[2024-01-24 13:31:33,656] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:31:33,658] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:31:33,658] [INFO] DQC Reference Directory: /var/lib/cwl/stg7231d244-16b2-4d34-b46f-2205a3689827/dqc_reference
[2024-01-24 13:31:35,021] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:31:35,022] [INFO] Task started: Prodigal
[2024-01-24 13:31:35,023] [INFO] Running command: gunzip -c /var/lib/cwl/stgbc3585d0-4085-4111-a642-4b8dda250ed7/GCF_900155435.1_PRJEB18758_genomic.fna.gz | prodigal -d GCF_900155435.1_PRJEB18758_genomic.fna/cds.fna -a GCF_900155435.1_PRJEB18758_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:31:45,865] [INFO] Task succeeded: Prodigal
[2024-01-24 13:31:45,866] [INFO] Task started: HMMsearch
[2024-01-24 13:31:45,866] [INFO] Running command: hmmsearch --tblout GCF_900155435.1_PRJEB18758_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7231d244-16b2-4d34-b46f-2205a3689827/dqc_reference/reference_markers.hmm GCF_900155435.1_PRJEB18758_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:31:46,143] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:31:46,144] [INFO] Found 6/6 markers.
[2024-01-24 13:31:46,182] [INFO] Query marker FASTA was written to GCF_900155435.1_PRJEB18758_genomic.fna/markers.fasta
[2024-01-24 13:31:46,183] [INFO] Task started: Blastn
[2024-01-24 13:31:46,183] [INFO] Running command: blastn -query GCF_900155435.1_PRJEB18758_genomic.fna/markers.fasta -db /var/lib/cwl/stg7231d244-16b2-4d34-b46f-2205a3689827/dqc_reference/reference_markers.fasta -out GCF_900155435.1_PRJEB18758_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:31:47,284] [INFO] Task succeeded: Blastn
[2024-01-24 13:31:47,288] [INFO] Selected 25 target genomes.
[2024-01-24 13:31:47,289] [INFO] Target genome list was writen to GCF_900155435.1_PRJEB18758_genomic.fna/target_genomes.txt
[2024-01-24 13:31:47,296] [INFO] Task started: fastANI
[2024-01-24 13:31:47,296] [INFO] Running command: fastANI --query /var/lib/cwl/stgbc3585d0-4085-4111-a642-4b8dda250ed7/GCF_900155435.1_PRJEB18758_genomic.fna.gz --refList GCF_900155435.1_PRJEB18758_genomic.fna/target_genomes.txt --output GCF_900155435.1_PRJEB18758_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:32:02,033] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:02,034] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7231d244-16b2-4d34-b46f-2205a3689827/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:32:02,034] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7231d244-16b2-4d34-b46f-2205a3689827/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:32:02,052] [INFO] Found 25 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:32:02,052] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:32:02,053] [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
Actinomyces provencensis	strain=SN12	GCA_900155435.1	1720198	1720198	type	True	99.9998	1106	1107	95	conclusive
Actinomyces polynesiensis	strain=MS2	GCA_000820725.1	1325934	1325934	type	True	88.5573	632	1107	95	below_threshold
Schaalia hyovaginalis	strain=DSM 10695	GCA_014208035.1	29316	29316	type	True	78.7359	281	1107	95	below_threshold
Actinomyces haliotis	strain=JCM 18848	GCA_015355765.1	1280843	1280843	type	True	78.3486	244	1107	95	below_threshold
Actinomyces viscosus	strain=CCUG 14476	GCA_004525795.1	1656	1656	type	True	78.1707	243	1107	95	below_threshold
Schaalia meyeri	strain=FDAARGOS_985	GCA_016127995.1	52773	52773	type	True	78.1186	182	1107	95	below_threshold
Actinomyces viscosus	strain=NCTC10951	GCA_900637975.1	1656	1656	type	True	78.0799	251	1107	95	below_threshold
Actinomyces radicidentis	strain=CCUG 36733	GCA_001553565.1	111015	111015	type	True	78.0424	287	1107	95	below_threshold
Actinomyces urogenitalis	strain=DSM 15434	GCA_000159035.1	103621	103621	type	True	78.0147	204	1107	95	below_threshold
Schaalia meyeri	strain=DSM 20733	GCA_900105015.1	52773	52773	type	True	77.9955	189	1107	95	below_threshold
Actinomyces faecalis	strain=ZJ34	GCA_013184985.2	2722820	2722820	type	True	77.9743	192	1107	95	below_threshold
Actinomyces dentalis	strain=DSM 19115	GCA_000429225.1	272548	272548	type	True	77.9289	266	1107	95	below_threshold
Actinomyces weissii	strain=CCUG 61299	GCA_016598775.1	675090	675090	type	True	77.8025	202	1107	95	below_threshold
Actinomyces israelii	strain=DSM 43320	GCA_000711965.1	1659	1659	type	True	77.7988	271	1107	95	below_threshold
Actinomyces ruminicola	strain=DSM 27982	GCA_900103885.1	332524	332524	type	True	77.7731	227	1107	95	below_threshold
Georgenia yuyongxinii	strain=Z443	GCA_006352065.1	2589797	2589797	type	True	77.6846	246	1107	95	below_threshold
Georgenia thermotolerans	strain=NBRC 104148	GCA_009193185.1	527326	527326	type	True	77.6761	280	1107	95	below_threshold
Georgenia subflava	strain=JCM 19765	GCA_009362315.1	1622177	1622177	type	True	77.6278	236	1107	95	below_threshold
Georgenia subflava	strain=CGMCC 1.12782	GCA_009193155.1	1622177	1622177	type	True	77.5626	247	1107	95	below_threshold
Oceanitalea stevensii	strain=Sa1BUA1	GCA_014837105.1	2763072	2763072	type	True	77.5594	251	1107	95	below_threshold
Actinomyces procaprae	strain=dk561	GCA_004798665.1	2560010	2560010	type	True	77.4328	218	1107	95	below_threshold
Micrococcus luteus	strain=ATCC 4698	GCA_003417425.1	1270	1270	type	True	77.1877	141	1107	95	below_threshold
Oerskovia douganii	strain=Sa1BUA8	GCA_015142735.1	2762210	2762210	type	True	76.8419	207	1107	95	below_threshold
Actinotalea solisilvae	strain=KACC 19191	GCA_016464425.1	2072922	2072922	type	True	76.5864	203	1107	95	below_threshold
