[2023-06-28 19:49:40,769] [INFO] DFAST_QC pipeline started.
[2023-06-28 19:49:40,773] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 19:49:40,773] [INFO] DQC Reference Directory: /var/lib/cwl/stgf99d3e6c-8328-4d5b-b763-0501fab1a48d/dqc_reference
[2023-06-28 19:49:42,415] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 19:49:42,417] [INFO] Task started: Prodigal
[2023-06-28 19:49:42,417] [INFO] Running command: gunzip -c /var/lib/cwl/stg13b8df24-d10b-493e-b4dd-a12285695f06/GCA_027446845.1_ASM2744684v1_genomic.fna.gz | prodigal -d GCA_027446845.1_ASM2744684v1_genomic.fna/cds.fna -a GCA_027446845.1_ASM2744684v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 19:49:51,107] [INFO] Task succeeded: Prodigal
[2023-06-28 19:49:51,107] [INFO] Task started: HMMsearch
[2023-06-28 19:49:51,107] [INFO] Running command: hmmsearch --tblout GCA_027446845.1_ASM2744684v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf99d3e6c-8328-4d5b-b763-0501fab1a48d/dqc_reference/reference_markers.hmm GCA_027446845.1_ASM2744684v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 19:49:51,374] [INFO] Task succeeded: HMMsearch
[2023-06-28 19:49:51,376] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg13b8df24-d10b-493e-b4dd-a12285695f06/GCA_027446845.1_ASM2744684v1_genomic.fna.gz]
[2023-06-28 19:49:51,419] [INFO] Query marker FASTA was written to GCA_027446845.1_ASM2744684v1_genomic.fna/markers.fasta
[2023-06-28 19:49:51,419] [INFO] Task started: Blastn
[2023-06-28 19:49:51,420] [INFO] Running command: blastn -query GCA_027446845.1_ASM2744684v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf99d3e6c-8328-4d5b-b763-0501fab1a48d/dqc_reference/reference_markers.fasta -out GCA_027446845.1_ASM2744684v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 19:49:52,242] [INFO] Task succeeded: Blastn
[2023-06-28 19:49:52,247] [INFO] Selected 22 target genomes.
[2023-06-28 19:49:52,248] [INFO] Target genome list was writen to GCA_027446845.1_ASM2744684v1_genomic.fna/target_genomes.txt
[2023-06-28 19:49:52,250] [INFO] Task started: fastANI
[2023-06-28 19:49:52,250] [INFO] Running command: fastANI --query /var/lib/cwl/stg13b8df24-d10b-493e-b4dd-a12285695f06/GCA_027446845.1_ASM2744684v1_genomic.fna.gz --refList GCA_027446845.1_ASM2744684v1_genomic.fna/target_genomes.txt --output GCA_027446845.1_ASM2744684v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 19:50:12,027] [INFO] Task succeeded: fastANI
[2023-06-28 19:50:12,027] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf99d3e6c-8328-4d5b-b763-0501fab1a48d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 19:50:12,028] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf99d3e6c-8328-4d5b-b763-0501fab1a48d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 19:50:12,045] [INFO] Found 22 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 19:50:12,045] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 19:50:12,045] [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
Acidiphilium multivorum	strain=AIU301	GCA_000964345.1	62140	62140	type	True	78.0736	269	956	95	below_threshold
Rhodovastum atsumiense	strain=G2-11	GCA_937425535.1	504468	504468	type	True	77.9923	409	956	95	below_threshold
Acidiphilium multivorum	strain=AIU301	GCA_000202835.1	62140	62140	type	True	77.8196	313	956	95	below_threshold
Roseomonas rhizosphaerae	strain=YW11	GCA_002631185.1	1335062	1335062	type	True	77.5482	338	956	95	below_threshold
Rhodopila globiformis	strain=DSM 161	GCA_002937115.1	1071	1071	type	True	77.4568	338	956	95	below_threshold
