[2024-01-24 15:06:36,949] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:06:36,950] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:06:36,951] [INFO] DQC Reference Directory: /var/lib/cwl/stged9319a1-00a0-4e75-baee-42b6d25cdfe3/dqc_reference
[2024-01-24 15:06:38,300] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:06:38,301] [INFO] Task started: Prodigal
[2024-01-24 15:06:38,301] [INFO] Running command: gunzip -c /var/lib/cwl/stg0c21cd33-4c77-4625-b5df-139866c957ec/GCF_002105555.1_ASM210555v1_genomic.fna.gz | prodigal -d GCF_002105555.1_ASM210555v1_genomic.fna/cds.fna -a GCF_002105555.1_ASM210555v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:06:48,161] [INFO] Task succeeded: Prodigal
[2024-01-24 15:06:48,161] [INFO] Task started: HMMsearch
[2024-01-24 15:06:48,161] [INFO] Running command: hmmsearch --tblout GCF_002105555.1_ASM210555v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stged9319a1-00a0-4e75-baee-42b6d25cdfe3/dqc_reference/reference_markers.hmm GCF_002105555.1_ASM210555v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:06:48,428] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:06:48,429] [INFO] Found 6/6 markers.
[2024-01-24 15:06:48,468] [INFO] Query marker FASTA was written to GCF_002105555.1_ASM210555v1_genomic.fna/markers.fasta
[2024-01-24 15:06:48,468] [INFO] Task started: Blastn
[2024-01-24 15:06:48,468] [INFO] Running command: blastn -query GCF_002105555.1_ASM210555v1_genomic.fna/markers.fasta -db /var/lib/cwl/stged9319a1-00a0-4e75-baee-42b6d25cdfe3/dqc_reference/reference_markers.fasta -out GCF_002105555.1_ASM210555v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:06:49,538] [INFO] Task succeeded: Blastn
[2024-01-24 15:06:49,541] [INFO] Selected 15 target genomes.
[2024-01-24 15:06:49,542] [INFO] Target genome list was writen to GCF_002105555.1_ASM210555v1_genomic.fna/target_genomes.txt
[2024-01-24 15:06:49,549] [INFO] Task started: fastANI
[2024-01-24 15:06:49,549] [INFO] Running command: fastANI --query /var/lib/cwl/stg0c21cd33-4c77-4625-b5df-139866c957ec/GCF_002105555.1_ASM210555v1_genomic.fna.gz --refList GCF_002105555.1_ASM210555v1_genomic.fna/target_genomes.txt --output GCF_002105555.1_ASM210555v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:07:02,202] [INFO] Task succeeded: fastANI
[2024-01-24 15:07:02,202] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stged9319a1-00a0-4e75-baee-42b6d25cdfe3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:07:02,203] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stged9319a1-00a0-4e75-baee-42b6d25cdfe3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:07:02,221] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:07:02,221] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:07:02,221] [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 contaminans	strain=RKI 16-01929T=LMG 29738T=CCM 8701T=CIP 111112T	GCA_002105555.1	1945662	1945662	type	True	100.0	1009	1010	95	conclusive
Paracoccus sphaerophysae	strain=HAMBI 3106	GCA_000763805.1	690417	690417	type	True	83.7482	680	1010	95	below_threshold
Paracoccus luteus	strain=CFH 10530	GCA_004522155.1	2508543	2508543	type	True	82.9536	660	1010	95	below_threshold
Paracoccus sanguinis	strain=DSM 29303	GCA_900106665.1	1545044	1545044	type	True	82.7479	705	1010	95	below_threshold
Paracoccus endophyticus	strain=SYSUP0003	GCA_003286075.1	2233774	2233774	type	True	82.225	645	1010	95	below_threshold
Paracoccus solventivorans	strain=DSM 6637	GCA_900142875.1	53463	53463	type	True	82.0544	602	1010	95	below_threshold
Paracoccus salipaludis	strain=WN007	GCA_002287065.1	2032623	2032623	type	True	81.9	646	1010	95	below_threshold
Paracoccus chinensis	strain=CGMCC 1.7655	GCA_900102885.1	525640	525640	type	True	81.885	637	1010	95	below_threshold
Paracoccus aeridis	strain=JC501	GCA_004923205.2	1966466	1966466	type	True	81.022	581	1010	95	below_threshold
Paracoccus binzhouensis	strain=wg1	GCA_016446475.1	2796149	2796149	type	True	80.8476	582	1010	95	below_threshold
Paracoccus mutanolyticus	strain=RSP-02	GCA_003285265.1	1499308	1499308	type	True	80.426	520	1010	95	below_threshold
Paracoccus shandongensis	strain=wg2	GCA_017315735.1	2816048	2816048	type	True	80.2376	520	1010	95	below_threshold
Paracoccus everestensis	strain=S8-55	GCA_021491915.1	2903900	2903900	type	True	79.5735	438	1010	95	below_threshold
