[2024-01-24 14:19:46,178] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:19:46,192] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:19:46,192] [INFO] DQC Reference Directory: /var/lib/cwl/stg1419d106-55cd-4960-b85b-92b3205b324f/dqc_reference
[2024-01-24 14:19:47,548] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:19:47,549] [INFO] Task started: Prodigal
[2024-01-24 14:19:47,549] [INFO] Running command: gunzip -c /var/lib/cwl/stg6e64ff6e-8b4f-435a-8557-4c1a9c6ed59a/GCF_000420745.1_ASM42074v1_genomic.fna.gz | prodigal -d GCF_000420745.1_ASM42074v1_genomic.fna/cds.fna -a GCF_000420745.1_ASM42074v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:19:59,257] [INFO] Task succeeded: Prodigal
[2024-01-24 14:19:59,257] [INFO] Task started: HMMsearch
[2024-01-24 14:19:59,257] [INFO] Running command: hmmsearch --tblout GCF_000420745.1_ASM42074v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1419d106-55cd-4960-b85b-92b3205b324f/dqc_reference/reference_markers.hmm GCF_000420745.1_ASM42074v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:19:59,525] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:19:59,527] [INFO] Found 6/6 markers.
[2024-01-24 14:19:59,571] [INFO] Query marker FASTA was written to GCF_000420745.1_ASM42074v1_genomic.fna/markers.fasta
[2024-01-24 14:19:59,571] [INFO] Task started: Blastn
[2024-01-24 14:19:59,571] [INFO] Running command: blastn -query GCF_000420745.1_ASM42074v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1419d106-55cd-4960-b85b-92b3205b324f/dqc_reference/reference_markers.fasta -out GCF_000420745.1_ASM42074v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:20:00,442] [INFO] Task succeeded: Blastn
[2024-01-24 14:20:00,445] [INFO] Selected 13 target genomes.
[2024-01-24 14:20:00,445] [INFO] Target genome list was writen to GCF_000420745.1_ASM42074v1_genomic.fna/target_genomes.txt
[2024-01-24 14:20:00,494] [INFO] Task started: fastANI
[2024-01-24 14:20:00,495] [INFO] Running command: fastANI --query /var/lib/cwl/stg6e64ff6e-8b4f-435a-8557-4c1a9c6ed59a/GCF_000420745.1_ASM42074v1_genomic.fna.gz --refList GCF_000420745.1_ASM42074v1_genomic.fna/target_genomes.txt --output GCF_000420745.1_ASM42074v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:20:10,755] [INFO] Task succeeded: fastANI
[2024-01-24 14:20:10,755] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1419d106-55cd-4960-b85b-92b3205b324f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:20:10,756] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1419d106-55cd-4960-b85b-92b3205b324f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:20:10,802] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:20:10,803] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:20:10,803] [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
Pseudorhodobacter ferrugineus	strain=DSM 5888	GCA_000420745.1	77008	77008	type	True	100.0	1121	1123	95	conclusive
Pseudorhodobacter wandonensis	strain=KCTC 23672	GCA_001202035.1	1120568	1120568	type	True	81.4847	736	1123	95	below_threshold
Pseudorhodobacter antarcticus	strain=CGMCC 1.10836	GCA_900110135.1	1077947	1077947	type	True	80.6158	687	1123	95	below_threshold
Pseudorhodobacter antarcticus	strain=KCTC 23700	GCA_001202015.1	1077947	1077947	type	True	80.5369	691	1123	95	below_threshold
Pseudorhodobacter turbinis	strain=S12M18	GCA_005234135.1	2500533	2500533	type	True	79.2995	520	1123	95	below_threshold
Tabrizicola sediminis	strain=DRYC-M-16	GCA_004745575.1	2486418	2486418	type	True	77.5541	346	1123	95	below_threshold
Gemmobacter fulva	strain=con5	GCA_018798885.1	2840474	2840474	type	True	77.446	355	1123	95	below_threshold
Tabrizicola alkalilacus	strain=DJC	GCA_003443995.1	2305252	2305252	type	True	77.362	356	1123	95	below_threshold
Rhodobacter ruber	strain=CCP-1	GCA_009908315.1	1985673	1985673	type	True	76.9139	279	1123	95	below_threshold
Actibacterium mucosum	strain=KCTC 23349	GCA_000647975.1	1087332	1087332	type	True	76.6489	154	1123	95	below_threshold
Celeribacter baekdonensis	strain=DSM 27375	GCA_900102315.1	875171	875171	type	True	76.6463	158	1123	95	below_threshold
Tritonibacter litoralis	strain=SM1979	GCA_009496005.1	2662264	2662264	type	True	76.414	122	1123	95	below_threshold
Cereibacter sediminicola	strain=JA983	GCA_007668225.1	2584941	2584941	type	True	76.3623	176	1123	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:20:10,806] [INFO] DFAST Taxonomy check result was written to GCF_000420745.1_ASM42074v1_genomic.fna/tc_result.tsv