Roseomonas cervicalis	strain=ATCC 49957	GCA_000164635.1	204525	204525	type	True	77.3281	330	956	95	below_threshold
Roseomonas coralli	strain=M0104	GCA_009829925.1	2545983	2545983	type	True	77.328	322	956	95	below_threshold
Roseomonas alkaliterrae	strain=DSM 25895	GCA_014199195.1	1452450	1452450	type	True	77.2612	392	956	95	below_threshold
Roseomonas oryzicola	strain=KCTC 22478	GCA_012163135.1	535904	535904	type	True	77.2215	383	956	95	below_threshold
Roseomonas rubea	strain=MO17	GCA_016106015.1	2748666	2748666	type	True	77.2011	310	956	95	below_threshold
Roseomonas mucosa	strain=NCTC13291	GCA_900455935.1	207340	207340	type	True	77.1394	301	956	95	below_threshold
Roseomonas hellenica	strain=LMG 31523	GCA_018129085.1	2687306	2687306	type	True	77.0854	370	956	95	below_threshold
Roseomonas mucosa	strain=ATCC BAA-692	GCA_000622225.1	207340	207340	type	True	77.066	309	956	95	below_threshold
Roseomonas oryzae	strain=KCTC 42542	GCA_008386565.1	1608942	1608942	type	True	77.0634	271	956	95	below_threshold
Belnapia moabensis	strain=DSM 16746	GCA_000745835.1	365533	365533	type	True	77.0507	327	956	95	below_threshold
Roseomonas haemaphysalidis	strain=546	GCA_017355405.1	2768162	2768162	type	True	77.0466	271	956	95	below_threshold
Roseococcus pinisoli	strain=XZZS9	GCA_018413645.1	2835040	2835040	type	True	77.0143	277	956	95	below_threshold
Roseomonas pecuniae	strain=DSM 25622	GCA_014199205.1	693023	693023	type	True	77.0122	298	956	95	below_threshold
Acidiphilium iwatense	strain=KCTC 23505	GCA_021556475.1	768198	768198	type	True	76.99	229	956	95	below_threshold
Belnapia arida	strain=T18	GCA_016773205.1	2804533	2804533	type	True	76.9706	317	956	95	below_threshold
Roseomonas aerilata	strain=DSM 19363	GCA_000711725.1	452982	452982	type	True	76.7766	310	956	95	below_threshold
Rhodovarius lipocyclicus	strain=CCUG 44693	GCA_009900765.1	268410	268410	type	True	76.6433	268	956	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 19:50:12,047] [INFO] DFAST Taxonomy check result was written to GCA_027446845.1_ASM2744684v1_genomic.fna/tc_result.tsv
[2023-06-28 19:50:12,048] [INFO] ===== Taxonomy check completed =====
[2023-06-28 19:50:12,048] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 19:50:12,048] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf99d3e6c-8328-4d5b-b763-0501fab1a48d/dqc_reference/checkm_data
[2023-06-28 19:50:12,050] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 19:50:12,083] [INFO] Task started: CheckM
[2023-06-28 19:50:12,083] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_027446845.1_ASM2744684v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_027446845.1_ASM2744684v1_genomic.fna/checkm_input GCA_027446845.1_ASM2744684v1_genomic.fna/checkm_result
[2023-06-28 19:50:42,061] [INFO] Task succeeded: CheckM
[2023-06-28 19:50:42,062] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 19:50:42,083] [INFO] ===== Completeness check finished =====
[2023-06-28 19:50:42,083] [INFO] ===== Start GTDB Search =====
[2023-06-28 19:50:42,084] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_027446845.1_ASM2744684v1_genomic.fna/markers.fasta)
[2023-06-28 19:50:42,084] [INFO] Task started: Blastn
[2023-06-28 19:50:42,084] [INFO] Running command: blastn -query GCA_027446845.1_ASM2744684v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf99d3e6c-8328-4d5b-b763-0501fab1a48d/dqc_reference/reference_markers_gtdb.fasta -out GCA_027446845.1_ASM2744684v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 19:50:43,500] [INFO] Task succeeded: Blastn
[2023-06-28 19:50:43,506] [INFO] Selected 27 target genomes.
