[2023-06-29 16:04:12,422] [INFO] DFAST_QC pipeline started.
[2023-06-29 16:04:12,427] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 16:04:12,427] [INFO] DQC Reference Directory: /var/lib/cwl/stg949dcebf-a081-4818-a971-9e8607f62d63/dqc_reference
[2023-06-29 16:04:15,004] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 16:04:15,005] [INFO] Task started: Prodigal
[2023-06-29 16:04:15,006] [INFO] Running command: gunzip -c /var/lib/cwl/stge6d2b683-0efb-4b2f-aaec-199b7e3c42e5/GCA_021832865.1_ASM2183286v1_genomic.fna.gz | prodigal -d GCA_021832865.1_ASM2183286v1_genomic.fna/cds.fna -a GCA_021832865.1_ASM2183286v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 16:04:20,949] [INFO] Task succeeded: Prodigal
[2023-06-29 16:04:20,949] [INFO] Task started: HMMsearch
[2023-06-29 16:04:20,950] [INFO] Running command: hmmsearch --tblout GCA_021832865.1_ASM2183286v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg949dcebf-a081-4818-a971-9e8607f62d63/dqc_reference/reference_markers.hmm GCA_021832865.1_ASM2183286v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 16:04:21,169] [INFO] Task succeeded: HMMsearch
[2023-06-29 16:04:21,170] [WARNING] Found 5/6 markers. [/var/lib/cwl/stge6d2b683-0efb-4b2f-aaec-199b7e3c42e5/GCA_021832865.1_ASM2183286v1_genomic.fna.gz]
[2023-06-29 16:04:21,204] [INFO] Query marker FASTA was written to GCA_021832865.1_ASM2183286v1_genomic.fna/markers.fasta
[2023-06-29 16:04:21,205] [INFO] Task started: Blastn
[2023-06-29 16:04:21,205] [INFO] Running command: blastn -query GCA_021832865.1_ASM2183286v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg949dcebf-a081-4818-a971-9e8607f62d63/dqc_reference/reference_markers.fasta -out GCA_021832865.1_ASM2183286v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 16:04:21,729] [INFO] Task succeeded: Blastn
[2023-06-29 16:04:21,734] [INFO] Selected 22 target genomes.
[2023-06-29 16:04:21,735] [INFO] Target genome list was writen to GCA_021832865.1_ASM2183286v1_genomic.fna/target_genomes.txt
[2023-06-29 16:04:21,736] [INFO] Task started: fastANI
[2023-06-29 16:04:21,736] [INFO] Running command: fastANI --query /var/lib/cwl/stge6d2b683-0efb-4b2f-aaec-199b7e3c42e5/GCA_021832865.1_ASM2183286v1_genomic.fna.gz --refList GCA_021832865.1_ASM2183286v1_genomic.fna/target_genomes.txt --output GCA_021832865.1_ASM2183286v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 16:04:38,277] [INFO] Task succeeded: fastANI
[2023-06-29 16:04:38,278] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg949dcebf-a081-4818-a971-9e8607f62d63/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 16:04:38,278] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg949dcebf-a081-4818-a971-9e8607f62d63/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 16:04:38,297] [INFO] Found 22 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 16:04:38,298] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 16:04:38,298] [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	77.5976	169	576	95	below_threshold
Rhodopila globiformis	strain=DSM 161	GCA_002937115.1	1071	1071	type	True	77.4859	199	576	95	below_threshold
Rhodovastum atsumiense	strain=G2-11	GCA_937425535.1	504468	504468	type	True	77.374	238	576	95	below_threshold
Roseomonas cervicalis	strain=ATCC 49957	GCA_000164635.1	204525	204525	type	True	77.3316	197	576	95	below_threshold
Roseomonas alkaliterrae	strain=DSM 25895	GCA_014199195.1	1452450	1452450	type	True	77.2725	225	576	95	below_threshold
Endobacter medicaginis	strain=LMG 26838	GCA_013376135.1	1181271	1181271	type	True	77.2403	86	576	95	below_threshold
Roseomonas oryzicola	strain=KCTC 22478	GCA_012163135.1	535904	535904	type	True	77.2246	204	576	95	below_threshold
Roseomonas coralli	strain=M0104	GCA_009829925.1	2545983	2545983	type	True	76.9573	204	576	95	below_threshold
Roseomonas aerilata	strain=DSM 19363	GCA_000711725.1	452982	452982	type	True	76.9447	160	576	95	below_threshold
Roseomonas aerophila	strain=NBRC 108923	GCA_014490485.1	1224513	1224513	type	True	76.9398	144	576	95	below_threshold
Endobacter medicaginis	strain=CECT 8088	GCA_014192375.1	1181271	1181271	type	True	76.9022	135	576	95	below_threshold
Belnapia arida	strain=T18	GCA_016773205.1	2804533	2804533	type	True	76.8709	180	576	95	below_threshold
Roseomonas rubea	strain=MO17	GCA_016106015.1	2748666	2748666	type	True	76.8277	187	576	95	below_threshold
Acidiphilium iwatense	strain=KCTC 23505	GCA_021556475.1	768198	768198	type	True	76.7439	128	576	95	below_threshold
Belnapia moabensis	strain=DSM 16746	GCA_000745835.1	365533	365533	type	True	76.7238	185	576	95	below_threshold
Roseococcus pinisoli	strain=XZZS9	GCA_018413645.1	2835040	2835040	type	True	76.7187	163	576	95	below_threshold
Roseomonas haemaphysalidis	strain=546	GCA_017355405.1	2768162	2768162	type	True	76.6749	173	576	95	below_threshold
Belnapia mucosa	strain=T6	GCA_016775475.1	2804532	2804532	type	True	76.609	199	576	95	below_threshold
Gluconacetobacter diazotrophicus	strain=PAl 5; ATCC 49037	GCA_000021325.1	33996	33996	type	True	76.6067	89	576	95	below_threshold
Gluconacetobacter diazotrophicus	strain=LMG 7603	GCA_014174315.1	33996	33996	type	True	76.5344	89	576	95	below_threshold
Roseomonas marmotae	strain=1318	GCA_017654485.1	2768161	2768161	type	True	76.526	149	576	95	below_threshold
Gluconacetobacter diazotrophicus	strain=PAl 5	GCA_000067045.1	33996	33996	type	True	76.5195	91	576	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 16:04:38,314] [INFO] DFAST Taxonomy check result was written to GCA_021832865.1_ASM2183286v1_genomic.fna/tc_result.tsv
[2023-06-29 16:04:38,315] [INFO] ===== Taxonomy check completed =====
