[2023-06-19 13:30:59,138] [INFO] DFAST_QC pipeline started.
[2023-06-19 13:30:59,140] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 13:30:59,140] [INFO] DQC Reference Directory: /var/lib/cwl/stg9b29986e-fb52-4b60-9451-18b064bfa8d4/dqc_reference
[2023-06-19 13:31:00,571] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 13:31:00,572] [INFO] Task started: Prodigal
[2023-06-19 13:31:00,572] [INFO] Running command: gunzip -c /var/lib/cwl/stgc5d6ba36-d15b-4a44-8d3d-8a36006ab14e/GCA_018971455.1_ASM1897145v1_genomic.fna.gz | prodigal -d GCA_018971455.1_ASM1897145v1_genomic.fna/cds.fna -a GCA_018971455.1_ASM1897145v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 13:31:08,481] [INFO] Task succeeded: Prodigal
[2023-06-19 13:31:08,481] [INFO] Task started: HMMsearch
[2023-06-19 13:31:08,481] [INFO] Running command: hmmsearch --tblout GCA_018971455.1_ASM1897145v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9b29986e-fb52-4b60-9451-18b064bfa8d4/dqc_reference/reference_markers.hmm GCA_018971455.1_ASM1897145v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 13:31:08,758] [INFO] Task succeeded: HMMsearch
[2023-06-19 13:31:08,760] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgc5d6ba36-d15b-4a44-8d3d-8a36006ab14e/GCA_018971455.1_ASM1897145v1_genomic.fna.gz]
[2023-06-19 13:31:08,801] [INFO] Query marker FASTA was written to GCA_018971455.1_ASM1897145v1_genomic.fna/markers.fasta
[2023-06-19 13:31:08,801] [INFO] Task started: Blastn
[2023-06-19 13:31:08,801] [INFO] Running command: blastn -query GCA_018971455.1_ASM1897145v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9b29986e-fb52-4b60-9451-18b064bfa8d4/dqc_reference/reference_markers.fasta -out GCA_018971455.1_ASM1897145v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 13:31:09,680] [INFO] Task succeeded: Blastn
[2023-06-19 13:31:09,684] [INFO] Selected 15 target genomes.
[2023-06-19 13:31:09,684] [INFO] Target genome list was writen to GCA_018971455.1_ASM1897145v1_genomic.fna/target_genomes.txt
[2023-06-19 13:31:09,688] [INFO] Task started: fastANI
[2023-06-19 13:31:09,688] [INFO] Running command: fastANI --query /var/lib/cwl/stgc5d6ba36-d15b-4a44-8d3d-8a36006ab14e/GCA_018971455.1_ASM1897145v1_genomic.fna.gz --refList GCA_018971455.1_ASM1897145v1_genomic.fna/target_genomes.txt --output GCA_018971455.1_ASM1897145v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 13:31:21,038] [INFO] Task succeeded: fastANI
[2023-06-19 13:31:21,038] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9b29986e-fb52-4b60-9451-18b064bfa8d4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 13:31:21,039] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9b29986e-fb52-4b60-9451-18b064bfa8d4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 13:31:21,052] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 13:31:21,052] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-19 13:31:21,053] [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	79.2235	328	647	95	below_threshold
Acidisphaera rubrifaciens	strain=HS-AP3	GCA_000964365.1	50715	50715	type	True	78.5766	202	647	95	below_threshold
Roseomonas coralli	strain=M0104	GCA_009829925.1	2545983	2545983	type	True	78.2606	247	647	95	below_threshold
Endobacter medicaginis	strain=LMG 26838	GCA_013376135.1	1181271	1181271	type	True	78.2215	125	647	95	below_threshold
Rhodopila globiformis	strain=DSM 161	GCA_002937115.1	1071	1071	type	True	78.1657	263	647	95	below_threshold
Endobacter medicaginis	strain=CECT 8088	GCA_014192375.1	1181271	1181271	type	True	78.0021	191	647	95	below_threshold
Roseomonas alkaliterrae	strain=DSM 25895	GCA_014199195.1	1452450	1452450	type	True	77.8259	269	647	95	below_threshold
Roseomonas haemaphysalidis	strain=546	GCA_017355405.1	2768162	2768162	type	True	77.5135	230	647	95	below_threshold
Roseococcus pinisoli	strain=XZZS9	GCA_018413645.1	2835040	2835040	type	True	77.49	217	647	95	below_threshold
Roseomonas gilardii subsp. rosea	strain=NCTC13290	GCA_900455865.1	243956	257708	type	True	77.4458	232	647	95	below_threshold
Roseomonas rubea	strain=MO17	GCA_016106015.1	2748666	2748666	type	True	77.4134	229	647	95	below_threshold
Roseococcus thiosulfatophilus	strain=RB-3	GCA_017311575.1	35813	35813	type	True	77.1563	238	647	95	below_threshold
Acidisoma cellulosilyticum	strain=HW T5.17	GCA_020621385.1	2802395	2802395	type	True	77.1409	143	647	95	below_threshold
Novacetimonas maltaceti	strain=LMG 1529	GCA_002906255.1	1203393	1203393	type	True	76.9555	92	647	95	below_threshold
Novacetimonas maltaceti	strain=LMG 1529	GCA_003206475.1	1203393	1203393	type	True	76.9544	92	647	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-19 13:31:21,055] [INFO] DFAST Taxonomy check result was written to GCA_018971455.1_ASM1897145v1_genomic.fna/tc_result.tsv
