[2024-01-24 13:37:40,814] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:37:40,816] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:37:40,816] [INFO] DQC Reference Directory: /var/lib/cwl/stgadd01ef0-219e-4c06-a3f9-b1f6c1bcaf33/dqc_reference
[2024-01-24 13:37:42,107] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:37:42,108] [INFO] Task started: Prodigal
[2024-01-24 13:37:42,108] [INFO] Running command: gunzip -c /var/lib/cwl/stge0eaf2bc-100a-43e7-aa16-86720510825a/GCF_014201825.1_ASM1420182v1_genomic.fna.gz | prodigal -d GCF_014201825.1_ASM1420182v1_genomic.fna/cds.fna -a GCF_014201825.1_ASM1420182v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:37:51,866] [INFO] Task succeeded: Prodigal
[2024-01-24 13:37:51,867] [INFO] Task started: HMMsearch
[2024-01-24 13:37:51,867] [INFO] Running command: hmmsearch --tblout GCF_014201825.1_ASM1420182v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgadd01ef0-219e-4c06-a3f9-b1f6c1bcaf33/dqc_reference/reference_markers.hmm GCF_014201825.1_ASM1420182v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:37:52,122] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:37:52,123] [INFO] Found 6/6 markers.
[2024-01-24 13:37:52,156] [INFO] Query marker FASTA was written to GCF_014201825.1_ASM1420182v1_genomic.fna/markers.fasta
[2024-01-24 13:37:52,156] [INFO] Task started: Blastn
[2024-01-24 13:37:52,156] [INFO] Running command: blastn -query GCF_014201825.1_ASM1420182v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgadd01ef0-219e-4c06-a3f9-b1f6c1bcaf33/dqc_reference/reference_markers.fasta -out GCF_014201825.1_ASM1420182v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:37:52,977] [INFO] Task succeeded: Blastn
[2024-01-24 13:37:52,981] [INFO] Selected 17 target genomes.
[2024-01-24 13:37:52,982] [INFO] Target genome list was writen to GCF_014201825.1_ASM1420182v1_genomic.fna/target_genomes.txt
[2024-01-24 13:37:52,992] [INFO] Task started: fastANI
[2024-01-24 13:37:52,992] [INFO] Running command: fastANI --query /var/lib/cwl/stge0eaf2bc-100a-43e7-aa16-86720510825a/GCF_014201825.1_ASM1420182v1_genomic.fna.gz --refList GCF_014201825.1_ASM1420182v1_genomic.fna/target_genomes.txt --output GCF_014201825.1_ASM1420182v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:38:05,885] [INFO] Task succeeded: fastANI
[2024-01-24 13:38:05,886] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgadd01ef0-219e-4c06-a3f9-b1f6c1bcaf33/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:38:05,886] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgadd01ef0-219e-4c06-a3f9-b1f6c1bcaf33/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:38:05,905] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:38:05,906] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:38:05,906] [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
Acidocella aromatica	strain=DSM 27026	GCA_014201825.1	1303579	1303579	type	True	100.0	944	944	95	conclusive
Acidocella facilis	strain=ATCC 35904	GCA_000687875.1	525	525	type	True	80.3007	504	944	95	below_threshold
Acidocella aminolytica	strain=DSM 11237	GCA_900129125.1	33998	33998	type	True	78.9548	375	944	95	below_threshold
Acidiphilium multivorum	strain=AIU301	GCA_000964345.1	62140	62140	type	True	78.1923	259	944	95	below_threshold
Acidiphilium multivorum	strain=AIU301	GCA_000202835.1	62140	62140	type	True	78.1585	284	944	95	below_threshold
Roseomonas mucosa	strain=ATCC BAA-692	GCA_000622225.1	207340	207340	type	True	77.7399	240	944	95	below_threshold
Roseomonas rhizosphaerae	strain=YW11	GCA_002631185.1	1335062	1335062	type	True	77.617	265	944	95	below_threshold
Rhodovastum atsumiense	strain=G2-11	GCA_937425535.1	504468	504468	type	True	77.5685	270	944	95	below_threshold
Rhodovarius lipocyclicus	strain=CCUG 44693	GCA_009900765.1	268410	268410	type	True	77.5179	222	944	95	below_threshold
Roseomonas haemaphysalidis	strain=546	GCA_017355405.1	2768162	2768162	type	True	77.4961	237	944	95	below_threshold
Roseomonas oryzae	strain=KCTC 42542	GCA_008386565.1	1608942	1608942	type	True	77.4735	225	944	95	below_threshold
Roseomonas rubea	strain=MO17	GCA_016106015.1	2748666	2748666	type	True	77.4038	166	944	95	below_threshold
Roseomonas alkaliterrae	strain=DSM 25895	GCA_014199195.1	1452450	1452450	type	True	77.3684	218	944	95	below_threshold
Roseococcus microcysteis	strain=NIBR12	GCA_014764365.1	2771361	2771361	type	True	77.3517	224	944	95	below_threshold
Roseococcus pinisoli	strain=XZZS9	GCA_018413645.1	2835040	2835040	type	True	77.2892	204	944	95	below_threshold
Acidiphilium iwatense	strain=KCTC 23505	GCA_021556475.1	768198	768198	type	True	77.242	246	944	95	below_threshold