Occultella gossypii	strain=N2-46	GCA_019947135.1	2800820	2800820	type	True	76.5215	188	1107	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:32:02,054] [INFO] DFAST Taxonomy check result was written to GCF_900155435.1_PRJEB18758_genomic.fna/tc_result.tsv
[2024-01-24 13:32:02,055] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:32:02,055] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:32:02,055] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7231d244-16b2-4d34-b46f-2205a3689827/dqc_reference/checkm_data
[2024-01-24 13:32:02,057] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:32:02,092] [INFO] Task started: CheckM
[2024-01-24 13:32:02,092] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900155435.1_PRJEB18758_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900155435.1_PRJEB18758_genomic.fna/checkm_input GCF_900155435.1_PRJEB18758_genomic.fna/checkm_result
[2024-01-24 13:33:26,248] [INFO] Task succeeded: CheckM
[2024-01-24 13:33:26,249] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:33:26,265] [INFO] ===== Completeness check finished =====
[2024-01-24 13:33:26,265] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:33:26,265] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900155435.1_PRJEB18758_genomic.fna/markers.fasta)
[2024-01-24 13:33:26,266] [INFO] Task started: Blastn
[2024-01-24 13:33:26,266] [INFO] Running command: blastn -query GCF_900155435.1_PRJEB18758_genomic.fna/markers.fasta -db /var/lib/cwl/stg7231d244-16b2-4d34-b46f-2205a3689827/dqc_reference/reference_markers_gtdb.fasta -out GCF_900155435.1_PRJEB18758_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:33:27,902] [INFO] Task succeeded: Blastn
[2024-01-24 13:33:27,906] [INFO] Selected 16 target genomes.
[2024-01-24 13:33:27,907] [INFO] Target genome list was writen to GCF_900155435.1_PRJEB18758_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:33:27,926] [INFO] Task started: fastANI
[2024-01-24 13:33:27,927] [INFO] Running command: fastANI --query /var/lib/cwl/stgbc3585d0-4085-4111-a642-4b8dda250ed7/GCF_900155435.1_PRJEB18758_genomic.fna.gz --refList GCF_900155435.1_PRJEB18758_genomic.fna/target_genomes_gtdb.txt --output GCF_900155435.1_PRJEB18758_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:33:36,490] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:36,509] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:33:36,509] [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_900155435.1	s__Pauljensenia provencensis	99.9998	1106	1107	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Pauljensenia	95.0	96.43	96.43	0.91	0.91	2	conclusive
GCF_000820725.1	s__Pauljensenia polynesiensis	88.6246	629	1107	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Pauljensenia	95.0	100.00	100.00	0.98	0.98	2	-
GCF_900499005.1	s__Pauljensenia culturomici	79.1342	326	1107	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Pauljensenia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001746855.1	s__Pauljensenia hongkongensis	79.0066	242	1107	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Pauljensenia	95.0	98.51	97.69	0.81	0.72	5	-
GCF_000429245.1	s__Pauljensenia georgiae	78.8521	254	1107	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Pauljensenia	95.0	97.90	96.98	0.94	0.93	3	-
GCF_014208035.1	s__Pauljensenia hyovaginalis	78.7654	279	1107	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Pauljensenia	95.0	95.48	95.48	0.88	0.88	2	-
GCF_018986735.1	s__Pauljensenia sp018986735	78.7412	301	1107	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Pauljensenia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001072465.1	s__Pauljensenia sp001072465	78.5732	229	1107	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Pauljensenia	95.0	97.78	97.78	0.94	0.94	2	-
GCF_000278725.1	s__Pauljensenia sp000278725	78.5178	188	1107	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Pauljensenia	95.0	96.30	95.28	0.90	0.88	4	-
GCA_015655375.1	s__Pauljensenia sp015655375	78.4441	349	1107	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Pauljensenia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900155595.1	s__Pauljensenia mediterranea	78.2235	203	1107	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Pauljensenia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_903645355.1	s__Pauljensenia sp903645355	78.0712	164	1107	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Pauljensenia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000195595.1	s__Actinomyces sp000195595	78.0514	224	1107	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000711965.1	s__Actinomyces israelii	77.8092	269	1107	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	99.26	99.26	0.94	0.94	2	-
GCF_900103885.1	s__Actinomyces ruminicola	77.7731	227	1107	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	96.80	96.66	0.89	0.87	3	-
GCA_900106055.1	s__Pauljensenia radingae_A	77.2434	105	1107	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Pauljensenia	95.0	98.95	98.90	0.90	0.87	6	-
--------------------------------------------------------------------------------
[2024-01-24 13:33:36,511] [INFO] GTDB search result was written to GCF_900155435.1_PRJEB18758_genomic.fna/result_gtdb.tsv
[2024-01-24 13:33:36,512] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:33:36,516] [INFO] DFAST_QC result json was written to GCF_900155435.1_PRJEB18758_genomic.fna/dqc_result.json
[2024-01-24 13:33:36,516] [INFO] DFAST_QC completed!
[2024-01-24 13:33:36,516] [INFO] Total running time: 0h2m3s