[2024-01-24 10:47:40,963] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:47:40,969] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:47:40,969] [INFO] DQC Reference Directory: /var/lib/cwl/stg0b1fb552-cded-483a-a5e1-4f8d0b3c0fbc/dqc_reference
[2024-01-24 10:47:44,787] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:47:44,789] [INFO] Task started: Prodigal
[2024-01-24 10:47:44,790] [INFO] Running command: gunzip -c /var/lib/cwl/stgbf34f40e-d90a-4ce6-8f74-861eed7681c9/GCF_016919705.1_ASM1691970v1_genomic.fna.gz | prodigal -d GCF_016919705.1_ASM1691970v1_genomic.fna/cds.fna -a GCF_016919705.1_ASM1691970v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:47:58,631] [INFO] Task succeeded: Prodigal
[2024-01-24 10:47:58,632] [INFO] Task started: HMMsearch
[2024-01-24 10:47:58,632] [INFO] Running command: hmmsearch --tblout GCF_016919705.1_ASM1691970v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0b1fb552-cded-483a-a5e1-4f8d0b3c0fbc/dqc_reference/reference_markers.hmm GCF_016919705.1_ASM1691970v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:47:58,910] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:47:58,911] [INFO] Found 6/6 markers.
[2024-01-24 10:47:58,960] [INFO] Query marker FASTA was written to GCF_016919705.1_ASM1691970v1_genomic.fna/markers.fasta
[2024-01-24 10:47:58,960] [INFO] Task started: Blastn
[2024-01-24 10:47:58,961] [INFO] Running command: blastn -query GCF_016919705.1_ASM1691970v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0b1fb552-cded-483a-a5e1-4f8d0b3c0fbc/dqc_reference/reference_markers.fasta -out GCF_016919705.1_ASM1691970v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:47:59,888] [INFO] Task succeeded: Blastn
[2024-01-24 10:47:59,892] [INFO] Selected 13 target genomes.
[2024-01-24 10:47:59,893] [INFO] Target genome list was writen to GCF_016919705.1_ASM1691970v1_genomic.fna/target_genomes.txt
[2024-01-24 10:47:59,910] [INFO] Task started: fastANI
[2024-01-24 10:47:59,910] [INFO] Running command: fastANI --query /var/lib/cwl/stgbf34f40e-d90a-4ce6-8f74-861eed7681c9/GCF_016919705.1_ASM1691970v1_genomic.fna.gz --refList GCF_016919705.1_ASM1691970v1_genomic.fna/target_genomes.txt --output GCF_016919705.1_ASM1691970v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:48:11,998] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:11,999] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0b1fb552-cded-483a-a5e1-4f8d0b3c0fbc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:48:12,000] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0b1fb552-cded-483a-a5e1-4f8d0b3c0fbc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:48:12,015] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 10:48:12,015] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 10:48:12,016] [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 denitrificans	strain=NBRC 102528	GCA_007989485.1	266	266	type	True	87.1627	1048	1457	95	below_threshold
Paracoccus denitrificans	strain=DSM 413	GCA_900100045.1	266	266	type	True	87.1548	1073	1457	95	below_threshold
Paracoccus pantotrophus	strain=DSM 2944	GCA_003633525.1	82367	82367	type	True	86.4569	977	1457	95	below_threshold
Paracoccus pantotrophus	strain=DSM 2944	GCA_008824185.1	82367	82367	type	True	86.4473	984	1457	95	below_threshold
Paracoccus versutus	strain=DSM 582	GCA_003387045.1	34007	34007	type	True	86.3223	1019	1457	95	below_threshold
Paracoccus versutus	strain=DSM 582	GCA_000763885.1	34007	34007	type	True	86.319	986	1457	95	below_threshold
Paracoccus thiocyanatus	strain=ATCC 700171	GCA_900156255.1	34006	34006	type	True	85.5043	850	1457	95	below_threshold
Paracoccus binzhouensis	strain=wg1	GCA_016446475.1	2796149	2796149	type	True	84.91	844	1457	95	below_threshold
Paracoccus mutanolyticus	strain=RSP-02	GCA_003285265.1	1499308	1499308	type	True	82.0745	708	1457	95	below_threshold
Paracoccus shandongensis	strain=wg2	GCA_017315735.1	2816048	2816048	type	True	79.4657	573	1457	95	below_threshold
Paracoccus nototheniae	strain=I-41R45	GCA_004335005.1	2489002	2489002	type	True	78.9629	515	1457	95	below_threshold
