[2024-01-24 13:57:42,988] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:57:42,990] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:57:42,990] [INFO] DQC Reference Directory: /var/lib/cwl/stg209cf8c0-4226-4e86-93c9-a65a69842f1d/dqc_reference
[2024-01-24 13:57:44,259] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:57:44,260] [INFO] Task started: Prodigal
[2024-01-24 13:57:44,260] [INFO] Running command: gunzip -c /var/lib/cwl/stg58ece378-0355-4362-8e4e-bb679d926c51/GCF_019130055.1_ASM1913005v1_genomic.fna.gz | prodigal -d GCF_019130055.1_ASM1913005v1_genomic.fna/cds.fna -a GCF_019130055.1_ASM1913005v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:57:56,812] [INFO] Task succeeded: Prodigal
[2024-01-24 13:57:56,813] [INFO] Task started: HMMsearch
[2024-01-24 13:57:56,813] [INFO] Running command: hmmsearch --tblout GCF_019130055.1_ASM1913005v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg209cf8c0-4226-4e86-93c9-a65a69842f1d/dqc_reference/reference_markers.hmm GCF_019130055.1_ASM1913005v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:57:57,086] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:57:57,087] [INFO] Found 6/6 markers.
[2024-01-24 13:57:57,137] [INFO] Query marker FASTA was written to GCF_019130055.1_ASM1913005v1_genomic.fna/markers.fasta
[2024-01-24 13:57:57,138] [INFO] Task started: Blastn
[2024-01-24 13:57:57,138] [INFO] Running command: blastn -query GCF_019130055.1_ASM1913005v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg209cf8c0-4226-4e86-93c9-a65a69842f1d/dqc_reference/reference_markers.fasta -out GCF_019130055.1_ASM1913005v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:57:58,161] [INFO] Task succeeded: Blastn
[2024-01-24 13:57:58,164] [INFO] Selected 12 target genomes.
[2024-01-24 13:57:58,165] [INFO] Target genome list was writen to GCF_019130055.1_ASM1913005v1_genomic.fna/target_genomes.txt
[2024-01-24 13:57:58,173] [INFO] Task started: fastANI
[2024-01-24 13:57:58,173] [INFO] Running command: fastANI --query /var/lib/cwl/stg58ece378-0355-4362-8e4e-bb679d926c51/GCF_019130055.1_ASM1913005v1_genomic.fna.gz --refList GCF_019130055.1_ASM1913005v1_genomic.fna/target_genomes.txt --output GCF_019130055.1_ASM1913005v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:58:09,166] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:09,167] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg209cf8c0-4226-4e86-93c9-a65a69842f1d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:58:09,167] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg209cf8c0-4226-4e86-93c9-a65a69842f1d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:58:09,177] [INFO] Found 12 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:58:09,177] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:58:09,178] [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
Rhodobacter amnigenus	strain=HSP-20	GCA_019130055.1	2852097	2852097	type	True	100.0	1362	1363	95	conclusive
Rhodobacter amnigenus	strain=HSP-20	GCA_009908265.2	2852097	2852097	type	True	100.0	1362	1363	95	conclusive
Rhodobacter ruber	strain=CCP-1	GCA_009908315.1	1985673	1985673	type	True	84.5495	875	1363	95	below_threshold
Gemmobacter straminiformis	strain=CAM-8	GCA_014243445.1	2045119	2045119	type	True	82.3083	836	1363	95	below_threshold
Gemmobacter aquarius	strain=HYN0069	GCA_003060865.1	2169400	2169400	type	True	81.3939	792	1363	95	below_threshold
Rhodobacter flagellatus	strain=SYSU G03088	GCA_008271465.1	2593021	2593021	type	True	80.4151	675	1363	95	below_threshold
Gemmobacter aquatilis	strain=DSM 3857	GCA_900110025.1	933059	933059	type	True	80.1623	661	1363	95	below_threshold
Gemmobacter lutimaris	strain=YJ-T1-11	GCA_003570715.1	2306023	2306023	type	True	79.8698	643	1363	95	below_threshold
Gemmobacter fulva	strain=con5	GCA_018798885.1	2840474	2840474	type	True	79.7708	626	1363	95	below_threshold
Cereibacter ovatus	strain=JA234	GCA_900207575.1	439529	439529	type	True	79.5173	558	1363	95	below_threshold
