[2024-01-24 11:26:12,753] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:26:12,755] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:26:12,756] [INFO] DQC Reference Directory: /var/lib/cwl/stg3f8a323b-cfbb-41a9-b1e1-89c04fe26e61/dqc_reference
[2024-01-24 11:26:14,060] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:26:14,061] [INFO] Task started: Prodigal
[2024-01-24 11:26:14,061] [INFO] Running command: gunzip -c /var/lib/cwl/stg5ed43c0c-24af-45a6-9cc2-1213b920797a/GCF_014490725.1_ASM1449072v1_genomic.fna.gz | prodigal -d GCF_014490725.1_ASM1449072v1_genomic.fna/cds.fna -a GCF_014490725.1_ASM1449072v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:26:26,128] [INFO] Task succeeded: Prodigal
[2024-01-24 11:26:26,129] [INFO] Task started: HMMsearch
[2024-01-24 11:26:26,129] [INFO] Running command: hmmsearch --tblout GCF_014490725.1_ASM1449072v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3f8a323b-cfbb-41a9-b1e1-89c04fe26e61/dqc_reference/reference_markers.hmm GCF_014490725.1_ASM1449072v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:26:26,416] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:26:26,417] [INFO] Found 6/6 markers.
[2024-01-24 11:26:26,450] [INFO] Query marker FASTA was written to GCF_014490725.1_ASM1449072v1_genomic.fna/markers.fasta
[2024-01-24 11:26:26,450] [INFO] Task started: Blastn
[2024-01-24 11:26:26,451] [INFO] Running command: blastn -query GCF_014490725.1_ASM1449072v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3f8a323b-cfbb-41a9-b1e1-89c04fe26e61/dqc_reference/reference_markers.fasta -out GCF_014490725.1_ASM1449072v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:26:27,315] [INFO] Task succeeded: Blastn
[2024-01-24 11:26:27,318] [INFO] Selected 18 target genomes.
[2024-01-24 11:26:27,318] [INFO] Target genome list was writen to GCF_014490725.1_ASM1449072v1_genomic.fna/target_genomes.txt
[2024-01-24 11:26:27,325] [INFO] Task started: fastANI
[2024-01-24 11:26:27,325] [INFO] Running command: fastANI --query /var/lib/cwl/stg5ed43c0c-24af-45a6-9cc2-1213b920797a/GCF_014490725.1_ASM1449072v1_genomic.fna.gz --refList GCF_014490725.1_ASM1449072v1_genomic.fna/target_genomes.txt --output GCF_014490725.1_ASM1449072v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:26:41,643] [INFO] Task succeeded: fastANI
[2024-01-24 11:26:41,644] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3f8a323b-cfbb-41a9-b1e1-89c04fe26e61/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:26:41,644] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3f8a323b-cfbb-41a9-b1e1-89c04fe26e61/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:26:41,665] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:26:41,666] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:26:41,666] [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 amoyensis	strain=11-3	GCA_014490725.1	2760093	2760093	type	True	100.0	1235	1235	95	conclusive
Paracoccus caeni	strain=MJ17	GCA_016629665.1	657651	657651	type	True	80.0999	672	1235	95	below_threshold
Paracoccus homiensis	strain=DSM 17862	GCA_900111675.1	364199	364199	type	True	79.7591	565	1235	95	below_threshold
Paracoccus alcaliphilus	strain=DSM 8512	GCA_900110285.1	34002	34002	type	True	79.7359	539	1235	95	below_threshold
Paracoccus tegillarcae	strain=BM15	GCA_002847305.1	1529068	1529068	type	True	79.5359	492	1235	95	below_threshold
Paracoccus siganidrum	strain=DSM 26381	GCA_003594835.1	1276757	1276757	type	True	79.4323	554	1235	95	below_threshold
Paracoccus siganidrum	strain=M26	GCA_003709565.1	1276757	1276757	type	True	79.3767	579	1235	95	below_threshold
Paracoccus shandongensis	strain=wg2	GCA_017315735.1	2816048	2816048	type	True	79.263	541	1235	95	below_threshold
Paracoccus everestensis	strain=S8-55	GCA_021491915.1	2903900	2903900	type	True	79.1751	491	1235	95	below_threshold
Paracoccus nototheniae	strain=I-41R45	GCA_004335005.1	2489002	2489002	type	True	79.1469	545	1235	95	below_threshold
Paracoccus sediminilitoris	strain=DSL-16	GCA_003259195.1	2202419	2202419	type	True	79.0729	491	1235	95	below_threshold
Paracoccus indicus	strain=IO390502	GCA_003056335.1	2079229	2079229	type	True	78.9235	495	1235	95	below_threshold
Paracoccus salsus	strain=EGI L200073	GCA_021556615.1	2911061	2911061	type	True	78.8522	463	1235	95	below_threshold
Paracoccus seriniphilus	strain=DSM 14827	GCA_900199195.1	184748	184748	type	True	78.6611	469	1235	95	below_threshold
Paracoccus pantotrophus	strain=DSM 2944	GCA_003633525.1	82367	82367	type	True	78.5823	416	1235	95	below_threshold
Paracoccus pantotrophus	strain=DSM 2944	GCA_008824185.1	82367	82367	type	True	78.5334	417	1235	95	below_threshold
Paracoccus onubensis	strain=1011MAR3C25	GCA_003591515.1	1675788	1675788	type	True	78.4038	457	1235	95	below_threshold