Falsiroseomonas frigidaquae	strain=JCM 15073	GCA_012163145.1	487318	487318	type	True	77.1115	230	944	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:38:05,908] [INFO] DFAST Taxonomy check result was written to GCF_014201825.1_ASM1420182v1_genomic.fna/tc_result.tsv
[2024-01-24 13:38:05,908] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:38:05,908] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:38:05,909] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgadd01ef0-219e-4c06-a3f9-b1f6c1bcaf33/dqc_reference/checkm_data
[2024-01-24 13:38:05,910] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:38:05,939] [INFO] Task started: CheckM
[2024-01-24 13:38:05,940] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014201825.1_ASM1420182v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014201825.1_ASM1420182v1_genomic.fna/checkm_input GCF_014201825.1_ASM1420182v1_genomic.fna/checkm_result
[2024-01-24 13:38:36,136] [INFO] Task succeeded: CheckM
[2024-01-24 13:38:36,138] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:38:36,159] [INFO] ===== Completeness check finished =====
[2024-01-24 13:38:36,159] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:38:36,160] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014201825.1_ASM1420182v1_genomic.fna/markers.fasta)
[2024-01-24 13:38:36,160] [INFO] Task started: Blastn
[2024-01-24 13:38:36,161] [INFO] Running command: blastn -query GCF_014201825.1_ASM1420182v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgadd01ef0-219e-4c06-a3f9-b1f6c1bcaf33/dqc_reference/reference_markers_gtdb.fasta -out GCF_014201825.1_ASM1420182v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:38:37,628] [INFO] Task succeeded: Blastn
[2024-01-24 13:38:37,634] [INFO] Selected 11 target genomes.
[2024-01-24 13:38:37,635] [INFO] Target genome list was writen to GCF_014201825.1_ASM1420182v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:38:37,660] [INFO] Task started: fastANI
[2024-01-24 13:38:37,661] [INFO] Running command: fastANI --query /var/lib/cwl/stge0eaf2bc-100a-43e7-aa16-86720510825a/GCF_014201825.1_ASM1420182v1_genomic.fna.gz --refList GCF_014201825.1_ASM1420182v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014201825.1_ASM1420182v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:38:44,597] [INFO] Task succeeded: fastANI
[2024-01-24 13:38:44,617] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:38:44,617] [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_014201825.1	s__Acidocella aromatica	100.0	944	944	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acidocella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000687875.1	s__Acidocella facilis	80.3215	503	944	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acidocella	95.0	98.02	98.02	0.93	0.93	2	-
GCA_018971725.1	s__Acidocella sp018971725	79.7388	295	944	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acidocella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018971905.1	s__Acidocella sp018971905	79.287	243	944	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acidocella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018971565.1	s__Acidocella sp018971565	79.2217	300	944	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acidocella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129125.1	s__Acidocella aminolytica	78.9546	375	944	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acidocella	95.0	99.99	99.99	0.99	0.99	2	-
GCA_003164135.1	s__Acidocella sp003164135	78.8453	381	944	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acidocella	95.0	99.77	99.73	0.97	0.95	5	-
GCA_013044125.1	s__Acidocella sp013044125	78.7939	367	944	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acidocella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003133265.1	s__PALSA-911 sp003133265	77.8062	175	944	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_018240635.1	s__JAFEFJ01 sp018240635	77.4532	210	944	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__JAFEFJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903924855.1	s__CAIQQQ01 sp903924855	77.3961	208	944	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__CAIQQQ01	95.0	99.77	99.77	0.89	0.89	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:38:44,620] [INFO] GTDB search result was written to GCF_014201825.1_ASM1420182v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:38:44,620] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:38:44,624] [INFO] DFAST_QC result json was written to GCF_014201825.1_ASM1420182v1_genomic.fna/dqc_result.json
[2024-01-24 13:38:44,624] [INFO] DFAST_QC completed!
[2024-01-24 13:38:44,625] [INFO] Total running time: 0h1m4s