[2024-01-25 19:54:50,509] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:54:50,511] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:54:50,511] [INFO] DQC Reference Directory: /var/lib/cwl/stg26c71dc4-a552-4825-aa8b-41cb3d46480c/dqc_reference
[2024-01-25 19:54:51,719] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:54:51,720] [INFO] Task started: Prodigal
[2024-01-25 19:54:51,720] [INFO] Running command: gunzip -c /var/lib/cwl/stg10388543-6361-44d6-9d2a-e3d1df080440/GCF_012927745.1_ASM1292774v1_genomic.fna.gz | prodigal -d GCF_012927745.1_ASM1292774v1_genomic.fna/cds.fna -a GCF_012927745.1_ASM1292774v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:55:04,823] [INFO] Task succeeded: Prodigal
[2024-01-25 19:55:04,824] [INFO] Task started: HMMsearch
[2024-01-25 19:55:04,824] [INFO] Running command: hmmsearch --tblout GCF_012927745.1_ASM1292774v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg26c71dc4-a552-4825-aa8b-41cb3d46480c/dqc_reference/reference_markers.hmm GCF_012927745.1_ASM1292774v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:55:05,146] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:55:05,147] [INFO] Found 6/6 markers.
[2024-01-25 19:55:05,192] [INFO] Query marker FASTA was written to GCF_012927745.1_ASM1292774v1_genomic.fna/markers.fasta
[2024-01-25 19:55:05,192] [INFO] Task started: Blastn
[2024-01-25 19:55:05,192] [INFO] Running command: blastn -query GCF_012927745.1_ASM1292774v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg26c71dc4-a552-4825-aa8b-41cb3d46480c/dqc_reference/reference_markers.fasta -out GCF_012927745.1_ASM1292774v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:55:06,091] [INFO] Task succeeded: Blastn
[2024-01-25 19:55:06,095] [INFO] Selected 14 target genomes.
[2024-01-25 19:55:06,095] [INFO] Target genome list was writen to GCF_012927745.1_ASM1292774v1_genomic.fna/target_genomes.txt
[2024-01-25 19:55:06,096] [INFO] Task started: fastANI
[2024-01-25 19:55:06,096] [INFO] Running command: fastANI --query /var/lib/cwl/stg10388543-6361-44d6-9d2a-e3d1df080440/GCF_012927745.1_ASM1292774v1_genomic.fna.gz --refList GCF_012927745.1_ASM1292774v1_genomic.fna/target_genomes.txt --output GCF_012927745.1_ASM1292774v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:55:23,052] [INFO] Task succeeded: fastANI
[2024-01-25 19:55:23,052] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg26c71dc4-a552-4825-aa8b-41cb3d46480c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:55:23,052] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg26c71dc4-a552-4825-aa8b-41cb3d46480c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:55:23,062] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 19:55:23,062] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 19:55:23,062] [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
Roseomonas oryzicola	strain=KCTC 22478	GCA_012163135.1	535904	535904	type	True	93.1806	1472	1703	95	below_threshold
Roseomonas alkaliterrae	strain=DSM 25895	GCA_014199195.1	1452450	1452450	type	True	84.1815	1084	1703	95	below_threshold
Roseomonas rubea	strain=MO17	GCA_016106015.1	2748666	2748666	type	True	83.8892	924	1703	95	below_threshold
Roseomonas lacus	strain=CGMCC 1.3617	GCA_014644535.1	287609	287609	type	True	82.7343	1210	1703	95	below_threshold
Roseomonas hellenica	strain=LMG 31523	GCA_018129085.1	2687306	2687306	type	True	79.5859	895	1703	95	below_threshold
Roseomonas coralli	strain=M0104	GCA_009829925.1	2545983	2545983	type	True	78.9972	659	1703	95	below_threshold
Belnapia mucosa	strain=T6	GCA_016775475.1	2804532	2804532	type	True	78.9674	801	1703	95	below_threshold
Siccirubricoccus deserti	strain=CGMCC 1.15936	GCA_014644195.1	2013562	2013562	type	True	78.8821	755	1703	95	below_threshold
Roseomonas gilardii subsp. rosea	strain=NCTC13290	GCA_900455865.1	243956	257708	type	True	78.8737	557	1703	95	below_threshold
Siccirubricoccus deserti	strain=SYSU D8009	GCA_014283215.1	2013562	2013562	type	True	78.8282	766	1703	95	below_threshold
Roseococcus pinisoli	strain=XZZS9	GCA_018413645.1	2835040	2835040	type	True	78.8104	712	1703	95	below_threshold
Rhodovarius crocodyli	strain=CCP-6	GCA_004005855.1	1979269	1979269	type	True	78.4488	659	1703	95	below_threshold
