[2024-01-25 19:58:35,667] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:58:35,668] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:58:35,668] [INFO] DQC Reference Directory: /var/lib/cwl/stge33faeae-640f-45f7-b6fc-2baabefdd002/dqc_reference
[2024-01-25 19:58:36,794] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:58:36,795] [INFO] Task started: Prodigal
[2024-01-25 19:58:36,795] [INFO] Running command: gunzip -c /var/lib/cwl/stg9fbdd83a-6cfe-4c27-b319-5eacf4416c39/GCF_001403735.1_J.rubraCECT5088_SeqMan_Prokka_genomic.fna.gz | prodigal -d GCF_001403735.1_J.rubraCECT5088_SeqMan_Prokka_genomic.fna/cds.fna -a GCF_001403735.1_J.rubraCECT5088_SeqMan_Prokka_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:58:46,238] [INFO] Task succeeded: Prodigal
[2024-01-25 19:58:46,238] [INFO] Task started: HMMsearch
[2024-01-25 19:58:46,238] [INFO] Running command: hmmsearch --tblout GCF_001403735.1_J.rubraCECT5088_SeqMan_Prokka_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge33faeae-640f-45f7-b6fc-2baabefdd002/dqc_reference/reference_markers.hmm GCF_001403735.1_J.rubraCECT5088_SeqMan_Prokka_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:58:46,456] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:58:46,457] [INFO] Found 6/6 markers.
[2024-01-25 19:58:46,489] [INFO] Query marker FASTA was written to GCF_001403735.1_J.rubraCECT5088_SeqMan_Prokka_genomic.fna/markers.fasta
[2024-01-25 19:58:46,489] [INFO] Task started: Blastn
[2024-01-25 19:58:46,489] [INFO] Running command: blastn -query GCF_001403735.1_J.rubraCECT5088_SeqMan_Prokka_genomic.fna/markers.fasta -db /var/lib/cwl/stge33faeae-640f-45f7-b6fc-2baabefdd002/dqc_reference/reference_markers.fasta -out GCF_001403735.1_J.rubraCECT5088_SeqMan_Prokka_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:58:47,409] [INFO] Task succeeded: Blastn
[2024-01-25 19:58:47,412] [INFO] Selected 16 target genomes.
[2024-01-25 19:58:47,412] [INFO] Target genome list was writen to GCF_001403735.1_J.rubraCECT5088_SeqMan_Prokka_genomic.fna/target_genomes.txt
[2024-01-25 19:58:47,422] [INFO] Task started: fastANI
[2024-01-25 19:58:47,422] [INFO] Running command: fastANI --query /var/lib/cwl/stg9fbdd83a-6cfe-4c27-b319-5eacf4416c39/GCF_001403735.1_J.rubraCECT5088_SeqMan_Prokka_genomic.fna.gz --refList GCF_001403735.1_J.rubraCECT5088_SeqMan_Prokka_genomic.fna/target_genomes.txt --output GCF_001403735.1_J.rubraCECT5088_SeqMan_Prokka_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:59:01,048] [INFO] Task succeeded: fastANI
[2024-01-25 19:59:01,048] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge33faeae-640f-45f7-b6fc-2baabefdd002/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:59:01,048] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge33faeae-640f-45f7-b6fc-2baabefdd002/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:59:01,061] [INFO] Found 16 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 19:59:01,061] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:59:01,061] [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
Jannaschia rubra	strain=CECT 5088	GCA_001403735.1	282197	282197	type	True	100.0	1208	1209	95	conclusive
Jannaschia rubra	strain=DSM 16279	GCA_900113265.1	282197	282197	type	True	99.9893	1164	1209	95	conclusive
Jannaschia formosa	strain=12N15	GCA_003340555.1	2259592	2259592	type	True	80.1042	664	1209	95	below_threshold
Jannaschia pohangensis	strain=DSM 19073	GCA_900113875.1	390807	390807	type	True	80.0371	633	1209	95	below_threshold
Jannaschia marina	strain=SHC163	GCA_013404595.1	2741674	2741674	type	True	80.0343	650	1209	95	below_threshold
Jannaschia helgolandensis	strain=DSM 14858	GCA_900109285.1	188906	188906	type	True	79.2922	571	1209	95	below_threshold
Jannaschia seohaensis	strain=DSM 25227	GCA_900116765.1	475081	475081	type	True	79.1804	570	1209	95	below_threshold
Jannaschia seohaensis	strain=DSM 25227	GCA_003149265.1	475081	475081	type	True	79.1769	571	1209	95	below_threshold
Palleronia rufa	strain=MOLA 401	GCA_000743715.1	1530186	1530186	type	True	78.5181	384	1209	95	below_threshold
Wenxinia saemankumensis	strain=DSM 100565	GCA_900141735.1	1447782	1447782	type	True	77.8687	411	1209	95	below_threshold
Paracoccus gahaiensis	strain=KCTC 42687	GCA_005048225.1	1706839	1706839	type	True	77.7592	371	1209	95	below_threshold
Cereibacter ovatus	strain=JA234	GCA_900207575.1	439529	439529	type	True	77.5973	342	1209	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_019130055.1	2852097	2852097	type	True	77.4503	345	1209	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_009908265.2	2852097	2852097	type	True	77.4421	346	1209	95	below_threshold
Rhodobacter ruber	strain=CCP-1	GCA_009908315.1	1985673	1985673	type	True	77.1102	321	1209	95	below_threshold
Phaeovulum veldkampii	strain=DSM 11550	GCA_003034995.1	33049	33049	type	True	76.9172	251	1209	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:59:01,065] [INFO] DFAST Taxonomy check result was written to GCF_001403735.1_J.rubraCECT5088_SeqMan_Prokka_genomic.fna/tc_result.tsv
