[2023-06-28 12:02:31,221] [INFO] DFAST_QC pipeline started.
[2023-06-28 12:02:31,224] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 12:02:31,224] [INFO] DQC Reference Directory: /var/lib/cwl/stg059ef3ee-64e3-4b85-9a66-d48e993d4702/dqc_reference
[2023-06-28 12:02:32,581] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 12:02:32,582] [INFO] Task started: Prodigal
[2023-06-28 12:02:32,582] [INFO] Running command: gunzip -c /var/lib/cwl/stg0603cffd-4f66-409a-9d71-064a304a1db9/GCA_027326445.1_ASM2732644v1_genomic.fna.gz | prodigal -d GCA_027326445.1_ASM2732644v1_genomic.fna/cds.fna -a GCA_027326445.1_ASM2732644v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 12:02:42,385] [INFO] Task succeeded: Prodigal
[2023-06-28 12:02:42,386] [INFO] Task started: HMMsearch
[2023-06-28 12:02:42,386] [INFO] Running command: hmmsearch --tblout GCA_027326445.1_ASM2732644v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg059ef3ee-64e3-4b85-9a66-d48e993d4702/dqc_reference/reference_markers.hmm GCA_027326445.1_ASM2732644v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 12:02:42,646] [INFO] Task succeeded: HMMsearch
[2023-06-28 12:02:42,648] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg0603cffd-4f66-409a-9d71-064a304a1db9/GCA_027326445.1_ASM2732644v1_genomic.fna.gz]
[2023-06-28 12:02:42,687] [INFO] Query marker FASTA was written to GCA_027326445.1_ASM2732644v1_genomic.fna/markers.fasta
[2023-06-28 12:02:42,688] [INFO] Task started: Blastn
[2023-06-28 12:02:42,688] [INFO] Running command: blastn -query GCA_027326445.1_ASM2732644v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg059ef3ee-64e3-4b85-9a66-d48e993d4702/dqc_reference/reference_markers.fasta -out GCA_027326445.1_ASM2732644v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 12:02:43,336] [INFO] Task succeeded: Blastn
[2023-06-28 12:02:43,340] [INFO] Selected 18 target genomes.
[2023-06-28 12:02:43,340] [INFO] Target genome list was writen to GCA_027326445.1_ASM2732644v1_genomic.fna/target_genomes.txt
[2023-06-28 12:02:43,344] [INFO] Task started: fastANI
[2023-06-28 12:02:43,344] [INFO] Running command: fastANI --query /var/lib/cwl/stg0603cffd-4f66-409a-9d71-064a304a1db9/GCA_027326445.1_ASM2732644v1_genomic.fna.gz --refList GCA_027326445.1_ASM2732644v1_genomic.fna/target_genomes.txt --output GCA_027326445.1_ASM2732644v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 12:02:58,336] [INFO] Task succeeded: fastANI
[2023-06-28 12:02:58,336] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg059ef3ee-64e3-4b85-9a66-d48e993d4702/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 12:02:58,337] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg059ef3ee-64e3-4b85-9a66-d48e993d4702/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 12:02:58,359] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 12:02:58,359] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 12:02:58,360] [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
Rhodovastum atsumiense	strain=G2-11	GCA_937425535.1	504468	504468	type	True	78.2514	397	995	95	below_threshold
Acidisphaera rubrifaciens	strain=HS-AP3	GCA_000964365.1	50715	50715	type	True	77.961	228	995	95	below_threshold
Rhodopila globiformis	strain=DSM 161	GCA_002937115.1	1071	1071	type	True	77.644	365	995	95	below_threshold
Roseomonas gilardii subsp. rosea	strain=NCTC13290	GCA_900455865.1	243956	257708	type	True	76.9994	264	995	95	below_threshold
Roseomonas coralli	strain=M0104	GCA_009829925.1	2545983	2545983	type	True	76.9707	315	995	95	below_threshold
Roseomonas mucosa	strain=ATCC BAA-692	GCA_000622225.1	207340	207340	type	True	76.9623	274	995	95	below_threshold
Roseomonas gilardii subsp. rosea	strain=ATCC BAA-691	GCA_000518625.1	243956	257708	type	True	76.947	274	995	95	below_threshold
Roseomonas mucosa	strain=NCTC13291	GCA_900455935.1	207340	207340	type	True	76.9029	276	995	95	below_threshold
Siccirubricoccus deserti	strain=CGMCC 1.15936	GCA_014644195.1	2013562	2013562	type	True	76.7027	319	995	95	below_threshold
Roseomonas haemaphysalidis	strain=546	GCA_017355405.1	2768162	2768162	type	True	76.6939	294	995	95	below_threshold
Siccirubricoccus deserti	strain=SYSU D8009	GCA_014283215.1	2013562	2013562	type	True	76.6921	322	995	95	below_threshold
Roseomonas oryzicola	strain=KCTC 22478	GCA_012163135.1	535904	535904	type	True	76.6845	320	995	95	below_threshold
Roseomonas rubea	strain=MO17	GCA_016106015.1	2748666	2748666	type	True	76.6164	253	995	95	below_threshold
Roseococcus pinisoli	strain=XZZS9	GCA_018413645.1	2835040	2835040	type	True	76.6154	214	995	95	below_threshold
Roseococcus microcysteis	strain=NIBR12	GCA_014764365.1	2771361	2771361	type	True	76.5765	243	995	95	below_threshold
Belnapia arida	strain=T18	GCA_016773205.1	2804533	2804533	type	True	76.5644	304	995	95	below_threshold
Roseococcus thiosulfatophilus	strain=RB-3	GCA_017311575.1	35813	35813	type	True	76.403	247	995	95	below_threshold
Rhodovarius crocodyli	strain=CCP-6	GCA_004005855.1	1979269	1979269	type	True	76.4027	267	995	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 12:02:58,364] [INFO] DFAST Taxonomy check result was written to GCA_027326445.1_ASM2732644v1_genomic.fna/tc_result.tsv
