[2024-01-24 14:38:48,215] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:38:48,217] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:38:48,217] [INFO] DQC Reference Directory: /var/lib/cwl/stg52d1e61d-3659-45f9-a043-b1dc411e56a9/dqc_reference
[2024-01-24 14:38:50,451] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:38:50,455] [INFO] Task started: Prodigal
[2024-01-24 14:38:50,455] [INFO] Running command: gunzip -c /var/lib/cwl/stga9babb53-021b-410c-9dbe-fd32af5e253a/GCF_016446475.1_ASM1644647v1_genomic.fna.gz | prodigal -d GCF_016446475.1_ASM1644647v1_genomic.fna/cds.fna -a GCF_016446475.1_ASM1644647v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:39:04,175] [INFO] Task succeeded: Prodigal
[2024-01-24 14:39:04,175] [INFO] Task started: HMMsearch
[2024-01-24 14:39:04,175] [INFO] Running command: hmmsearch --tblout GCF_016446475.1_ASM1644647v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg52d1e61d-3659-45f9-a043-b1dc411e56a9/dqc_reference/reference_markers.hmm GCF_016446475.1_ASM1644647v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:39:04,541] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:39:04,543] [INFO] Found 6/6 markers.
[2024-01-24 14:39:04,588] [INFO] Query marker FASTA was written to GCF_016446475.1_ASM1644647v1_genomic.fna/markers.fasta
[2024-01-24 14:39:04,588] [INFO] Task started: Blastn
[2024-01-24 14:39:04,588] [INFO] Running command: blastn -query GCF_016446475.1_ASM1644647v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg52d1e61d-3659-45f9-a043-b1dc411e56a9/dqc_reference/reference_markers.fasta -out GCF_016446475.1_ASM1644647v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:39:05,721] [INFO] Task succeeded: Blastn
[2024-01-24 14:39:05,725] [INFO] Selected 14 target genomes.
[2024-01-24 14:39:05,726] [INFO] Target genome list was writen to GCF_016446475.1_ASM1644647v1_genomic.fna/target_genomes.txt
[2024-01-24 14:39:05,733] [INFO] Task started: fastANI
[2024-01-24 14:39:05,734] [INFO] Running command: fastANI --query /var/lib/cwl/stga9babb53-021b-410c-9dbe-fd32af5e253a/GCF_016446475.1_ASM1644647v1_genomic.fna.gz --refList GCF_016446475.1_ASM1644647v1_genomic.fna/target_genomes.txt --output GCF_016446475.1_ASM1644647v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:39:20,973] [INFO] Task succeeded: fastANI
[2024-01-24 14:39:20,974] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg52d1e61d-3659-45f9-a043-b1dc411e56a9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:39:20,974] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg52d1e61d-3659-45f9-a043-b1dc411e56a9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:39:20,988] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:39:20,989] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:39:20,989] [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 binzhouensis	strain=wg1	GCA_016446475.1	2796149	2796149	type	True	100.0	1471	1483	95	conclusive
Paracoccus pantotrophus	strain=DSM 2944	GCA_003633525.1	82367	82367	type	True	89.957	955	1483	95	below_threshold
Paracoccus pantotrophus	strain=DSM 2944	GCA_008824185.1	82367	82367	type	True	89.91	954	1483	95	below_threshold
Paracoccus versutus	strain=DSM 582	GCA_003387045.1	34007	34007	type	True	89.6344	992	1483	95	below_threshold
Paracoccus versutus	strain=DSM 582	GCA_000763885.1	34007	34007	type	True	89.587	974	1483	95	below_threshold
Paracoccus denitrificans	strain=DSM 413	GCA_900100045.1	266	266	type	True	89.2476	990	1483	95	below_threshold
Paracoccus denitrificans	strain=NBRC 102528	GCA_007989485.1	266	266	type	True	89.2386	969	1483	95	below_threshold
Paracoccus aminovorans	strain=DSM 8537	GCA_900113565.1	34004	34004	type	True	88.1604	876	1483	95	below_threshold
Paracoccus aminovorans		GCA_900005615.1	34004	34004	type	True	88.1382	887	1483	95	below_threshold
Paracoccus mutanolyticus	strain=RSP-02	GCA_003285265.1	1499308	1499308	type	True	84.9093	729	1483	95	below_threshold
Paracoccus shandongensis	strain=wg2	GCA_017315735.1	2816048	2816048	type	True	81.7813	697	1483	95	below_threshold
Paracoccus salsus	strain=EGI L200073	GCA_021556615.1	2911061	2911061	type	True	80.5076	537	1483	95	below_threshold