[2024-01-25 19:59:01,066] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:59:01,067] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:59:01,067] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge33faeae-640f-45f7-b6fc-2baabefdd002/dqc_reference/checkm_data
[2024-01-25 19:59:01,068] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:59:01,116] [INFO] Task started: CheckM
[2024-01-25 19:59:01,117] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001403735.1_J.rubraCECT5088_SeqMan_Prokka_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001403735.1_J.rubraCECT5088_SeqMan_Prokka_genomic.fna/checkm_input GCF_001403735.1_J.rubraCECT5088_SeqMan_Prokka_genomic.fna/checkm_result
[2024-01-25 19:59:39,161] [INFO] Task succeeded: CheckM
[2024-01-25 19:59:39,162] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:59:39,214] [INFO] ===== Completeness check finished =====
[2024-01-25 19:59:39,214] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:59:39,215] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001403735.1_J.rubraCECT5088_SeqMan_Prokka_genomic.fna/markers.fasta)
[2024-01-25 19:59:39,215] [INFO] Task started: Blastn
[2024-01-25 19:59:39,215] [INFO] Running command: blastn -query GCF_001403735.1_J.rubraCECT5088_SeqMan_Prokka_genomic.fna/markers.fasta -db /var/lib/cwl/stge33faeae-640f-45f7-b6fc-2baabefdd002/dqc_reference/reference_markers_gtdb.fasta -out GCF_001403735.1_J.rubraCECT5088_SeqMan_Prokka_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:59:41,174] [INFO] Task succeeded: Blastn
[2024-01-25 19:59:41,177] [INFO] Selected 13 target genomes.
[2024-01-25 19:59:41,177] [INFO] Target genome list was writen to GCF_001403735.1_J.rubraCECT5088_SeqMan_Prokka_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:59:41,196] [INFO] Task started: fastANI
[2024-01-25 19:59:41,196] [INFO] Running command: fastANI --query /var/lib/cwl/stg9fbdd83a-6cfe-4c27-b319-5eacf4416c39/GCF_001403735.1_J.rubraCECT5088_SeqMan_Prokka_genomic.fna.gz --refList GCF_001403735.1_J.rubraCECT5088_SeqMan_Prokka_genomic.fna/target_genomes_gtdb.txt --output GCF_001403735.1_J.rubraCECT5088_SeqMan_Prokka_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:59:51,729] [INFO] Task succeeded: fastANI
[2024-01-25 19:59:51,737] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:59:51,738] [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_001403735.1	s__Jannaschia rubra	100.0	1208	1209	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Jannaschia	95.0	99.99	99.99	0.99	0.99	2	conclusive
GCF_003340555.1	s__Jannaschia formosa	80.1054	663	1209	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Jannaschia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013404595.1	s__Jannaschia marina	80.0474	648	1209	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Jannaschia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900113875.1	s__Jannaschia pohangensis	80.0423	632	1209	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Jannaschia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001408515.1	s__Jannaschia seosinensis	79.8482	532	1209	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Jannaschia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001403795.1	s__Jannaschia donghaensis	79.5055	589	1209	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Jannaschia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109285.1	s__Jannaschia helgolandensis	79.2923	571	1209	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Jannaschia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900116765.1	s__Jannaschia seohaensis	79.1884	569	1209	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Jannaschia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900107415.1	s__Jannaschia faecimaris	78.6184	514	1209	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Jannaschia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900141735.1	s__Wenxinia saemankumensis	77.8468	413	1209	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Wenxinia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005048225.1	s__Paracoccus gahaiensis	77.7573	372	1209	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004005435.1	s__CCMM004 sp004005435	77.7465	442	1209	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__CCMM004	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003034995.1	s__Phaeovulum veldkampii	76.9189	252	1209	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Phaeovulum	95.0	99.98	99.97	0.97	0.94	3	-
--------------------------------------------------------------------------------
[2024-01-25 19:59:51,739] [INFO] GTDB search result was written to GCF_001403735.1_J.rubraCECT5088_SeqMan_Prokka_genomic.fna/result_gtdb.tsv
[2024-01-25 19:59:51,740] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:59:51,746] [INFO] DFAST_QC result json was written to GCF_001403735.1_J.rubraCECT5088_SeqMan_Prokka_genomic.fna/dqc_result.json
[2024-01-25 19:59:51,746] [INFO] DFAST_QC completed!
[2024-01-25 19:59:51,746] [INFO] Total running time: 0h1m16s