[2024-01-24 15:27:10,804] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:27:10,806] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:27:10,806] [INFO] DQC Reference Directory: /var/lib/cwl/stg9a1b88a3-de36-4b0a-a46a-6878d77f32c9/dqc_reference
[2024-01-24 15:27:12,108] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:27:12,115] [INFO] Task started: Prodigal
[2024-01-24 15:27:12,115] [INFO] Running command: gunzip -c /var/lib/cwl/stgcab3d4a5-d530-4245-a056-86ae884bf2cb/GCF_003076755.1_ASM307675v1_genomic.fna.gz | prodigal -d GCF_003076755.1_ASM307675v1_genomic.fna/cds.fna -a GCF_003076755.1_ASM307675v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:27:25,891] [INFO] Task succeeded: Prodigal
[2024-01-24 15:27:25,891] [INFO] Task started: HMMsearch
[2024-01-24 15:27:25,891] [INFO] Running command: hmmsearch --tblout GCF_003076755.1_ASM307675v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9a1b88a3-de36-4b0a-a46a-6878d77f32c9/dqc_reference/reference_markers.hmm GCF_003076755.1_ASM307675v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:27:26,262] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:27:26,263] [INFO] Found 6/6 markers.
[2024-01-24 15:27:26,328] [INFO] Query marker FASTA was written to GCF_003076755.1_ASM307675v1_genomic.fna/markers.fasta
[2024-01-24 15:27:26,329] [INFO] Task started: Blastn
[2024-01-24 15:27:26,329] [INFO] Running command: blastn -query GCF_003076755.1_ASM307675v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9a1b88a3-de36-4b0a-a46a-6878d77f32c9/dqc_reference/reference_markers.fasta -out GCF_003076755.1_ASM307675v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:27:27,415] [INFO] Task succeeded: Blastn
[2024-01-24 15:27:27,427] [INFO] Selected 15 target genomes.
[2024-01-24 15:27:27,427] [INFO] Target genome list was writen to GCF_003076755.1_ASM307675v1_genomic.fna/target_genomes.txt
[2024-01-24 15:27:27,433] [INFO] Task started: fastANI
[2024-01-24 15:27:27,433] [INFO] Running command: fastANI --query /var/lib/cwl/stgcab3d4a5-d530-4245-a056-86ae884bf2cb/GCF_003076755.1_ASM307675v1_genomic.fna.gz --refList GCF_003076755.1_ASM307675v1_genomic.fna/target_genomes.txt --output GCF_003076755.1_ASM307675v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:27:40,156] [INFO] Task succeeded: fastANI
[2024-01-24 15:27:40,156] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9a1b88a3-de36-4b0a-a46a-6878d77f32c9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:27:40,156] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9a1b88a3-de36-4b0a-a46a-6878d77f32c9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:27:40,169] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:27:40,169] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:27:40,169] [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
Pararhodobacter oceanensis	strain=AM505	GCA_003076755.1	2172121	2172121	type	True	100.0	1343	1345	95	conclusive
Pararhodobacter zhoushanensis	strain=ZQ420	GCA_003990445.1	2479545	2479545	type	True	79.1869	636	1345	95	below_threshold
Pararhodobacter aggregans	strain=DSM 18938	GCA_003054005.1	404875	404875	type	True	79.0717	634	1345	95	below_threshold
Pararhodobacter aggregans	strain=D1-19	GCA_003075525.1	404875	404875	type	True	79.0602	632	1345	95	below_threshold
Pararhodobacter marinus	strain=CIC4N-9	GCA_003122215.1	2184063	2184063	type	True	78.7677	609	1345	95	below_threshold
Paracoccus aminovorans		GCA_900005615.1	34004	34004	type	True	77.5234	283	1345	95	below_threshold
Gemmobacter fulva	strain=con5	GCA_018798885.1	2840474	2840474	type	True	77.4793	348	1345	95	below_threshold
Paracoccus aminovorans	strain=DSM 8537	GCA_900113565.1	34004	34004	type	True	77.4483	283	1345	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	77.3609	287	1345	95	below_threshold
Cereibacter ovatus	strain=JA234	GCA_900207575.1	439529	439529	type	True	77.3207	295	1345	95	below_threshold
Tabrizicola sediminis	strain=DRYC-M-16	GCA_004745575.1	2486418	2486418	type	True	77.3178	288	1345	95	below_threshold
Pseudogemmobacter bohemicus	strain=Cd-10	GCA_003290025.1	2250708	2250708	type	True	77.3037	299	1345	95	below_threshold
Gemmobacter aquarius	strain=HYN0069	GCA_003060865.1	2169400	2169400	type	True	77.2339	266	1345	95	below_threshold
Thalassobius aquimarinus	strain=KMM 8518	GCA_018219815.1	2785917	2785917	type	True	77.1683	289	1345	95	below_threshold
Maritimibacter alexandrii	strain=LZ-17	GCA_005871115.1	2570355	2570355	type	True	77.0561	251	1345	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:27:40,171] [INFO] DFAST Taxonomy check result was written to GCF_003076755.1_ASM307675v1_genomic.fna/tc_result.tsv
[2024-01-24 15:27:40,171] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:27:40,171] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:27:40,172] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9a1b88a3-de36-4b0a-a46a-6878d77f32c9/dqc_reference/checkm_data
[2024-01-24 15:27:40,173] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:27:40,218] [INFO] Task started: CheckM