Cereibacter sediminicola	strain=JA983	GCA_007668225.1	2584941	2584941	type	True	79.4389	552	1363	95	below_threshold
Roseicitreum antarcticum	strain=ZS2-28	GCA_014681765.1	564137	564137	type	True	77.5605	342	1363	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:58:09,179] [INFO] DFAST Taxonomy check result was written to GCF_019130055.1_ASM1913005v1_genomic.fna/tc_result.tsv
[2024-01-24 13:58:09,180] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:58:09,180] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:58:09,180] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg209cf8c0-4226-4e86-93c9-a65a69842f1d/dqc_reference/checkm_data
[2024-01-24 13:58:09,181] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:58:09,227] [INFO] Task started: CheckM
[2024-01-24 13:58:09,227] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019130055.1_ASM1913005v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019130055.1_ASM1913005v1_genomic.fna/checkm_input GCF_019130055.1_ASM1913005v1_genomic.fna/checkm_result
[2024-01-24 13:58:55,731] [INFO] Task succeeded: CheckM
[2024-01-24 13:58:55,732] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:58:55,756] [INFO] ===== Completeness check finished =====
[2024-01-24 13:58:55,756] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:58:55,756] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019130055.1_ASM1913005v1_genomic.fna/markers.fasta)
[2024-01-24 13:58:55,757] [INFO] Task started: Blastn
[2024-01-24 13:58:55,757] [INFO] Running command: blastn -query GCF_019130055.1_ASM1913005v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg209cf8c0-4226-4e86-93c9-a65a69842f1d/dqc_reference/reference_markers_gtdb.fasta -out GCF_019130055.1_ASM1913005v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:57,716] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:57,720] [INFO] Selected 8 target genomes.
[2024-01-24 13:58:57,721] [INFO] Target genome list was writen to GCF_019130055.1_ASM1913005v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:58:57,728] [INFO] Task started: fastANI
[2024-01-24 13:58:57,728] [INFO] Running command: fastANI --query /var/lib/cwl/stg58ece378-0355-4362-8e4e-bb679d926c51/GCF_019130055.1_ASM1913005v1_genomic.fna.gz --refList GCF_019130055.1_ASM1913005v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019130055.1_ASM1913005v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:59:05,837] [INFO] Task succeeded: fastANI
[2024-01-24 13:59:05,844] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:59:05,845] [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
GCA_009908265.2	s__Gemmobacter_B sp009908265	100.0	1362	1363	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter_B	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCA_000500915.1	s__Gemmobacter_B sp000500915	86.7096	828	1363	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011059185.1	s__Gemmobacter_B sp011059185	85.6988	947	1363	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002855575.1	s__Gemmobacter_B sp002855575	85.3816	961	1363	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014654775.1	s__Gemmobacter_B sp014654775	84.6338	914	1363	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009908315.1	s__Gemmobacter_B sp009908315	84.5703	873	1363	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014859945.1	s__UBA1943 sp014859945	80.4749	516	1363	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__UBA1943	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002256185.1	s__Gemmobacter_B sp002256185	80.1681	671	1363	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter_B	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:59:05,846] [INFO] GTDB search result was written to GCF_019130055.1_ASM1913005v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:59:05,847] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:59:05,850] [INFO] DFAST_QC result json was written to GCF_019130055.1_ASM1913005v1_genomic.fna/dqc_result.json
[2024-01-24 13:59:05,851] [INFO] DFAST_QC completed!
[2024-01-24 13:59:05,851] [INFO] Total running time: 0h1m23s