[2024-01-25 18:11:05,834] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:11:05,835] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:11:05,835] [INFO] DQC Reference Directory: /var/lib/cwl/stg7aada84c-a8bd-4e60-af5c-0ab585ce4bd9/dqc_reference
[2024-01-25 18:11:06,967] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:11:06,968] [INFO] Task started: Prodigal
[2024-01-25 18:11:06,968] [INFO] Running command: gunzip -c /var/lib/cwl/stga8c4011d-1cf0-4972-8ab2-c0c5928dcf27/GCF_028553785.1_ASM2855378v1_genomic.fna.gz | prodigal -d GCF_028553785.1_ASM2855378v1_genomic.fna/cds.fna -a GCF_028553785.1_ASM2855378v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:11:16,762] [INFO] Task succeeded: Prodigal
[2024-01-25 18:11:16,762] [INFO] Task started: HMMsearch
[2024-01-25 18:11:16,762] [INFO] Running command: hmmsearch --tblout GCF_028553785.1_ASM2855378v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7aada84c-a8bd-4e60-af5c-0ab585ce4bd9/dqc_reference/reference_markers.hmm GCF_028553785.1_ASM2855378v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:11:16,974] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:11:16,975] [INFO] Found 6/6 markers.
[2024-01-25 18:11:17,009] [INFO] Query marker FASTA was written to GCF_028553785.1_ASM2855378v1_genomic.fna/markers.fasta
[2024-01-25 18:11:17,010] [INFO] Task started: Blastn
[2024-01-25 18:11:17,010] [INFO] Running command: blastn -query GCF_028553785.1_ASM2855378v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7aada84c-a8bd-4e60-af5c-0ab585ce4bd9/dqc_reference/reference_markers.fasta -out GCF_028553785.1_ASM2855378v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:11:17,919] [INFO] Task succeeded: Blastn
[2024-01-25 18:11:17,925] [INFO] Selected 18 target genomes.
[2024-01-25 18:11:17,925] [INFO] Target genome list was writen to GCF_028553785.1_ASM2855378v1_genomic.fna/target_genomes.txt
[2024-01-25 18:11:17,932] [INFO] Task started: fastANI
[2024-01-25 18:11:17,932] [INFO] Running command: fastANI --query /var/lib/cwl/stga8c4011d-1cf0-4972-8ab2-c0c5928dcf27/GCF_028553785.1_ASM2855378v1_genomic.fna.gz --refList GCF_028553785.1_ASM2855378v1_genomic.fna/target_genomes.txt --output GCF_028553785.1_ASM2855378v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:11:32,311] [INFO] Task succeeded: fastANI
[2024-01-25 18:11:32,311] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7aada84c-a8bd-4e60-af5c-0ab585ce4bd9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:11:32,311] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7aada84c-a8bd-4e60-af5c-0ab585ce4bd9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:11:32,322] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 18:11:32,322] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 18:11:32,322] [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	82.5457	814	1240	95	below_threshold
Paracoccus homiensis	strain=DSM 17862	GCA_900111675.1	364199	364199	type	True	81.5639	663	1240	95	below_threshold
Paracoccus caeni	strain=MJ17	GCA_016629665.1	657651	657651	type	True	81.4599	719	1240	95	below_threshold
Paracoccus siganidrum	strain=M26	GCA_003709565.1	1276757	1276757	type	True	81.4259	730	1240	95	below_threshold
Paracoccus alcaliphilus	strain=DSM 8512	GCA_900110285.1	34002	34002	type	True	81.3928	663	1240	95	below_threshold
Paracoccus siganidrum	strain=DSM 26381	GCA_003594835.1	1276757	1276757	type	True	81.3913	679	1240	95	below_threshold
Paracoccus shandongensis	strain=wg2	GCA_017315735.1	2816048	2816048	type	True	81.0407	630	1240	95	below_threshold
Paracoccus nototheniae	strain=I-41R45	GCA_004335005.1	2489002	2489002	type	True	81.0196	644	1240	95	below_threshold
Paracoccus acridae	strain=CGMCC 1.15419	GCA_014642735.1	1795310	1795310	type	True	80.8157	638	1240	95	below_threshold
Paracoccus fontiphilus	strain=MVW-1	GCA_017356265.1	1815556	1815556	type	True	80.5992	631	1240	95	below_threshold
Paracoccus indicus	strain=IO390502	GCA_003056335.1	2079229	2079229	type	True	80.5661	611	1240	95	below_threshold
Paracoccus salsus	strain=EGI L200073	GCA_021556615.1	2911061	2911061	type	True	80.5537	590	1240	95	below_threshold
Paracoccus zeaxanthinifaciens	strain=ATCC 21588	GCA_000420145.1	187400	187400	type	True	80.5218	564	1240	95	below_threshold
Paracoccus subflavus	strain=GY0581	GCA_004310345.1	2528244	2528244	type	True	80.4646	598	1240	95	below_threshold
Paracoccus everestensis	strain=S8-55	GCA_021491915.1	2903900	2903900	type	True	80.4401	597	1240	95	below_threshold
Paracoccus tegillarcae	strain=BM15	GCA_002847305.1	1529068	1529068	type	True	80.1987	624	1240	95	below_threshold