[2024-01-24 15:27:40,218] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003076755.1_ASM307675v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003076755.1_ASM307675v1_genomic.fna/checkm_input GCF_003076755.1_ASM307675v1_genomic.fna/checkm_result
[2024-01-24 15:28:20,473] [INFO] Task succeeded: CheckM
[2024-01-24 15:28:20,474] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:28:20,499] [INFO] ===== Completeness check finished =====
[2024-01-24 15:28:20,499] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:28:20,499] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003076755.1_ASM307675v1_genomic.fna/markers.fasta)
[2024-01-24 15:28:20,500] [INFO] Task started: Blastn
[2024-01-24 15:28:20,500] [INFO] Running command: blastn -query GCF_003076755.1_ASM307675v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9a1b88a3-de36-4b0a-a46a-6878d77f32c9/dqc_reference/reference_markers_gtdb.fasta -out GCF_003076755.1_ASM307675v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:28:22,373] [INFO] Task succeeded: Blastn
[2024-01-24 15:28:22,378] [INFO] Selected 17 target genomes.
[2024-01-24 15:28:22,379] [INFO] Target genome list was writen to GCF_003076755.1_ASM307675v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:28:22,398] [INFO] Task started: fastANI
[2024-01-24 15:28:22,398] [INFO] Running command: fastANI --query /var/lib/cwl/stgcab3d4a5-d530-4245-a056-86ae884bf2cb/GCF_003076755.1_ASM307675v1_genomic.fna.gz --refList GCF_003076755.1_ASM307675v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003076755.1_ASM307675v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:28:35,157] [INFO] Task succeeded: fastANI
[2024-01-24 15:28:35,177] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:28:35,177] [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_003076755.1	s__Pararhodobacter oceanensis	100.0	1343	1345	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pararhodobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003990445.1	s__Pararhodobacter zhoushanensis	79.1984	635	1345	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pararhodobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003075525.1	s__Pararhodobacter aggregans	79.0423	634	1345	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pararhodobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCA_905479725.1	s__Pararhodobacter sp905479725	78.9162	342	1345	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pararhodobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017303295.1	s__Pararhodobacter sp017303295	78.8087	605	1345	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pararhodobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003122215.1	s__Pararhodobacter marinus	78.7887	605	1345	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pararhodobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001691415.1	s__Pararhodobacter sp001691415	78.7605	573	1345	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pararhodobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001314715.1	s__Pararhodobacter sp001314715	78.0314	415	1345	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pararhodobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007131945.1	s__Pararhodobacter sp007131945	77.632	353	1345	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pararhodobacter	95.0	99.16	99.15	0.86	0.82	3	-
GCF_018139985.1	s__JAGSOU01 sp018139985	77.6138	332	1345	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JAGSOU01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900005615.1	s__Paracoccus aminovorans	77.5451	281	1345	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	99.98	99.98	1.00	1.00	2	-
GCA_007134865.1	s__Roseinatronobacter sp007134865	77.3628	279	1345	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseinatronobacter	95.0	99.54	99.18	0.88	0.81	5	-
GCF_000744955.1	s__Actibacterium sp000744955	77.1056	291	1345	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Actibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002708925.1	s__Thalassobius sp002708925	76.9889	250	1345	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	99.91	99.91	0.84	0.84	2	-
GCA_007694945.1	s__Roseinatronobacter sp007694945	76.8419	265	1345	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseinatronobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018279165.1	s__Falsirhodobacter sp018279165	76.8021	205	1345	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Falsirhodobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007131465.1	s__Roseinatronobacter sp007131465	76.6985	165	1345	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseinatronobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:28:35,179] [INFO] GTDB search result was written to GCF_003076755.1_ASM307675v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:28:35,180] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:28:35,183] [INFO] DFAST_QC result json was written to GCF_003076755.1_ASM307675v1_genomic.fna/dqc_result.json
[2024-01-24 15:28:35,184] [INFO] DFAST_QC completed!
[2024-01-24 15:28:35,184] [INFO] Total running time: 0h1m24s