[2024-01-24 14:11:46,274] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:11:46,278] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:11:46,278] [INFO] DQC Reference Directory: /var/lib/cwl/stgea643dec-b2e5-49e3-a536-99c1abeeb2d0/dqc_reference
[2024-01-24 14:11:48,877] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:11:48,879] [INFO] Task started: Prodigal
[2024-01-24 14:11:48,879] [INFO] Running command: gunzip -c /var/lib/cwl/stg6458c255-d170-4640-9296-8f3ac005c376/GCF_001552735.1_ASM155273v1_genomic.fna.gz | prodigal -d GCF_001552735.1_ASM155273v1_genomic.fna/cds.fna -a GCF_001552735.1_ASM155273v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:12:00,589] [INFO] Task succeeded: Prodigal
[2024-01-24 14:12:00,590] [INFO] Task started: HMMsearch
[2024-01-24 14:12:00,590] [INFO] Running command: hmmsearch --tblout GCF_001552735.1_ASM155273v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgea643dec-b2e5-49e3-a536-99c1abeeb2d0/dqc_reference/reference_markers.hmm GCF_001552735.1_ASM155273v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:12:00,986] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:12:00,987] [INFO] Found 6/6 markers.
[2024-01-24 14:12:01,028] [INFO] Query marker FASTA was written to GCF_001552735.1_ASM155273v1_genomic.fna/markers.fasta
[2024-01-24 14:12:01,029] [INFO] Task started: Blastn
[2024-01-24 14:12:01,029] [INFO] Running command: blastn -query GCF_001552735.1_ASM155273v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgea643dec-b2e5-49e3-a536-99c1abeeb2d0/dqc_reference/reference_markers.fasta -out GCF_001552735.1_ASM155273v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:12:02,626] [INFO] Task succeeded: Blastn
[2024-01-24 14:12:02,629] [INFO] Selected 12 target genomes.
[2024-01-24 14:12:02,629] [INFO] Target genome list was writen to GCF_001552735.1_ASM155273v1_genomic.fna/target_genomes.txt
[2024-01-24 14:12:02,635] [INFO] Task started: fastANI
[2024-01-24 14:12:02,636] [INFO] Running command: fastANI --query /var/lib/cwl/stg6458c255-d170-4640-9296-8f3ac005c376/GCF_001552735.1_ASM155273v1_genomic.fna.gz --refList GCF_001552735.1_ASM155273v1_genomic.fna/target_genomes.txt --output GCF_001552735.1_ASM155273v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:12:14,657] [INFO] Task succeeded: fastANI
[2024-01-24 14:12:14,658] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgea643dec-b2e5-49e3-a536-99c1abeeb2d0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:12:14,658] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgea643dec-b2e5-49e3-a536-99c1abeeb2d0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:12:14,670] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:12:14,671] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:12:14,671] [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
Sanguibacter suarezii	strain=NBRC 16159	GCA_001552735.1	60921	60921	type	True	100.0	1249	1253	95	conclusive
Sanguibacter gelidistatuariae	strain=ISLP-3	GCA_900096585.1	1814289	1814289	type	True	85.963	939	1253	95	below_threshold
Sanguibacter inulinus	strain=DSM 100099	GCA_013415325.1	60922	60922	type	True	81.7228	691	1253	95	below_threshold
Sanguibacter keddieii	strain=DSM 10542	GCA_000024925.1	60920	60920	type	True	81.708	746	1253	95	below_threshold
Sanguibacter suaedae	strain=YZGR15	GCA_016342785.1	2795737	2795737	type	True	80.5892	592	1253	95	below_threshold
Oerskovia merdavium	strain=Sa2CUA9	GCA_014836755.1	2762227	2762227	type	True	79.624	523	1253	95	below_threshold
Oerskovia rustica	strain=Sa4CUA1	GCA_014836555.1	2762237	2762237	type	True	79.5617	529	1253	95	below_threshold
Oerskovia douganii	strain=Sa1BUA8	GCA_015142735.1	2762210	2762210	type	True	79.4315	554	1253	95	below_threshold
Cellulomonas humilata	strain=ATCC 25174	GCA_013359775.1	144055	144055	type	True	78.568	472	1253	95	below_threshold
Actinotalea solisilvae	strain=KACC 19191	GCA_016464425.1	2072922	2072922	type	True	78.5385	464	1253	95	below_threshold
Cellulomonas hominis	strain=DSM 9581	GCA_014201095.1	156981	156981	suspected-type	True	78.5032	483	1253	95	below_threshold
Cellulomonas palmilytica	strain=EW123	GCA_021590045.1	2608402	2608402	type	True	78.3335	459	1253	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:12:14,672] [INFO] DFAST Taxonomy check result was written to GCF_001552735.1_ASM155273v1_genomic.fna/tc_result.tsv