[2023-06-28 12:02:58,365] [INFO] ===== Taxonomy check completed =====
[2023-06-28 12:02:58,365] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 12:02:58,366] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg059ef3ee-64e3-4b85-9a66-d48e993d4702/dqc_reference/checkm_data
[2023-06-28 12:02:58,367] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 12:02:58,403] [INFO] Task started: CheckM
[2023-06-28 12:02:58,403] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_027326445.1_ASM2732644v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_027326445.1_ASM2732644v1_genomic.fna/checkm_input GCA_027326445.1_ASM2732644v1_genomic.fna/checkm_result
[2023-06-28 12:03:31,953] [INFO] Task succeeded: CheckM
[2023-06-28 12:03:31,954] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 58.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 12:03:31,983] [INFO] ===== Completeness check finished =====
[2023-06-28 12:03:31,983] [INFO] ===== Start GTDB Search =====
[2023-06-28 12:03:31,984] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_027326445.1_ASM2732644v1_genomic.fna/markers.fasta)
[2023-06-28 12:03:31,985] [INFO] Task started: Blastn
[2023-06-28 12:03:31,985] [INFO] Running command: blastn -query GCA_027326445.1_ASM2732644v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg059ef3ee-64e3-4b85-9a66-d48e993d4702/dqc_reference/reference_markers_gtdb.fasta -out GCA_027326445.1_ASM2732644v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 12:03:32,989] [INFO] Task succeeded: Blastn
[2023-06-28 12:03:32,994] [INFO] Selected 14 target genomes.
[2023-06-28 12:03:32,994] [INFO] Target genome list was writen to GCA_027326445.1_ASM2732644v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 12:03:33,001] [INFO] Task started: fastANI
[2023-06-28 12:03:33,002] [INFO] Running command: fastANI --query /var/lib/cwl/stg0603cffd-4f66-409a-9d71-064a304a1db9/GCA_027326445.1_ASM2732644v1_genomic.fna.gz --refList GCA_027326445.1_ASM2732644v1_genomic.fna/target_genomes_gtdb.txt --output GCA_027326445.1_ASM2732644v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 12:03:46,578] [INFO] Task succeeded: fastANI
[2023-06-28 12:03:46,591] [INFO] Found 14 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 12:03:46,591] [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_903970625.1	s__CAJCJG01 sp903970625	80.6878	554	995	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__CAJCJG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903864895.1	s__CAIPHQ01 sp903864895	79.6147	482	995	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__CAIPHQ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017307335.1	s__JAFKFJ01 sp017307335	78.9896	398	995	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__JAFKFJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001899585.1	s__70-18 sp001899585	78.9873	441	995	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__70-18	95.0	99.94	99.94	0.98	0.98	2	-
GCA_003133265.1	s__PALSA-911 sp003133265	78.6993	266	995	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__PALSA-911	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903918195.1	s__BOG-930 sp903918195	78.5035	343	995	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__BOG-930	95.0	99.84	99.84	0.94	0.94	2	-
GCA_903907955.1	s__BOG-930 sp903907955	78.4811	347	995	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__BOG-930	95.0	99.93	99.75	0.97	0.94	12	-
GCF_008630155.1	s__Rhodovastum atsumiense	78.2602	395	995	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Rhodovastum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017304945.1	s__69-11 sp017304945	77.8066	348	995	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__69-11	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019240395.1	s__JAFAYA01 sp019240395	77.6593	308	995	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__JAFAYA01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002937115.1	s__Rhodopila globiformis	77.657	363	995	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Rhodopila	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001898425.1	s__69-11 sp001898425	77.4995	342	995	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__69-11	95.0	99.84	99.84	0.96	0.96	2	-
GCF_014644455.1	s__Caldovatus sediminis	76.8977	367	995	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Caldovatus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006704265.1	s__Elioraea sp006704265	76.5907	252	995	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Elioraea	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 12:03:46,593] [INFO] GTDB search result was written to GCA_027326445.1_ASM2732644v1_genomic.fna/result_gtdb.tsv
[2023-06-28 12:03:46,594] [INFO] ===== GTDB Search completed =====
[2023-06-28 12:03:46,599] [INFO] DFAST_QC result json was written to GCA_027326445.1_ASM2732644v1_genomic.fna/dqc_result.json
[2023-06-28 12:03:46,599] [INFO] DFAST_QC completed!
[2023-06-28 12:03:46,599] [INFO] Total running time: 0h1m15s