Paracoccus seriniphilus	strain=DSM 14827	GCA_900199195.1	184748	184748	type	True	80.0654	580	1240	95	below_threshold
Paracoccus onubensis	strain=1011MAR3C25	GCA_003591515.1	1675788	1675788	type	True	79.5298	530	1240	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:11:32,324] [INFO] DFAST Taxonomy check result was written to GCF_028553785.1_ASM2855378v1_genomic.fna/tc_result.tsv
[2024-01-25 18:11:32,325] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:11:32,325] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:11:32,325] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7aada84c-a8bd-4e60-af5c-0ab585ce4bd9/dqc_reference/checkm_data
[2024-01-25 18:11:32,326] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:11:32,363] [INFO] Task started: CheckM
[2024-01-25 18:11:32,363] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_028553785.1_ASM2855378v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_028553785.1_ASM2855378v1_genomic.fna/checkm_input GCF_028553785.1_ASM2855378v1_genomic.fna/checkm_result
[2024-01-25 18:12:06,458] [INFO] Task succeeded: CheckM
[2024-01-25 18:12:06,459] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:12:06,475] [INFO] ===== Completeness check finished =====
[2024-01-25 18:12:06,475] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:12:06,476] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_028553785.1_ASM2855378v1_genomic.fna/markers.fasta)
[2024-01-25 18:12:06,476] [INFO] Task started: Blastn
[2024-01-25 18:12:06,476] [INFO] Running command: blastn -query GCF_028553785.1_ASM2855378v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7aada84c-a8bd-4e60-af5c-0ab585ce4bd9/dqc_reference/reference_markers_gtdb.fasta -out GCF_028553785.1_ASM2855378v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:12:08,206] [INFO] Task succeeded: Blastn
[2024-01-25 18:12:08,208] [INFO] Selected 16 target genomes.
[2024-01-25 18:12:08,209] [INFO] Target genome list was writen to GCF_028553785.1_ASM2855378v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:12:08,224] [INFO] Task started: fastANI
[2024-01-25 18:12:08,224] [INFO] Running command: fastANI --query /var/lib/cwl/stga8c4011d-1cf0-4972-8ab2-c0c5928dcf27/GCF_028553785.1_ASM2855378v1_genomic.fna.gz --refList GCF_028553785.1_ASM2855378v1_genomic.fna/target_genomes_gtdb.txt --output GCF_028553785.1_ASM2855378v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:12:21,953] [INFO] Task succeeded: fastANI
[2024-01-25 18:12:21,962] [INFO] Found 16 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 18:12:21,963] [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	82.5557	813	1240	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	81.6637	706	1240	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	81.5627	662	1240	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016629665.1	s__Paracoccus caeni	81.4365	721	1240	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	81.4091	662	1240	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	81.4011	663	1240	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	81.3827	736	1240	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	99.99	99.99	0.98	0.98	2	-
GCF_017744015.1	s__Paracoccus sp002732665	80.994	643	1240	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	99.29	98.58	0.98	0.95	3	-
GCF_003007735.2	s__Paracoccus marinus_A	80.7727	617	1240	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017356265.1	s__Paracoccus fontiphilus	80.6376	627	1240	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009711265.1	s__Paracoccus sp009711265	80.6318	613	1240	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000420145.1	s__Paracoccus zeaxanthinifaciens	80.537	563	1240	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004310345.1	s__Paracoccus subflavus	80.455	598	1240	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900199195.1	s__Paracoccus seriniphilus	80.0557	581	1240	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900156835.1	s__Paracoccus saliphilus	80.0422	578	1240	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	79.9993	551	1240	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 18:12:21,965] [INFO] GTDB search result was written to GCF_028553785.1_ASM2855378v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:12:21,968] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:12:21,976] [INFO] DFAST_QC result json was written to GCF_028553785.1_ASM2855378v1_genomic.fna/dqc_result.json
[2024-01-25 18:12:21,976] [INFO] DFAST_QC completed!
[2024-01-25 18:12:21,976] [INFO] Total running time: 0h1m16s