[2024-01-24 12:57:49,089] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:57:49,091] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:57:49,091] [INFO] DQC Reference Directory: /var/lib/cwl/stg69bd4015-05bb-47d9-aaee-4679081060c8/dqc_reference
[2024-01-24 12:57:50,285] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:57:50,286] [INFO] Task started: Prodigal
[2024-01-24 12:57:50,286] [INFO] Running command: gunzip -c /var/lib/cwl/stg6b11a583-c271-4ff4-b700-6981dc2b5e9a/GCF_900109285.1_IMG-taxon_2622736446_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900109285.1_IMG-taxon_2622736446_annotated_assembly_genomic.fna/cds.fna -a GCF_900109285.1_IMG-taxon_2622736446_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:58:01,356] [INFO] Task succeeded: Prodigal
[2024-01-24 12:58:01,356] [INFO] Task started: HMMsearch
[2024-01-24 12:58:01,356] [INFO] Running command: hmmsearch --tblout GCF_900109285.1_IMG-taxon_2622736446_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg69bd4015-05bb-47d9-aaee-4679081060c8/dqc_reference/reference_markers.hmm GCF_900109285.1_IMG-taxon_2622736446_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:58:01,549] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:58:01,550] [INFO] Found 6/6 markers.
[2024-01-24 12:58:01,578] [INFO] Query marker FASTA was written to GCF_900109285.1_IMG-taxon_2622736446_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 12:58:01,578] [INFO] Task started: Blastn
[2024-01-24 12:58:01,578] [INFO] Running command: blastn -query GCF_900109285.1_IMG-taxon_2622736446_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg69bd4015-05bb-47d9-aaee-4679081060c8/dqc_reference/reference_markers.fasta -out GCF_900109285.1_IMG-taxon_2622736446_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:58:02,379] [INFO] Task succeeded: Blastn
[2024-01-24 12:58:02,382] [INFO] Selected 17 target genomes.
[2024-01-24 12:58:02,382] [INFO] Target genome list was writen to GCF_900109285.1_IMG-taxon_2622736446_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 12:58:02,388] [INFO] Task started: fastANI
[2024-01-24 12:58:02,388] [INFO] Running command: fastANI --query /var/lib/cwl/stg6b11a583-c271-4ff4-b700-6981dc2b5e9a/GCF_900109285.1_IMG-taxon_2622736446_annotated_assembly_genomic.fna.gz --refList GCF_900109285.1_IMG-taxon_2622736446_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900109285.1_IMG-taxon_2622736446_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:58:13,665] [INFO] Task succeeded: fastANI
[2024-01-24 12:58:13,665] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg69bd4015-05bb-47d9-aaee-4679081060c8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:58:13,665] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg69bd4015-05bb-47d9-aaee-4679081060c8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:58:13,678] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:58:13,678] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:58:13,679] [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 helgolandensis	strain=DSM 14858	GCA_900109285.1	188906	188906	type	True	100.0	1178	1181	95	conclusive
Jannaschia rubra	strain=DSM 16279	GCA_900113265.1	282197	282197	type	True	79.47	547	1181	95	below_threshold
Jannaschia pohangensis	strain=DSM 19073	GCA_900113875.1	390807	390807	type	True	79.3726	597	1181	95	below_threshold
Jannaschia rubra	strain=CECT 5088	GCA_001403735.1	282197	282197	type	True	79.3526	554	1181	95	below_threshold
Jannaschia marina	strain=SHC163	GCA_013404595.1	2741674	2741674	type	True	78.9084	568	1181	95	below_threshold
Jannaschia faecimaris	strain=DSM 100420	GCA_900107415.1	1244108	1244108	type	True	78.8556	556	1181	95	below_threshold
Jannaschia formosa	strain=12N15	GCA_003340555.1	2259592	2259592	type	True	78.4402	495	1181	95	below_threshold
Roseovarius indicus	strain=DSM 26383	GCA_008728195.1	540747	540747	type	True	78.3254	257	1181	95	below_threshold
Roseovarius indicus	strain=DSM 26383	GCA_900112725.1	540747	540747	type	True	78.1405	255	1181	95	below_threshold
Roseovarius indicus	strain=B108	GCA_001441635.1	540747	540747	type	True	77.9396	249	1181	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	77.6424	248	1181	95	below_threshold
Cereibacter ovatus	strain=JA234	GCA_900207575.1	439529	439529	type	True	77.4919	246	1181	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	77.4152	270	1181	95	below_threshold
Paracoccus lutimaris	strain=CECT 8525	GCA_003337565.1	1490030	1490030	type	True	77.2286	204	1181	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_019130055.1	2852097	2852097	type	True	77.194	243	1181	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_009908265.2	2852097	2852097	type	True	77.1723	245	1181	95	below_threshold
