[2024-01-24 12:06:24,695] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:06:24,697] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:06:24,697] [INFO] DQC Reference Directory: /var/lib/cwl/stg260638fd-7695-4186-9763-40e891b7b741/dqc_reference
[2024-01-24 12:06:25,951] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:06:25,952] [INFO] Task started: Prodigal
[2024-01-24 12:06:25,952] [INFO] Running command: gunzip -c /var/lib/cwl/stg1d2d8e0c-9bf2-4517-bc0a-b4f760ec4fc3/GCF_019430885.1_ASM1943088v1_genomic.fna.gz | prodigal -d GCF_019430885.1_ASM1943088v1_genomic.fna/cds.fna -a GCF_019430885.1_ASM1943088v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:06:45,203] [INFO] Task succeeded: Prodigal
[2024-01-24 12:06:45,203] [INFO] Task started: HMMsearch
[2024-01-24 12:06:45,204] [INFO] Running command: hmmsearch --tblout GCF_019430885.1_ASM1943088v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg260638fd-7695-4186-9763-40e891b7b741/dqc_reference/reference_markers.hmm GCF_019430885.1_ASM1943088v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:06:45,501] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:06:45,502] [INFO] Found 6/6 markers.
[2024-01-24 12:06:45,551] [INFO] Query marker FASTA was written to GCF_019430885.1_ASM1943088v1_genomic.fna/markers.fasta
[2024-01-24 12:06:45,551] [INFO] Task started: Blastn
[2024-01-24 12:06:45,551] [INFO] Running command: blastn -query GCF_019430885.1_ASM1943088v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg260638fd-7695-4186-9763-40e891b7b741/dqc_reference/reference_markers.fasta -out GCF_019430885.1_ASM1943088v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:06:46,392] [INFO] Task succeeded: Blastn
[2024-01-24 12:06:46,395] [INFO] Selected 18 target genomes.
[2024-01-24 12:06:46,396] [INFO] Target genome list was writen to GCF_019430885.1_ASM1943088v1_genomic.fna/target_genomes.txt
[2024-01-24 12:06:46,404] [INFO] Task started: fastANI
[2024-01-24 12:06:46,404] [INFO] Running command: fastANI --query /var/lib/cwl/stg1d2d8e0c-9bf2-4517-bc0a-b4f760ec4fc3/GCF_019430885.1_ASM1943088v1_genomic.fna.gz --refList GCF_019430885.1_ASM1943088v1_genomic.fna/target_genomes.txt --output GCF_019430885.1_ASM1943088v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:07:06,483] [INFO] Task succeeded: fastANI
[2024-01-24 12:07:06,484] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg260638fd-7695-4186-9763-40e891b7b741/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:07:06,484] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg260638fd-7695-4186-9763-40e891b7b741/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:07:06,500] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:07:06,500] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:07:06,500] [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	83.7684	1212	2094	95	below_threshold
Roseomonas lacus	strain=CGMCC 1.3617	GCA_014644535.1	287609	287609	type	True	83.2535	1395	2094	95	below_threshold
Roseomonas alkaliterrae	strain=DSM 25895	GCA_014199195.1	1452450	1452450	type	True	82.7868	1069	2094	95	below_threshold
Roseomonas rubea	strain=MO17	GCA_016106015.1	2748666	2748666	type	True	82.527	908	2094	95	below_threshold
Roseomonas hellenica	strain=LMG 31523	GCA_018129085.1	2687306	2687306	type	True	79.3465	928	2094	95	below_threshold
Siccirubricoccus deserti	strain=SYSU D8009	GCA_014283215.1	2013562	2013562	type	True	78.8783	795	2094	95	below_threshold
Roseomonas rhizosphaerae	strain=YW11	GCA_002631185.1	1335062	1335062	type	True	78.8252	719	2094	95	below_threshold
Belnapia rosea	strain=CPCC 100156	GCA_900101615.1	938405	938405	type	True	78.7705	798	2094	95	below_threshold
Belnapia mucosa	strain=T6	GCA_016775475.1	2804532	2804532	type	True	78.7188	839	2094	95	below_threshold
Rhodovarius lipocyclicus	strain=CCUG 44693	GCA_009900765.1	268410	268410	type	True	78.7152	711	2094	95	below_threshold
Roseococcus pinisoli	strain=XZZS9	GCA_018413645.1	2835040	2835040	type	True	78.5137	698	2094	95	below_threshold
Rhodovarius crocodyli	strain=CCP-6	GCA_004005855.1	1979269	1979269	type	True	78.3203	720	2094	95	below_threshold
Roseomonas marmotae	strain=1318	GCA_017654485.1	2768161	2768161	type	True	78.2859	583	2094	95	below_threshold
Roseomonas rosea	strain=DSM 14916	GCA_900141905.1	198092	198092	type	True	78.128	648	2094	95	below_threshold
Elioraea tepida	strain=MS-P2	GCA_019203965.1	2843330	2843330	type	True	76.7471	372	2094	95	below_threshold
Novosphingobium flavum	strain=NBRC 111647	GCA_014230315.1	1778672	1778672	type	True	75.7135	164	2094	95	below_threshold