Paracoccus nototheniae	strain=I-41R45	GCA_004335005.1	2489002	2489002	type	True	79.4446	467	1010	95	below_threshold
Paracoccus tegillarcae	strain=BM15	GCA_002847305.1	1529068	1529068	type	True	78.2782	405	1010	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:07:02,223] [INFO] DFAST Taxonomy check result was written to GCF_002105555.1_ASM210555v1_genomic.fna/tc_result.tsv
[2024-01-24 15:07:02,223] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:07:02,224] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:07:02,224] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stged9319a1-00a0-4e75-baee-42b6d25cdfe3/dqc_reference/checkm_data
[2024-01-24 15:07:02,225] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:07:02,255] [INFO] Task started: CheckM
[2024-01-24 15:07:02,255] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002105555.1_ASM210555v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002105555.1_ASM210555v1_genomic.fna/checkm_input GCF_002105555.1_ASM210555v1_genomic.fna/checkm_result
[2024-01-24 15:07:39,575] [INFO] Task succeeded: CheckM
[2024-01-24 15:07:39,577] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:07:39,599] [INFO] ===== Completeness check finished =====
[2024-01-24 15:07:39,600] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:07:39,600] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002105555.1_ASM210555v1_genomic.fna/markers.fasta)
[2024-01-24 15:07:39,601] [INFO] Task started: Blastn
[2024-01-24 15:07:39,601] [INFO] Running command: blastn -query GCF_002105555.1_ASM210555v1_genomic.fna/markers.fasta -db /var/lib/cwl/stged9319a1-00a0-4e75-baee-42b6d25cdfe3/dqc_reference/reference_markers_gtdb.fasta -out GCF_002105555.1_ASM210555v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:07:41,561] [INFO] Task succeeded: Blastn
[2024-01-24 15:07:41,566] [INFO] Selected 11 target genomes.
[2024-01-24 15:07:41,567] [INFO] Target genome list was writen to GCF_002105555.1_ASM210555v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:07:41,589] [INFO] Task started: fastANI
[2024-01-24 15:07:41,590] [INFO] Running command: fastANI --query /var/lib/cwl/stg0c21cd33-4c77-4625-b5df-139866c957ec/GCF_002105555.1_ASM210555v1_genomic.fna.gz --refList GCF_002105555.1_ASM210555v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002105555.1_ASM210555v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:07:51,098] [INFO] Task succeeded: fastANI
[2024-01-24 15:07:51,108] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:07:51,108] [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_002105555.1	s__Paracoccus contaminans	100.0	1009	1010	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_000763805.1	s__Paracoccus sphaerophysae	83.7527	680	1010	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004522155.1	s__Paracoccus luteus	82.9572	660	1010	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900106665.1	s__Paracoccus sanguinis	82.7677	704	1010	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	97.10	96.00	0.89	0.81	6	-
GCF_003286075.1	s__Paracoccus endophyticus	82.2249	645	1010	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142875.1	s__Paracoccus solventivorans	82.0725	600	1010	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	96.61	95.99	0.87	0.87	3	-
GCF_002287065.1	s__Paracoccus salipaludis	81.9247	642	1010	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102885.1	s__Paracoccus chinensis	81.8849	637	1010	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007018965.1	s__Paracoccus marinus	81.7681	607	1010	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004923205.2	s__Paracoccus aeridis	81.0116	582	1010	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016446475.1	s__Paracoccus binzhouensis	80.8136	583	1010	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 15:07:51,110] [INFO] GTDB search result was written to GCF_002105555.1_ASM210555v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:07:51,110] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:07:51,114] [INFO] DFAST_QC result json was written to GCF_002105555.1_ASM210555v1_genomic.fna/dqc_result.json
[2024-01-24 15:07:51,114] [INFO] DFAST_QC completed!
[2024-01-24 15:07:51,114] [INFO] Total running time: 0h1m14s