[2023-06-28 16:33:01,211] [INFO] DFAST_QC pipeline started.
[2023-06-28 16:33:01,213] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 16:33:01,213] [INFO] DQC Reference Directory: /var/lib/cwl/stgd09aecbc-df20-454b-b1a2-5a319de0c80f/dqc_reference
[2023-06-28 16:33:02,373] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 16:33:02,374] [INFO] Task started: Prodigal
[2023-06-28 16:33:02,374] [INFO] Running command: gunzip -c /var/lib/cwl/stg8b372bc5-f657-4ed3-8da2-ad4a25489c84/GCA_913778685.1_maxbin_SP398_2.010_cleaned_genomic.fna.gz | prodigal -d GCA_913778685.1_maxbin_SP398_2.010_cleaned_genomic.fna/cds.fna -a GCA_913778685.1_maxbin_SP398_2.010_cleaned_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 16:33:06,801] [INFO] Task succeeded: Prodigal
[2023-06-28 16:33:06,801] [INFO] Task started: HMMsearch
[2023-06-28 16:33:06,801] [INFO] Running command: hmmsearch --tblout GCA_913778685.1_maxbin_SP398_2.010_cleaned_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd09aecbc-df20-454b-b1a2-5a319de0c80f/dqc_reference/reference_markers.hmm GCA_913778685.1_maxbin_SP398_2.010_cleaned_genomic.fna/protein.faa > /dev/null
[2023-06-28 16:33:06,982] [INFO] Task succeeded: HMMsearch
[2023-06-28 16:33:06,983] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg8b372bc5-f657-4ed3-8da2-ad4a25489c84/GCA_913778685.1_maxbin_SP398_2.010_cleaned_genomic.fna.gz]
[2023-06-28 16:33:07,013] [INFO] Query marker FASTA was written to GCA_913778685.1_maxbin_SP398_2.010_cleaned_genomic.fna/markers.fasta
[2023-06-28 16:33:07,013] [INFO] Task started: Blastn
[2023-06-28 16:33:07,013] [INFO] Running command: blastn -query GCA_913778685.1_maxbin_SP398_2.010_cleaned_genomic.fna/markers.fasta -db /var/lib/cwl/stgd09aecbc-df20-454b-b1a2-5a319de0c80f/dqc_reference/reference_markers.fasta -out GCA_913778685.1_maxbin_SP398_2.010_cleaned_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 16:33:07,858] [INFO] Task succeeded: Blastn
[2023-06-28 16:33:07,861] [INFO] Selected 15 target genomes.
[2023-06-28 16:33:07,861] [INFO] Target genome list was writen to GCA_913778685.1_maxbin_SP398_2.010_cleaned_genomic.fna/target_genomes.txt
[2023-06-28 16:33:07,863] [INFO] Task started: fastANI
[2023-06-28 16:33:07,863] [INFO] Running command: fastANI --query /var/lib/cwl/stg8b372bc5-f657-4ed3-8da2-ad4a25489c84/GCA_913778685.1_maxbin_SP398_2.010_cleaned_genomic.fna.gz --refList GCA_913778685.1_maxbin_SP398_2.010_cleaned_genomic.fna/target_genomes.txt --output GCA_913778685.1_maxbin_SP398_2.010_cleaned_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 16:33:16,481] [INFO] Task succeeded: fastANI
[2023-06-28 16:33:16,482] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd09aecbc-df20-454b-b1a2-5a319de0c80f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 16:33:16,482] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd09aecbc-df20-454b-b1a2-5a319de0c80f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 16:33:16,489] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 16:33:16,489] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 16:33:16,489] [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
Sphingomonas yabuuchiae	strain=DSM 14562	GCA_014199595.1	172044	172044	type	True	94.1917	70	76	95	below_threshold
Sphingomonas yabuuchiae	strain=DSM 14562	GCA_017052455.1	172044	172044	type	True	94.1906	70	76	95	below_threshold
Sphingomonas parapaucimobilis	strain=NBRC 15100	GCA_000787715.1	28213	28213	type	True	92.9652	70	76	95	below_threshold
Sphingomonas sanguinis	strain=NBRC 13937	GCA_001591005.1	33051	33051	suspected-type	True	90.7456	66	76	95	below_threshold
Sphingomonas pseudosanguinis	strain=DSM 19512	GCA_014196255.1	413712	413712	type	True	89.965	66	76	95	below_threshold
Sphingomonas pseudosanguinis	strain=DSM 19512	GCA_017052355.1	413712	413712	type	True	89.8097	69	76	95	below_threshold
Sphingomonas paucimobilis	strain=NBRC 13935	GCA_000739895.2	13689	13689	type	True	89.1267	67	76	95	below_threshold
Sphingomonas paucimobilis	strain=FDAARGOS_908	GCA_016027095.1	13689	13689	type	True	89.093	68	76	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 16:33:16,491] [INFO] DFAST Taxonomy check result was written to GCA_913778685.1_maxbin_SP398_2.010_cleaned_genomic.fna/tc_result.tsv