Paracoccus everestensis	strain=S8-55	GCA_021491915.1	2903900	2903900	type	True	80.3436	560	1483	95	below_threshold
Paracoccus nototheniae	strain=I-41R45	GCA_004335005.1	2489002	2489002	type	True	79.9145	591	1483	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:39:20,991] [INFO] DFAST Taxonomy check result was written to GCF_016446475.1_ASM1644647v1_genomic.fna/tc_result.tsv
[2024-01-24 14:39:20,991] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:39:20,992] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:39:20,992] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg52d1e61d-3659-45f9-a043-b1dc411e56a9/dqc_reference/checkm_data
[2024-01-24 14:39:20,993] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:39:21,043] [INFO] Task started: CheckM
[2024-01-24 14:39:21,044] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016446475.1_ASM1644647v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016446475.1_ASM1644647v1_genomic.fna/checkm_input GCF_016446475.1_ASM1644647v1_genomic.fna/checkm_result
[2024-01-24 14:40:08,776] [INFO] Task succeeded: CheckM
[2024-01-24 14:40:08,778] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:40:08,798] [INFO] ===== Completeness check finished =====
[2024-01-24 14:40:08,798] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:40:08,799] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016446475.1_ASM1644647v1_genomic.fna/markers.fasta)
[2024-01-24 14:40:08,799] [INFO] Task started: Blastn
[2024-01-24 14:40:08,799] [INFO] Running command: blastn -query GCF_016446475.1_ASM1644647v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg52d1e61d-3659-45f9-a043-b1dc411e56a9/dqc_reference/reference_markers_gtdb.fasta -out GCF_016446475.1_ASM1644647v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:40:11,172] [INFO] Task succeeded: Blastn
[2024-01-24 14:40:11,177] [INFO] Selected 8 target genomes.
[2024-01-24 14:40:11,177] [INFO] Target genome list was writen to GCF_016446475.1_ASM1644647v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:40:11,184] [INFO] Task started: fastANI
[2024-01-24 14:40:11,184] [INFO] Running command: fastANI --query /var/lib/cwl/stga9babb53-021b-410c-9dbe-fd32af5e253a/GCF_016446475.1_ASM1644647v1_genomic.fna.gz --refList GCF_016446475.1_ASM1644647v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016446475.1_ASM1644647v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:40:21,923] [INFO] Task succeeded: fastANI
[2024-01-24 14:40:21,932] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:40:21,932] [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_016446475.1	s__Paracoccus binzhouensis	100.0	1471	1483	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_000518925.1	s__Paracoccus sp000518925	91.5299	960	1483	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	99.13	98.71	0.90	0.89	3	-
GCF_001447385.1	s__Paracoccus sp001447385	90.0941	1020	1483	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	89.8885	955	1483	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	99.22	98.98	0.90	0.84	8	-
GCF_000763885.1	s__Paracoccus versutus	89.5557	977	1483	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	98.67	98.17	0.87	0.76	7	-
GCF_900100045.1	s__Paracoccus denitrificans	89.2235	992	1483	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	99.78	98.70	0.97	0.88	7	-
GCF_001546115.1	s__Paracoccus aminovorans_B	88.598	972	1483	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	95.35	95.35	0.81	0.81	2	-
GCF_900005615.1	s__Paracoccus aminovorans	88.1577	886	1483	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	99.98	99.98	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:40:21,933] [INFO] GTDB search result was written to GCF_016446475.1_ASM1644647v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:40:21,934] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:40:21,937] [INFO] DFAST_QC result json was written to GCF_016446475.1_ASM1644647v1_genomic.fna/dqc_result.json
[2024-01-24 14:40:21,937] [INFO] DFAST_QC completed!
[2024-01-24 14:40:21,937] [INFO] Total running time: 0h1m34s