Mangrovicoccus algicola	strain=HB182678	GCA_014903745.1	2771008	2771008	type	True	77.0912	213	1181	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:58:13,680] [INFO] DFAST Taxonomy check result was written to GCF_900109285.1_IMG-taxon_2622736446_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 12:58:13,681] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:58:13,681] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:58:13,681] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg69bd4015-05bb-47d9-aaee-4679081060c8/dqc_reference/checkm_data
[2024-01-24 12:58:13,682] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:58:13,717] [INFO] Task started: CheckM
[2024-01-24 12:58:13,718] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900109285.1_IMG-taxon_2622736446_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900109285.1_IMG-taxon_2622736446_annotated_assembly_genomic.fna/checkm_input GCF_900109285.1_IMG-taxon_2622736446_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 12:58:48,560] [INFO] Task succeeded: CheckM
[2024-01-24 12:58:48,561] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:58:48,579] [INFO] ===== Completeness check finished =====
[2024-01-24 12:58:48,579] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:58:48,579] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900109285.1_IMG-taxon_2622736446_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 12:58:48,580] [INFO] Task started: Blastn
[2024-01-24 12:58:48,580] [INFO] Running command: blastn -query GCF_900109285.1_IMG-taxon_2622736446_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg69bd4015-05bb-47d9-aaee-4679081060c8/dqc_reference/reference_markers_gtdb.fasta -out GCF_900109285.1_IMG-taxon_2622736446_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:58:50,041] [INFO] Task succeeded: Blastn
[2024-01-24 12:58:50,044] [INFO] Selected 14 target genomes.
[2024-01-24 12:58:50,044] [INFO] Target genome list was writen to GCF_900109285.1_IMG-taxon_2622736446_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:58:50,052] [INFO] Task started: fastANI
[2024-01-24 12:58:50,052] [INFO] Running command: fastANI --query /var/lib/cwl/stg6b11a583-c271-4ff4-b700-6981dc2b5e9a/GCF_900109285.1_IMG-taxon_2622736446_annotated_assembly_genomic.fna.gz --refList GCF_900109285.1_IMG-taxon_2622736446_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900109285.1_IMG-taxon_2622736446_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:58:59,891] [INFO] Task succeeded: fastANI
[2024-01-24 12:58:59,902] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:58:59,903] [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_900109285.1	s__Jannaschia helgolandensis	100.0	1178	1181	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Jannaschia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001403795.1	s__Jannaschia donghaensis	79.5668	612	1181	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	79.3894	595	1181	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Jannaschia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001403735.1	s__Jannaschia rubra	79.3707	552	1181	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Jannaschia	95.0	99.99	99.99	0.99	0.99	2	-
GCF_013404595.1	s__Jannaschia marina	78.9156	568	1181	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Jannaschia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900107415.1	s__Jannaschia faecimaris	78.8639	555	1181	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	78.5629	386	1181	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Jannaschia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003340555.1	s__Jannaschia formosa	78.4565	493	1181	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Jannaschia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013155465.1	s__Alterinioella nitratireducens	77.7596	297	1181	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Alterinioella	95.0	97.91	97.83	0.91	0.91	3	-
GCF_009857745.1	s__Thalassobius mangrovi	77.3424	278	1181	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003337565.1	s__Paracoccus lutimaris	77.2286	204	1181	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001679925.1	s__Leisingera sp001679925	77.0309	201	1181	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000813745.1	s__Leisingera sp000813745	76.7571	181	1181	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015654855.1	s__JAATGA01 sp015654855	75.9967	122	1181	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JAATGA01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:58:59,905] [INFO] GTDB search result was written to GCF_900109285.1_IMG-taxon_2622736446_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 12:58:59,906] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:58:59,910] [INFO] DFAST_QC result json was written to GCF_900109285.1_IMG-taxon_2622736446_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 12:58:59,910] [INFO] DFAST_QC completed!
[2024-01-24 12:58:59,910] [INFO] Total running time: 0h1m11s