[2024-01-25 20:05:20,630] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:05:20,632] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:05:20,632] [INFO] DQC Reference Directory: /var/lib/cwl/stg12857ad6-fc7f-4864-988b-8e3bee478feb/dqc_reference
[2024-01-25 20:05:21,744] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:05:21,745] [INFO] Task started: Prodigal
[2024-01-25 20:05:21,745] [INFO] Running command: gunzip -c /var/lib/cwl/stga1377582-e628-4f08-b778-eae0d72fb05d/GCF_900110285.1_IMG-taxon_2636415977_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900110285.1_IMG-taxon_2636415977_annotated_assembly_genomic.fna/cds.fna -a GCF_900110285.1_IMG-taxon_2636415977_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:05:33,847] [INFO] Task succeeded: Prodigal
[2024-01-25 20:05:33,848] [INFO] Task started: HMMsearch
[2024-01-25 20:05:33,848] [INFO] Running command: hmmsearch --tblout GCF_900110285.1_IMG-taxon_2636415977_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg12857ad6-fc7f-4864-988b-8e3bee478feb/dqc_reference/reference_markers.hmm GCF_900110285.1_IMG-taxon_2636415977_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:05:34,148] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:05:34,149] [INFO] Found 6/6 markers.
[2024-01-25 20:05:34,188] [INFO] Query marker FASTA was written to GCF_900110285.1_IMG-taxon_2636415977_annotated_assembly_genomic.fna/markers.fasta
[2024-01-25 20:05:34,188] [INFO] Task started: Blastn
[2024-01-25 20:05:34,188] [INFO] Running command: blastn -query GCF_900110285.1_IMG-taxon_2636415977_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg12857ad6-fc7f-4864-988b-8e3bee478feb/dqc_reference/reference_markers.fasta -out GCF_900110285.1_IMG-taxon_2636415977_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:05:35,164] [INFO] Task succeeded: Blastn
[2024-01-25 20:05:35,167] [INFO] Selected 17 target genomes.
[2024-01-25 20:05:35,167] [INFO] Target genome list was writen to GCF_900110285.1_IMG-taxon_2636415977_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-25 20:05:35,172] [INFO] Task started: fastANI
[2024-01-25 20:05:35,172] [INFO] Running command: fastANI --query /var/lib/cwl/stga1377582-e628-4f08-b778-eae0d72fb05d/GCF_900110285.1_IMG-taxon_2636415977_annotated_assembly_genomic.fna.gz --refList GCF_900110285.1_IMG-taxon_2636415977_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900110285.1_IMG-taxon_2636415977_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:05:49,897] [INFO] Task succeeded: fastANI
[2024-01-25 20:05:49,897] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg12857ad6-fc7f-4864-988b-8e3bee478feb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:05:49,897] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg12857ad6-fc7f-4864-988b-8e3bee478feb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:05:49,908] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:05:49,909] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:05:49,909] [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 alcaliphilus	strain=DSM 8512	GCA_900110285.1	34002	34002	type	True	100.0	1461	1468	95	conclusive
Paracoccus siganidrum	strain=DSM 26381	GCA_003594835.1	1276757	1276757	type	True	85.5529	915	1468	95	below_threshold
Paracoccus siganidrum	strain=M26	GCA_003709565.1	1276757	1276757	type	True	85.5374	977	1468	95	below_threshold
Paracoccus shandongensis	strain=wg2	GCA_017315735.1	2816048	2816048	type	True	82.1319	672	1468	95	below_threshold
Paracoccus lichenicola	strain=YIM 132242	GCA_009708075.1	2665644	2665644	type	True	82.0186	656	1468	95	below_threshold
Paracoccus fontiphilus	strain=MVW-1	GCA_017356265.1	1815556	1815556	type	True	81.7286	667	1468	95	below_threshold
Paracoccus aerius	strain=KCTC 42845	GCA_016757275.1	1915382	1915382	type	True	81.5749	663	1468	95	below_threshold
Paracoccus aerius	strain=KCTC 42845	GCA_014656455.1	1915382	1915382	type	True	81.5583	666	1468	95	below_threshold
Paracoccus caeni	strain=MJ17	GCA_016629665.1	657651	657651	type	True	81.4155	691	1468	95	below_threshold
Paracoccus homiensis	strain=DSM 17862	GCA_900111675.1	364199	364199	type	True	81.3752	645	1468	95	below_threshold
Paracoccus everestensis	strain=S8-55	GCA_021491915.1	2903900	2903900	type	True	81.3538	599	1468	95	below_threshold
Paracoccus versutus	strain=DSM 582	GCA_000763885.1	34007	34007	type	True	81.2671	756	1468	95	below_threshold
Paracoccus zeaxanthinifaciens	strain=ATCC 21588	GCA_000420145.1	187400	187400	type	True	81.2109	585	1468	95	below_threshold
Paracoccus salsus	strain=EGI L200073	GCA_021556615.1	2911061	2911061	type	True	81.2053	590	1468	95	below_threshold