Roseomonas marmotae	strain=1318	GCA_017654485.1	2768161	2768161	type	True	78.2011	559	1703	95	below_threshold
Roseomonas haemaphysalidis	strain=546	GCA_017355405.1	2768162	2768162	type	True	78.1782	580	1703	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:55:23,063] [INFO] DFAST Taxonomy check result was written to GCF_012927745.1_ASM1292774v1_genomic.fna/tc_result.tsv
[2024-01-25 19:55:23,064] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:55:23,064] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:55:23,064] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg26c71dc4-a552-4825-aa8b-41cb3d46480c/dqc_reference/checkm_data
[2024-01-25 19:55:23,065] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:55:23,113] [INFO] Task started: CheckM
[2024-01-25 19:55:23,113] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_012927745.1_ASM1292774v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_012927745.1_ASM1292774v1_genomic.fna/checkm_input GCF_012927745.1_ASM1292774v1_genomic.fna/checkm_result
[2024-01-25 19:56:44,325] [INFO] Task succeeded: CheckM
[2024-01-25 19:56:44,326] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:56:44,342] [INFO] ===== Completeness check finished =====
[2024-01-25 19:56:44,342] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:56:44,343] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_012927745.1_ASM1292774v1_genomic.fna/markers.fasta)
[2024-01-25 19:56:44,343] [INFO] Task started: Blastn
[2024-01-25 19:56:44,344] [INFO] Running command: blastn -query GCF_012927745.1_ASM1292774v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg26c71dc4-a552-4825-aa8b-41cb3d46480c/dqc_reference/reference_markers_gtdb.fasta -out GCF_012927745.1_ASM1292774v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:56:46,057] [INFO] Task succeeded: Blastn
[2024-01-25 19:56:46,060] [INFO] Selected 10 target genomes.
[2024-01-25 19:56:46,060] [INFO] Target genome list was writen to GCF_012927745.1_ASM1292774v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:56:46,065] [INFO] Task started: fastANI
[2024-01-25 19:56:46,065] [INFO] Running command: fastANI --query /var/lib/cwl/stg10388543-6361-44d6-9d2a-e3d1df080440/GCF_012927745.1_ASM1292774v1_genomic.fna.gz --refList GCF_012927745.1_ASM1292774v1_genomic.fna/target_genomes_gtdb.txt --output GCF_012927745.1_ASM1292774v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:57:00,587] [INFO] Task succeeded: fastANI
[2024-01-25 19:57:00,594] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:57:00,595] [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_012927745.1	s__Roseomonas_B sp012927745	100.0	1701	1703	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas_B	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_012163135.1	s__Roseomonas_B oryzicola	93.1934	1471	1703	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas_B	95.0	99.99	99.99	1.00	1.00	2	-
GCF_018129065.1	s__Roseomonas_B soli	84.9674	1143	1703	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018129005.1	s__Roseomonas_B eburnea	84.7557	1229	1703	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017813355.1	s__Roseomonas_B sp017813355	84.355	1164	1703	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014199195.1	s__Roseomonas_B alkaliterrae	84.2213	1079	1703	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas_B	95.0	99.89	99.89	0.97	0.97	2	-
GCF_016106005.1	s__Roseomonas_B sp016106005	84.1233	996	1703	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005222755.1	s__Roseomonas_B sp005222755	83.8105	1195	1703	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018129025.1	s__Roseomonas_B terrae	82.9324	1108	1703	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014644535.1	s__Roseomonas_B lacus	82.7283	1211	1703	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas_B	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:57:00,596] [INFO] GTDB search result was written to GCF_012927745.1_ASM1292774v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:57:00,596] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:57:00,599] [INFO] DFAST_QC result json was written to GCF_012927745.1_ASM1292774v1_genomic.fna/dqc_result.json
[2024-01-25 19:57:00,599] [INFO] DFAST_QC completed!
[2024-01-25 19:57:00,599] [INFO] Total running time: 0h2m10s