[2024-01-24 14:12:14,673] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:12:14,673] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:12:14,674] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgea643dec-b2e5-49e3-a536-99c1abeeb2d0/dqc_reference/checkm_data
[2024-01-24 14:12:14,675] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:12:14,719] [INFO] Task started: CheckM
[2024-01-24 14:12:14,720] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001552735.1_ASM155273v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001552735.1_ASM155273v1_genomic.fna/checkm_input GCF_001552735.1_ASM155273v1_genomic.fna/checkm_result
[2024-01-24 14:13:12,576] [INFO] Task succeeded: CheckM
[2024-01-24 14:13:12,578] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:13:12,610] [INFO] ===== Completeness check finished =====
[2024-01-24 14:13:12,610] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:13:12,611] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001552735.1_ASM155273v1_genomic.fna/markers.fasta)
[2024-01-24 14:13:12,611] [INFO] Task started: Blastn
[2024-01-24 14:13:12,611] [INFO] Running command: blastn -query GCF_001552735.1_ASM155273v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgea643dec-b2e5-49e3-a536-99c1abeeb2d0/dqc_reference/reference_markers_gtdb.fasta -out GCF_001552735.1_ASM155273v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:13:14,696] [INFO] Task succeeded: Blastn
[2024-01-24 14:13:14,699] [INFO] Selected 11 target genomes.
[2024-01-24 14:13:14,700] [INFO] Target genome list was writen to GCF_001552735.1_ASM155273v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:13:14,712] [INFO] Task started: fastANI
[2024-01-24 14:13:14,713] [INFO] Running command: fastANI --query /var/lib/cwl/stg6458c255-d170-4640-9296-8f3ac005c376/GCF_001552735.1_ASM155273v1_genomic.fna.gz --refList GCF_001552735.1_ASM155273v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001552735.1_ASM155273v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:13:24,331] [INFO] Task succeeded: fastANI
[2024-01-24 14:13:24,561] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:13:24,561] [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_001552735.1	s__Sanguibacter suarezii	100.0	1249	1253	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Sanguibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900096585.1	s__Sanguibacter gelidistatuariae	85.9485	941	1253	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Sanguibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000024925.1	s__Sanguibacter keddieii	81.722	745	1253	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Sanguibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013415325.1	s__Sanguibacter inulinus	81.6816	695	1253	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Sanguibacter	95.0	98.94	97.89	0.97	0.94	3	-
GCF_016342785.1	s__Sanguibacter sp016342785	80.5999	591	1253	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Sanguibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014836755.1	s__Oerskovia sp014836755	79.6641	519	1253	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Oerskovia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001692445.1	s__Oerskovia enterophila	79.6306	536	1253	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Oerskovia	95.0	98.35	97.89	0.90	0.89	4	-
GCF_005937995.2	s__Oerskovia sp005937995	79.5605	544	1253	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Oerskovia	95.0	96.13	96.13	0.91	0.91	2	-
GCF_009429125.1	s__Luteimicrobium xylanilyticum	78.7273	449	1253	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Luteimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001429255.1	s__Cellulomonas sp001429255	78.6567	481	1253	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	98.79	98.79	0.94	0.94	2	-
GCA_002441315.1	s__Cellulomonas sp002441315	77.8362	326	1253	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:13:24,563] [INFO] GTDB search result was written to GCF_001552735.1_ASM155273v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:13:24,564] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:13:24,570] [INFO] DFAST_QC result json was written to GCF_001552735.1_ASM155273v1_genomic.fna/dqc_result.json
[2024-01-24 14:13:24,571] [INFO] DFAST_QC completed!
[2024-01-24 14:13:24,571] [INFO] Total running time: 0h1m38s