Paracoccus zhejiangensis	strain=J6	GCA_002847445.1	1077935	1077935	type	True	80.9997	709	1468	95	below_threshold
Paracoccus tegillarcae	strain=BM15	GCA_002847305.1	1529068	1529068	type	True	80.0079	554	1468	95	below_threshold
Paracoccus onubensis	strain=1011MAR3C25	GCA_003591515.1	1675788	1675788	type	True	79.921	583	1468	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:05:49,910] [INFO] DFAST Taxonomy check result was written to GCF_900110285.1_IMG-taxon_2636415977_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-25 20:05:49,912] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:05:49,912] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:05:49,912] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg12857ad6-fc7f-4864-988b-8e3bee478feb/dqc_reference/checkm_data
[2024-01-25 20:05:49,913] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:05:49,956] [INFO] Task started: CheckM
[2024-01-25 20:05:49,956] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900110285.1_IMG-taxon_2636415977_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900110285.1_IMG-taxon_2636415977_annotated_assembly_genomic.fna/checkm_input GCF_900110285.1_IMG-taxon_2636415977_annotated_assembly_genomic.fna/checkm_result
[2024-01-25 20:06:36,511] [INFO] Task succeeded: CheckM
[2024-01-25 20:06:36,512] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:06:36,555] [INFO] ===== Completeness check finished =====
[2024-01-25 20:06:36,555] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:06:36,556] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900110285.1_IMG-taxon_2636415977_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-25 20:06:36,556] [INFO] Task started: Blastn
[2024-01-25 20:06:36,556] [INFO] Running command: blastn -query GCF_900110285.1_IMG-taxon_2636415977_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg12857ad6-fc7f-4864-988b-8e3bee478feb/dqc_reference/reference_markers_gtdb.fasta -out GCF_900110285.1_IMG-taxon_2636415977_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:06:38,420] [INFO] Task succeeded: Blastn
[2024-01-25 20:06:38,424] [INFO] Selected 12 target genomes.
[2024-01-25 20:06:38,424] [INFO] Target genome list was writen to GCF_900110285.1_IMG-taxon_2636415977_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:06:38,427] [INFO] Task started: fastANI
[2024-01-25 20:06:38,427] [INFO] Running command: fastANI --query /var/lib/cwl/stga1377582-e628-4f08-b778-eae0d72fb05d/GCF_900110285.1_IMG-taxon_2636415977_annotated_assembly_genomic.fna.gz --refList GCF_900110285.1_IMG-taxon_2636415977_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900110285.1_IMG-taxon_2636415977_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:06:49,362] [INFO] Task succeeded: fastANI
[2024-01-25 20:06:49,370] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:06:49,370] [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_900110285.1	s__Paracoccus alcaliphilus	100.0	1461	1468	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_003709565.1	s__Paracoccus siganidrum	85.5636	975	1468	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	99.99	99.99	0.98	0.98	2	-
GCF_018860165.1	s__Paracoccus sp018860165	82.5236	711	1468	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	82.337	707	1468	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003007735.2	s__Paracoccus marinus_A	81.6582	653	1468	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002294185.1	s__Paracoccus sp002294185	81.5992	585	1468	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	99.77	99.74	0.93	0.89	5	-
GCF_016629665.1	s__Paracoccus caeni	81.4112	692	1468	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	81.4102	642	1468	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017744015.1	s__Paracoccus sp002732665	81.3257	643	1468	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	99.29	98.58	0.98	0.95	3	-
GCF_000420145.1	s__Paracoccus zeaxanthinifaciens	81.2345	583	1468	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003697785.1	s__Paracoccus alkanivorans	81.2006	645	1468	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002847445.1	s__Paracoccus zhejiangensis	80.9579	714	1468	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 20:06:49,372] [INFO] GTDB search result was written to GCF_900110285.1_IMG-taxon_2636415977_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-25 20:06:49,372] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:06:49,377] [INFO] DFAST_QC result json was written to GCF_900110285.1_IMG-taxon_2636415977_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-25 20:06:49,377] [INFO] DFAST_QC completed!
[2024-01-25 20:06:49,377] [INFO] Total running time: 0h1m29s