Novosphingobium percolationis	strain=c1	GCA_020179425.1	2871811	2871811	type	True	75.5445	185	2094	95	below_threshold
Pseudoduganella dura	strain=KCTC 12342	GCA_014651395.1	321982	321982	type	True	74.9669	215	2094	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:07:06,502] [INFO] DFAST Taxonomy check result was written to GCF_019430885.1_ASM1943088v1_genomic.fna/tc_result.tsv
[2024-01-24 12:07:06,503] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:07:06,503] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:07:06,504] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg260638fd-7695-4186-9763-40e891b7b741/dqc_reference/checkm_data
[2024-01-24 12:07:06,505] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:07:06,565] [INFO] Task started: CheckM
[2024-01-24 12:07:06,566] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019430885.1_ASM1943088v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019430885.1_ASM1943088v1_genomic.fna/checkm_input GCF_019430885.1_ASM1943088v1_genomic.fna/checkm_result
[2024-01-24 12:08:42,002] [INFO] Task succeeded: CheckM
[2024-01-24 12:08:42,004] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:08:42,023] [INFO] ===== Completeness check finished =====
[2024-01-24 12:08:42,024] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:08:42,024] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019430885.1_ASM1943088v1_genomic.fna/markers.fasta)
[2024-01-24 12:08:42,024] [INFO] Task started: Blastn
[2024-01-24 12:08:42,024] [INFO] Running command: blastn -query GCF_019430885.1_ASM1943088v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg260638fd-7695-4186-9763-40e891b7b741/dqc_reference/reference_markers_gtdb.fasta -out GCF_019430885.1_ASM1943088v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:08:43,334] [INFO] Task succeeded: Blastn
[2024-01-24 12:08:43,338] [INFO] Selected 14 target genomes.
[2024-01-24 12:08:43,338] [INFO] Target genome list was writen to GCF_019430885.1_ASM1943088v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:08:43,348] [INFO] Task started: fastANI
[2024-01-24 12:08:43,348] [INFO] Running command: fastANI --query /var/lib/cwl/stg1d2d8e0c-9bf2-4517-bc0a-b4f760ec4fc3/GCF_019430885.1_ASM1943088v1_genomic.fna.gz --refList GCF_019430885.1_ASM1943088v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019430885.1_ASM1943088v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:09:02,881] [INFO] Task succeeded: fastANI
[2024-01-24 12:09:02,893] [INFO] Found 14 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:09:02,893] [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_012163135.1	s__Roseomonas_B oryzicola	83.801	1208	2094	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_018129005.1	s__Roseomonas_B eburnea	83.7445	1318	2094	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_012927745.1	s__Roseomonas_B sp012927745	83.4027	1194	2094	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	83.3645	1256	2094	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_018129065.1	s__Roseomonas_B soli	83.2854	1170	2094	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	83.2534	1394	2094	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_016106005.1	s__Roseomonas_B sp016106005	82.9237	962	2094	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	82.7788	1069	2094	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_017813355.1	s__Roseomonas_B sp017813355	82.5804	1139	2094	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	82.062	1178	2094	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_003258945.1	s__Paracraurococcus frigidaeris	79.3131	888	2094	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Paracraurococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003173615.1	s__Roseomonas_A sp003173615	79.3031	887	2094	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014644455.1	s__Caldovatus sediminis	79.2864	791	2094	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Caldovatus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005222815.1	s__Roseomonas_A sp005222815	79.0974	888	2094	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:09:02,894] [INFO] GTDB search result was written to GCF_019430885.1_ASM1943088v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:09:02,895] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:09:02,899] [INFO] DFAST_QC result json was written to GCF_019430885.1_ASM1943088v1_genomic.fna/dqc_result.json
[2024-01-24 12:09:02,899] [INFO] DFAST_QC completed!
[2024-01-24 12:09:02,899] [INFO] Total running time: 0h2m38s