[2023-06-19 13:31:21,056] [INFO] ===== Taxonomy check completed =====
[2023-06-19 13:31:21,056] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 13:31:21,056] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9b29986e-fb52-4b60-9451-18b064bfa8d4/dqc_reference/checkm_data
[2023-06-19 13:31:21,058] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 13:31:21,093] [INFO] Task started: CheckM
[2023-06-19 13:31:21,093] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018971455.1_ASM1897145v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018971455.1_ASM1897145v1_genomic.fna/checkm_input GCA_018971455.1_ASM1897145v1_genomic.fna/checkm_result
[2023-06-19 13:31:49,350] [INFO] Task succeeded: CheckM
[2023-06-19 13:31:49,351] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.04%
Contamintation: 1.83%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-06-19 13:31:49,376] [INFO] ===== Completeness check finished =====
[2023-06-19 13:31:49,376] [INFO] ===== Start GTDB Search =====
[2023-06-19 13:31:49,377] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018971455.1_ASM1897145v1_genomic.fna/markers.fasta)
[2023-06-19 13:31:49,377] [INFO] Task started: Blastn
[2023-06-19 13:31:49,377] [INFO] Running command: blastn -query GCA_018971455.1_ASM1897145v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9b29986e-fb52-4b60-9451-18b064bfa8d4/dqc_reference/reference_markers_gtdb.fasta -out GCA_018971455.1_ASM1897145v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 13:31:50,982] [INFO] Task succeeded: Blastn
[2023-06-19 13:31:51,001] [INFO] Selected 13 target genomes.
[2023-06-19 13:31:51,001] [INFO] Target genome list was writen to GCA_018971455.1_ASM1897145v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 13:31:51,010] [INFO] Task started: fastANI
[2023-06-19 13:31:51,011] [INFO] Running command: fastANI --query /var/lib/cwl/stgc5d6ba36-d15b-4a44-8d3d-8a36006ab14e/GCA_018971455.1_ASM1897145v1_genomic.fna.gz --refList GCA_018971455.1_ASM1897145v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018971455.1_ASM1897145v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 13:32:01,452] [INFO] Task succeeded: fastANI
[2023-06-19 13:32:01,481] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 13:32:01,482] [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_018971455.1	s__REEB85 sp018971455	99.9999	639	647	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__REEB85	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_001899585.1	s__70-18 sp001899585	80.7932	416	647	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_903907955.1	s__BOG-930 sp903907955	79.4902	288	647	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	79.2033	323	647	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Rhodovastum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019240395.1	s__JAFAYA01 sp019240395	79.2007	286	647	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__JAFAYA01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903865895.1	s__CAIYPH01 sp903865895	79.1663	345	647	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__CAIYPH01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903918195.1	s__BOG-930 sp903918195	79.0451	278	647	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_018240635.1	s__JAFEFJ01 sp018240635	78.9153	274	647	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__JAFEFJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017304945.1	s__69-11 sp017304945	78.7416	286	647	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_017307285.1	s__JAFKFI01 sp017307285	78.6782	272	647	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__JAFKFI01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000964365.1	s__Acidisphaera rubrifaciens	78.6573	198	647	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acidisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017307335.1	s__JAFKFJ01 sp017307335	78.5256	261	647	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__JAFKFJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903928045.1	s__CAIYPH01 sp903928045	78.5159	253	647	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__CAIYPH01	95.0	98.55	98.55	0.76	0.76	2	-
--------------------------------------------------------------------------------
[2023-06-19 13:32:01,487] [INFO] GTDB search result was written to GCA_018971455.1_ASM1897145v1_genomic.fna/result_gtdb.tsv
[2023-06-19 13:32:01,488] [INFO] ===== GTDB Search completed =====
[2023-06-19 13:32:01,494] [INFO] DFAST_QC result json was written to GCA_018971455.1_ASM1897145v1_genomic.fna/dqc_result.json
[2023-06-19 13:32:01,494] [INFO] DFAST_QC completed!
[2023-06-19 13:32:01,494] [INFO] Total running time: 0h1m2s