Thalassobius mangrovi	strain=GS-10	GCA_009857745.1	2692236	2692236	type	True	77.1485	235	1235	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:26:41,668] [INFO] DFAST Taxonomy check result was written to GCF_014490725.1_ASM1449072v1_genomic.fna/tc_result.tsv
[2024-01-24 11:26:41,669] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:26:41,669] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:26:41,669] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3f8a323b-cfbb-41a9-b1e1-89c04fe26e61/dqc_reference/checkm_data
[2024-01-24 11:26:41,671] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:26:41,739] [INFO] Task started: CheckM
[2024-01-24 11:26:41,739] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014490725.1_ASM1449072v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014490725.1_ASM1449072v1_genomic.fna/checkm_input GCF_014490725.1_ASM1449072v1_genomic.fna/checkm_result
[2024-01-24 11:27:20,397] [INFO] Task succeeded: CheckM
[2024-01-24 11:27:20,399] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:27:20,421] [INFO] ===== Completeness check finished =====
[2024-01-24 11:27:20,422] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:27:20,422] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014490725.1_ASM1449072v1_genomic.fna/markers.fasta)
[2024-01-24 11:27:20,423] [INFO] Task started: Blastn
[2024-01-24 11:27:20,423] [INFO] Running command: blastn -query GCF_014490725.1_ASM1449072v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3f8a323b-cfbb-41a9-b1e1-89c04fe26e61/dqc_reference/reference_markers_gtdb.fasta -out GCF_014490725.1_ASM1449072v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:27:21,955] [INFO] Task succeeded: Blastn
[2024-01-24 11:27:21,958] [INFO] Selected 16 target genomes.
[2024-01-24 11:27:21,958] [INFO] Target genome list was writen to GCF_014490725.1_ASM1449072v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:27:21,971] [INFO] Task started: fastANI
[2024-01-24 11:27:21,972] [INFO] Running command: fastANI --query /var/lib/cwl/stg5ed43c0c-24af-45a6-9cc2-1213b920797a/GCF_014490725.1_ASM1449072v1_genomic.fna.gz --refList GCF_014490725.1_ASM1449072v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014490725.1_ASM1449072v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:27:34,336] [INFO] Task succeeded: fastANI
[2024-01-24 11:27:34,354] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:27:34,354] [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_014490725.1	s__Paracoccus amoyensis	100.0	1235	1235	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_016629665.1	s__Paracoccus caeni	80.0998	672	1235	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	79.778	563	1235	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110285.1	s__Paracoccus alcaliphilus	79.7257	540	1235	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	79.6659	550	1235	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	79.5401	576	1235	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	79.4028	575	1235	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	99.99	99.99	0.98	0.98	2	-
GCF_014642735.1	s__Paracoccus acridae	79.3115	552	1235	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	97.80	97.80	0.86	0.86	2	-
GCF_017744015.1	s__Paracoccus sp002732665	79.2858	553	1235	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	99.29	98.58	0.98	0.95	3	-
GCF_003594815.1	s__Paracoccus aestuarii	79.0835	439	1235	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003259195.1	s__Paracoccus sediminilitoris	79.0639	492	1235	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	95.17	95.17	0.89	0.89	2	-
GCF_003056335.1	s__Paracoccus indicus	78.9237	495	1235	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	78.8133	432	1235	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009711205.1	s__Paracoccus litorisediminis	78.7916	455	1235	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	97.39	97.39	0.92	0.92	2	-
GCF_900199195.1	s__Paracoccus seriniphilus	78.6608	468	1235	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008824185.1	s__Paracoccus pantotrophus	78.5338	417	1235	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	99.22	98.98	0.90	0.84	8	-
--------------------------------------------------------------------------------
[2024-01-24 11:27:34,356] [INFO] GTDB search result was written to GCF_014490725.1_ASM1449072v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:27:34,357] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:27:34,364] [INFO] DFAST_QC result json was written to GCF_014490725.1_ASM1449072v1_genomic.fna/dqc_result.json
[2024-01-24 11:27:34,365] [INFO] DFAST_QC completed!
[2024-01-24 11:27:34,365] [INFO] Total running time: 0h1m22s