[2023-06-29 16:04:38,315] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 16:04:38,316] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg949dcebf-a081-4818-a971-9e8607f62d63/dqc_reference/checkm_data
[2023-06-29 16:04:38,318] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 16:04:38,356] [INFO] Task started: CheckM
[2023-06-29 16:04:38,356] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_021832865.1_ASM2183286v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_021832865.1_ASM2183286v1_genomic.fna/checkm_input GCA_021832865.1_ASM2183286v1_genomic.fna/checkm_result
[2023-06-29 16:05:01,313] [INFO] Task succeeded: CheckM
[2023-06-29 16:05:01,314] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 80.30%
Contamintation: 5.21%
Strain heterogeneity: 33.33%
--------------------------------------------------------------------------------
[2023-06-29 16:05:01,339] [INFO] ===== Completeness check finished =====
[2023-06-29 16:05:01,339] [INFO] ===== Start GTDB Search =====
[2023-06-29 16:05:01,339] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_021832865.1_ASM2183286v1_genomic.fna/markers.fasta)
[2023-06-29 16:05:01,340] [INFO] Task started: Blastn
[2023-06-29 16:05:01,340] [INFO] Running command: blastn -query GCA_021832865.1_ASM2183286v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg949dcebf-a081-4818-a971-9e8607f62d63/dqc_reference/reference_markers_gtdb.fasta -out GCA_021832865.1_ASM2183286v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 16:05:01,896] [INFO] Task succeeded: Blastn
[2023-06-29 16:05:01,901] [INFO] Selected 23 target genomes.
[2023-06-29 16:05:01,901] [INFO] Target genome list was writen to GCA_021832865.1_ASM2183286v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 16:05:01,907] [INFO] Task started: fastANI
[2023-06-29 16:05:01,907] [INFO] Running command: fastANI --query /var/lib/cwl/stge6d2b683-0efb-4b2f-aaec-199b7e3c42e5/GCA_021832865.1_ASM2183286v1_genomic.fna.gz --refList GCA_021832865.1_ASM2183286v1_genomic.fna/target_genomes_gtdb.txt --output GCA_021832865.1_ASM2183286v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 16:05:23,918] [INFO] Task succeeded: fastANI
[2023-06-29 16:05:23,939] [INFO] Found 23 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 16:05:23,940] [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	78.4735	279	576	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	77.8134	194	576	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_014644455.1	s__Caldovatus sediminis	77.7767	248	576	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Caldovatus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000964365.1	s__Acidisphaera rubrifaciens	77.7575	132	576	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	77.7557	186	576	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__JAFKFI01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017304945.1	s__69-11 sp017304945	77.589	225	576	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__69-11	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004761865.1	s__Crenalkalicoccus roseus	77.483	239	576	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Crenalkalicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008630155.1	s__Rhodovastum atsumiense	77.3926	236	576	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Rhodovastum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903970625.1	s__CAJCJG01 sp903970625	77.3682	146	576	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__CAJCJG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903865895.1	s__CAIYPH01 sp903865895	77.3307	224	576	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__CAIYPH01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903881515.1	s__CAIRTN01 sp903881515	77.2401	173	576	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__CAIRTN01	95.0	99.60	99.60	0.90	0.90	2	-
GCF_004343615.1	s__Paracraurococcus sp004343615	77.1927	212	576	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Paracraurococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005844085.1	s__Lichenicoccus roseus	77.1613	141	576	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Lichenicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017813355.1	s__Roseomonas_B sp017813355	76.9812	230	576	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_009829925.1	s__Roseomonas coralli	76.9697	203	576	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005222755.1	s__Roseomonas_B sp005222755	76.9519	216	576	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903944925.1	s__Rhodopila sp903944925	76.9276	149	576	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Rhodopila	95.0	99.96	99.95	0.97	0.97	3	-
GCF_014490485.1	s__Roseomonas aerophila	76.9225	145	576	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	76.9147	162	576	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	76.8286	158	576	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__CAIYPH01	95.0	98.55	98.55	0.76	0.76	2	-
GCF_016107305.1	s__Roseomonas sp016107305	76.6076	159	576	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006438825.1	s__Roseomonas nepalensis	76.5498	209	576	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015223225.1	s__Roseomonas sp015223225	76.4252	149	576	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 16:05:23,942] [INFO] GTDB search result was written to GCA_021832865.1_ASM2183286v1_genomic.fna/result_gtdb.tsv
[2023-06-29 16:05:23,942] [INFO] ===== GTDB Search completed =====
[2023-06-29 16:05:23,947] [INFO] DFAST_QC result json was written to GCA_021832865.1_ASM2183286v1_genomic.fna/dqc_result.json
[2023-06-29 16:05:23,947] [INFO] DFAST_QC completed!
[2023-06-29 16:05:23,947] [INFO] Total running time: 0h1m12s