[2023-06-28 19:50:43,506] [INFO] Target genome list was writen to GCA_027446845.1_ASM2744684v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 19:50:43,518] [INFO] Task started: fastANI
[2023-06-28 19:50:43,519] [INFO] Running command: fastANI --query /var/lib/cwl/stg13b8df24-d10b-493e-b4dd-a12285695f06/GCA_027446845.1_ASM2744684v1_genomic.fna.gz --refList GCA_027446845.1_ASM2744684v1_genomic.fna/target_genomes_gtdb.txt --output GCA_027446845.1_ASM2744684v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 19:51:06,943] [INFO] Task succeeded: fastANI
[2023-06-28 19:51:06,966] [INFO] Found 27 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 19:51:06,966] [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_001899585.1	s__70-18 sp001899585	78.6943	491	956	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_018240635.1	s__JAFEFJ01 sp018240635	78.2794	331	956	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__JAFEFJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000964365.1	s__Acidisphaera rubrifaciens	78.068	249	956	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acidisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017307285.1	s__JAFKFI01 sp017307285	77.9463	340	956	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__JAFKFI01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014644455.1	s__Caldovatus sediminis	77.9038	414	956	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Caldovatus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000202835.1	s__Acidiphilium multivorum	77.8299	312	956	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acidiphilium	95.0	98.69	98.42	0.90	0.87	6	-
GCF_004761865.1	s__Crenalkalicoccus roseus	77.7803	398	956	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Crenalkalicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903865895.1	s__CAIYPH01 sp903865895	77.6929	358	956	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	77.6379	340	956	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__BOG-930	95.0	99.84	99.84	0.94	0.94	2	-
GCF_003116135.1	s__Roseomonas aestuarii	77.4934	364	956	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903928895.1	s__CAIYPH01 sp903928895	77.4786	332	956	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__CAIYPH01	95.0	99.93	99.91	0.97	0.97	4	-
GCA_003151425.1	s__Palsa-883 sp003151425	77.4617	360	956	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Palsa-883	95.0	99.82	99.82	0.94	0.94	2	-
GCA_903881515.1	s__CAIRTN01 sp903881515	77.4311	287	956	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__CAIRTN01	95.0	99.60	99.60	0.90	0.90	2	-
GCA_903970625.1	s__CAJCJG01 sp903970625	77.4224	250	956	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__CAJCJG01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000164635.1	s__Roseomonas cervicalis	77.3906	323	956	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014199195.1	s__Roseomonas_B alkaliterrae	77.3445	381	956	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_004343615.1	s__Paracraurococcus sp004343615	77.2729	379	956	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Paracraurococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012927745.1	s__Roseomonas_B sp012927745	77.1934	347	956	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_016106015.1	s__Roseomonas_B sp016106015	77.1927	310	956	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_018129085.1	s__Roseomonas_C hellenica	77.1491	361	956	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas_C	95.0	97.71	97.71	0.92	0.92	2	-
GCA_007129145.1	s__Roseococcus sp007129145	77.0812	175	956	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000622225.1	s__Roseomonas mucosa	77.0652	308	956	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas	95.0	99.41	98.67	0.95	0.89	8	-
GCF_006438825.1	s__Roseomonas nepalensis	77.0627	340	956	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903928045.1	s__CAIYPH01 sp903928045	76.9588	258	956	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__CAIYPH01	95.0	98.55	98.55	0.76	0.76	2	-
GCF_016773205.1	s__Belnapia sp016773205	76.953	319	956	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Belnapia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016107305.1	s__Roseomonas sp016107305	76.8024	289	956	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000711725.1	s__Roseomonas aerilata	76.7454	312	956	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 19:51:06,968] [INFO] GTDB search result was written to GCA_027446845.1_ASM2744684v1_genomic.fna/result_gtdb.tsv
[2023-06-28 19:51:06,969] [INFO] ===== GTDB Search completed =====
[2023-06-28 19:51:06,978] [INFO] DFAST_QC result json was written to GCA_027446845.1_ASM2744684v1_genomic.fna/dqc_result.json
[2023-06-28 19:51:06,978] [INFO] DFAST_QC completed!
[2023-06-28 19:51:06,978] [INFO] Total running time: 0h1m26s