Paracoccus salsus	strain=EGI L200073	GCA_021556615.1	2911061	2911061	type	True	78.8144	471	1457	95	below_threshold
Paracoccus tegillarcae	strain=BM15	GCA_002847305.1	1529068	1529068	type	True	78.5128	454	1457	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:48:12,017] [INFO] DFAST Taxonomy check result was written to GCF_016919705.1_ASM1691970v1_genomic.fna/tc_result.tsv
[2024-01-24 10:48:12,018] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:48:12,018] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:48:12,018] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0b1fb552-cded-483a-a5e1-4f8d0b3c0fbc/dqc_reference/checkm_data
[2024-01-24 10:48:12,019] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:48:12,059] [INFO] Task started: CheckM
[2024-01-24 10:48:12,059] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016919705.1_ASM1691970v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016919705.1_ASM1691970v1_genomic.fna/checkm_input GCF_016919705.1_ASM1691970v1_genomic.fna/checkm_result
[2024-01-24 10:48:56,546] [INFO] Task succeeded: CheckM
[2024-01-24 10:48:56,548] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:48:56,571] [INFO] ===== Completeness check finished =====
[2024-01-24 10:48:56,571] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:48:56,572] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016919705.1_ASM1691970v1_genomic.fna/markers.fasta)
[2024-01-24 10:48:56,572] [INFO] Task started: Blastn
[2024-01-24 10:48:56,572] [INFO] Running command: blastn -query GCF_016919705.1_ASM1691970v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0b1fb552-cded-483a-a5e1-4f8d0b3c0fbc/dqc_reference/reference_markers_gtdb.fasta -out GCF_016919705.1_ASM1691970v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:48:58,232] [INFO] Task succeeded: Blastn
[2024-01-24 10:48:58,238] [INFO] Selected 8 target genomes.
[2024-01-24 10:48:58,238] [INFO] Target genome list was writen to GCF_016919705.1_ASM1691970v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:48:58,245] [INFO] Task started: fastANI
[2024-01-24 10:48:58,245] [INFO] Running command: fastANI --query /var/lib/cwl/stgbf34f40e-d90a-4ce6-8f74-861eed7681c9/GCF_016919705.1_ASM1691970v1_genomic.fna.gz --refList GCF_016919705.1_ASM1691970v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016919705.1_ASM1691970v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:49:06,968] [INFO] Task succeeded: fastANI
[2024-01-24 10:49:06,981] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:49:06,981] [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_016919705.1	s__Paracoccus sp002359815	100.0	1456	1457	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	98.20	98.20	0.92	0.92	2	conclusive
GCF_900100045.1	s__Paracoccus denitrificans	87.1548	1073	1457	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	99.78	98.70	0.97	0.88	7	-
GCF_008824185.1	s__Paracoccus pantotrophus	86.3918	982	1457	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	86.32	984	1457	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	98.67	98.17	0.87	0.76	7	-
GCF_001447385.1	s__Paracoccus sp001447385	86.2491	988	1457	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000518925.1	s__Paracoccus sp000518925	85.9891	937	1457	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	99.13	98.71	0.90	0.89	3	-
GCF_900156255.1	s__Paracoccus thiocyanatus	85.5249	848	1457	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	97.14	97.14	0.86	0.86	2	-
GCF_016446475.1	s__Paracoccus binzhouensis	84.8915	844	1457	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 10:49:06,983] [INFO] GTDB search result was written to GCF_016919705.1_ASM1691970v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:49:06,983] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:49:06,986] [INFO] DFAST_QC result json was written to GCF_016919705.1_ASM1691970v1_genomic.fna/dqc_result.json
[2024-01-24 10:49:06,986] [INFO] DFAST_QC completed!
[2024-01-24 10:49:06,986] [INFO] Total running time: 0h1m26s