[2023-06-28 16:33:16,492] [INFO] ===== Taxonomy check completed =====
[2023-06-28 16:33:16,492] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 16:33:16,492] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd09aecbc-df20-454b-b1a2-5a319de0c80f/dqc_reference/checkm_data
[2023-06-28 16:33:16,493] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 16:33:16,520] [INFO] Task started: CheckM
[2023-06-28 16:33:16,521] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_913778685.1_maxbin_SP398_2.010_cleaned_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_913778685.1_maxbin_SP398_2.010_cleaned_genomic.fna/checkm_input GCA_913778685.1_maxbin_SP398_2.010_cleaned_genomic.fna/checkm_result
[2023-06-28 16:33:34,797] [INFO] Task succeeded: CheckM
[2023-06-28 16:33:34,798] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 8.54%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-06-28 16:33:34,822] [INFO] ===== Completeness check finished =====
[2023-06-28 16:33:34,822] [INFO] ===== Start GTDB Search =====
[2023-06-28 16:33:34,823] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_913778685.1_maxbin_SP398_2.010_cleaned_genomic.fna/markers.fasta)
[2023-06-28 16:33:34,823] [INFO] Task started: Blastn
[2023-06-28 16:33:34,823] [INFO] Running command: blastn -query GCA_913778685.1_maxbin_SP398_2.010_cleaned_genomic.fna/markers.fasta -db /var/lib/cwl/stgd09aecbc-df20-454b-b1a2-5a319de0c80f/dqc_reference/reference_markers_gtdb.fasta -out GCA_913778685.1_maxbin_SP398_2.010_cleaned_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 16:33:36,416] [INFO] Task succeeded: Blastn
[2023-06-28 16:33:36,445] [INFO] Selected 8 target genomes.
[2023-06-28 16:33:36,445] [INFO] Target genome list was writen to GCA_913778685.1_maxbin_SP398_2.010_cleaned_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 16:33:36,447] [INFO] Task started: fastANI
[2023-06-28 16:33:36,448] [INFO] Running command: fastANI --query /var/lib/cwl/stg8b372bc5-f657-4ed3-8da2-ad4a25489c84/GCA_913778685.1_maxbin_SP398_2.010_cleaned_genomic.fna.gz --refList GCA_913778685.1_maxbin_SP398_2.010_cleaned_genomic.fna/target_genomes_gtdb.txt --output GCA_913778685.1_maxbin_SP398_2.010_cleaned_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 16:33:40,873] [INFO] Task succeeded: fastANI
[2023-06-28 16:33:40,879] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 16:33:40,879] [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_001477495.1	s__Sphingomonas yabuuchiae_A	97.3226	72	76	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014199595.1	s__Sphingomonas yabuuchiae	94.1917	70	76	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	97.94	96.78	0.92	0.88	4	-
GCF_000787715.1	s__Sphingomonas parapaucimobilis	92.9652	70	76	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	97.90	97.90	0.87	0.87	2	-
GCA_019112965.1	s__Sphingomonas excrementigallinarum	91.7051	65	76	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001476905.1	s__Sphingomonas sanguinis_B	90.9612	65	76	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	96.13	96.11	0.83	0.82	3	-
GCF_001591005.1	s__Sphingomonas sanguinis	90.7456	66	76	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	98.09	96.84	0.89	0.83	8	-
GCF_014196255.1	s__Sphingomonas pseudosanguinis	89.965	66	76	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	99.99	99.99	1.00	1.00	2	-
GCF_000739895.2	s__Sphingomonas paucimobilis	89.1267	67	76	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	99.74	99.40	0.92	0.87	13	-
--------------------------------------------------------------------------------
[2023-06-28 16:33:40,881] [INFO] GTDB search result was written to GCA_913778685.1_maxbin_SP398_2.010_cleaned_genomic.fna/result_gtdb.tsv
[2023-06-28 16:33:40,881] [INFO] ===== GTDB Search completed =====
[2023-06-28 16:33:40,884] [INFO] DFAST_QC result json was written to GCA_913778685.1_maxbin_SP398_2.010_cleaned_genomic.fna/dqc_result.json
[2023-06-28 16:33:40,884] [INFO] DFAST_QC completed!
[2023-06-28 16:33:40,884] [INFO] Total running time: 0h0m40s