[2024-01-24 14:20:10,807] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:20:10,807] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:20:10,807] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1419d106-55cd-4960-b85b-92b3205b324f/dqc_reference/checkm_data
[2024-01-24 14:20:10,809] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:20:10,843] [INFO] Task started: CheckM
[2024-01-24 14:20:10,844] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000420745.1_ASM42074v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000420745.1_ASM42074v1_genomic.fna/checkm_input GCF_000420745.1_ASM42074v1_genomic.fna/checkm_result
[2024-01-24 14:20:48,913] [INFO] Task succeeded: CheckM
[2024-01-24 14:20:48,914] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:20:48,933] [INFO] ===== Completeness check finished =====
[2024-01-24 14:20:48,933] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:20:48,933] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000420745.1_ASM42074v1_genomic.fna/markers.fasta)
[2024-01-24 14:20:48,933] [INFO] Task started: Blastn
[2024-01-24 14:20:48,934] [INFO] Running command: blastn -query GCF_000420745.1_ASM42074v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1419d106-55cd-4960-b85b-92b3205b324f/dqc_reference/reference_markers_gtdb.fasta -out GCF_000420745.1_ASM42074v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:20:50,386] [INFO] Task succeeded: Blastn
[2024-01-24 14:20:50,389] [INFO] Selected 10 target genomes.
[2024-01-24 14:20:50,389] [INFO] Target genome list was writen to GCF_000420745.1_ASM42074v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:20:50,407] [INFO] Task started: fastANI
[2024-01-24 14:20:50,407] [INFO] Running command: fastANI --query /var/lib/cwl/stg6e64ff6e-8b4f-435a-8557-4c1a9c6ed59a/GCF_000420745.1_ASM42074v1_genomic.fna.gz --refList GCF_000420745.1_ASM42074v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000420745.1_ASM42074v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:20:58,177] [INFO] Task succeeded: fastANI
[2024-01-24 14:20:58,186] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:20:58,186] [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_000420745.1	s__Pseudorhodobacter ferrugineus	100.0	1121	1123	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudorhodobacter	95.0	99.99	99.99	0.99	0.99	2	conclusive
GCF_001202035.1	s__Pseudorhodobacter wandonensis	81.4847	736	1123	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudorhodobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003991405.1	s__Pseudorhodobacter sp003991405	81.2655	774	1123	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudorhodobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110135.1	s__Pseudorhodobacter antarcticus	80.6118	687	1123	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudorhodobacter	95.0	99.98	99.98	0.98	0.98	2	-
GCF_005234135.1	s__Pseudorhodobacter turbinis	79.2995	520	1123	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudorhodobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001202025.1	s__Pseudorhodobacter aquimaris	79.1919	500	1123	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudorhodobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002900965.1	s__ETT8 sp002900965	77.5424	309	1123	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__ETT8	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009773375.1	s__Cypionkella sp009773375	77.3205	325	1123	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cypionkella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110025.1	s__Gemmobacter aquatilis	77.2124	337	1123	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_008711135.1	s__LNNU-3342 sp008711135	76.5359	152	1123	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__LNNU-3342	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:20:58,188] [INFO] GTDB search result was written to GCF_000420745.1_ASM42074v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:20:58,189] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:20:58,193] [INFO] DFAST_QC result json was written to GCF_000420745.1_ASM42074v1_genomic.fna/dqc_result.json
[2024-01-24 14:20:58,193] [INFO] DFAST_QC completed!
[2024-01-24 14:20:58,193] [INFO] Total running time: 0h1m12s