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	88.3553	820	1267	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	97.50	96.78	0.86	0.75	9	-
GCF_003594815.1	s__Paracoccus aestuarii	87.1408	807	1267	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005048225.1	s__Paracoccus gahaiensis	86.3604	912	1267	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004683865.2	s__Paracoccus liaowanqingii	86.2286	946	1267	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	96.54	96.54	0.86	0.86	2	-
GCF_004335005.1	s__Paracoccus sp004335005	85.5872	883	1267	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003255745.1	s__Paracoccus saliphilus_A	84.1337	789	1267	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 13:44:11,295] [INFO] GTDB search result was written to GCF_005048265.1_ASM504826v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:44:11,295] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:44:11,301] [INFO] DFAST_QC result json was written to GCF_005048265.1_ASM504826v1_genomic.fna/dqc_result.json
[2024-01-24 13:44:11,301] [INFO] DFAST_QC completed!
[2024-01-24 13:44:11,301] [INFO] Total running time: 0h1m15s