[2023-06-18 22:14:26,527] [INFO] DFAST_QC pipeline started.
[2023-06-18 22:14:26,531] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 22:14:26,532] [INFO] DQC Reference Directory: /var/lib/cwl/stg92ecb74c-7d42-416f-99c4-51e39d39eb46/dqc_reference
[2023-06-18 22:14:27,705] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 22:14:27,706] [INFO] Task started: Prodigal
[2023-06-18 22:14:27,707] [INFO] Running command: gunzip -c /var/lib/cwl/stg698b99fa-338c-40bf-8794-fd66c4b73cf5/GCA_013822035.1_ASM1382203v1_genomic.fna.gz | prodigal -d GCA_013822035.1_ASM1382203v1_genomic.fna/cds.fna -a GCA_013822035.1_ASM1382203v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 22:14:40,733] [INFO] Task succeeded: Prodigal
[2023-06-18 22:14:40,733] [INFO] Task started: HMMsearch
[2023-06-18 22:14:40,733] [INFO] Running command: hmmsearch --tblout GCA_013822035.1_ASM1382203v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg92ecb74c-7d42-416f-99c4-51e39d39eb46/dqc_reference/reference_markers.hmm GCA_013822035.1_ASM1382203v1_genomic.fna/protein.faa > /dev/null
[2023-06-18 22:14:40,958] [INFO] Task succeeded: HMMsearch
[2023-06-18 22:14:40,960] [INFO] Found 6/6 markers.
[2023-06-18 22:14:40,992] [INFO] Query marker FASTA was written to GCA_013822035.1_ASM1382203v1_genomic.fna/markers.fasta
[2023-06-18 22:14:40,992] [INFO] Task started: Blastn
[2023-06-18 22:14:40,992] [INFO] Running command: blastn -query GCA_013822035.1_ASM1382203v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg92ecb74c-7d42-416f-99c4-51e39d39eb46/dqc_reference/reference_markers.fasta -out GCA_013822035.1_ASM1382203v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 22:14:41,620] [INFO] Task succeeded: Blastn
[2023-06-18 22:14:41,624] [INFO] Selected 14 target genomes.
[2023-06-18 22:14:41,624] [INFO] Target genome list was writen to GCA_013822035.1_ASM1382203v1_genomic.fna/target_genomes.txt
[2023-06-18 22:14:41,628] [INFO] Task started: fastANI
[2023-06-18 22:14:41,628] [INFO] Running command: fastANI --query /var/lib/cwl/stg698b99fa-338c-40bf-8794-fd66c4b73cf5/GCA_013822035.1_ASM1382203v1_genomic.fna.gz --refList GCA_013822035.1_ASM1382203v1_genomic.fna/target_genomes.txt --output GCA_013822035.1_ASM1382203v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 22:14:53,430] [INFO] Task succeeded: fastANI
[2023-06-18 22:14:53,431] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg92ecb74c-7d42-416f-99c4-51e39d39eb46/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 22:14:53,431] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg92ecb74c-7d42-416f-99c4-51e39d39eb46/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 22:14:53,439] [INFO] Found 7 fastANI hits (0 hits with ANI > threshold)
[2023-06-18 22:14:53,439] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-18 22:14:53,439] [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
Gemmatimonas aurantiaca	strain=T-27	GCA_000010305.1	173480	173480	type	True	79.3499	521	1224	95	below_threshold
Gemmatimonas phototrophica	strain=AP64	GCA_000695095.2	1379270	1379270	type	True	79.1272	523	1224	95	below_threshold
Gemmatimonas groenlandica	strain=TET16	GCA_013004105.1	2732249	2732249	type	True	78.4648	461	1224	95	below_threshold
Gemmatirosa kalamazoonensis	strain=KBS708	GCA_000522985.1	861299	861299	type	True	76.7552	241	1224	95	below_threshold
Longimicrobium terrae	strain=DSM 29007	GCA_014202995.1	1639882	1639882	type	True	75.4856	115	1224	95	below_threshold
Longimicrobium terrae	strain=CB-286315	GCA_013000925.1	1639882	1639882	type	True	75.4727	119	1224	95	below_threshold
Dokdonella fugitiva	strain=A3	GCA_004342425.1	328517	328517	type	True	75.0117	55	1224	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-18 22:14:53,443] [INFO] DFAST Taxonomy check result was written to GCA_013822035.1_ASM1382203v1_genomic.fna/tc_result.tsv
[2023-06-18 22:14:53,444] [INFO] ===== Taxonomy check completed =====
[2023-06-18 22:14:53,444] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 22:14:53,444] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg92ecb74c-7d42-416f-99c4-51e39d39eb46/dqc_reference/checkm_data
[2023-06-18 22:14:53,445] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 22:14:53,484] [INFO] Task started: CheckM
[2023-06-18 22:14:53,484] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_013822035.1_ASM1382203v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_013822035.1_ASM1382203v1_genomic.fna/checkm_input GCA_013822035.1_ASM1382203v1_genomic.fna/checkm_result
[2023-06-18 22:15:46,982] [INFO] Task succeeded: CheckM
[2023-06-18 22:15:46,983] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-18 22:15:47,007] [INFO] ===== Completeness check finished =====
[2023-06-18 22:15:47,007] [INFO] ===== Start GTDB Search =====
[2023-06-18 22:15:47,007] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_013822035.1_ASM1382203v1_genomic.fna/markers.fasta)
[2023-06-18 22:15:47,008] [INFO] Task started: Blastn
[2023-06-18 22:15:47,008] [INFO] Running command: blastn -query GCA_013822035.1_ASM1382203v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg92ecb74c-7d42-416f-99c4-51e39d39eb46/dqc_reference/reference_markers_gtdb.fasta -out GCA_013822035.1_ASM1382203v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 22:15:47,978] [INFO] Task succeeded: Blastn
[2023-06-18 22:15:47,984] [INFO] Selected 10 target genomes.
[2023-06-18 22:15:47,984] [INFO] Target genome list was writen to GCA_013822035.1_ASM1382203v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 22:15:47,991] [INFO] Task started: fastANI
[2023-06-18 22:15:47,991] [INFO] Running command: fastANI --query /var/lib/cwl/stg698b99fa-338c-40bf-8794-fd66c4b73cf5/GCA_013822035.1_ASM1382203v1_genomic.fna.gz --refList GCA_013822035.1_ASM1382203v1_genomic.fna/target_genomes_gtdb.txt --output GCA_013822035.1_ASM1382203v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 22:15:56,411] [INFO] Task succeeded: fastANI
[2023-06-18 22:15:56,422] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-18 22:15:56,423] [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_002483225.1	s__Gemmatimonas sp002483225	97.6982	1170	1224	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__Gemmatimonadaceae;g__Gemmatimonas	95.0	97.70	97.70	0.96	0.96	2	conclusive
GCA_016741895.1	s__Gemmatimonas sp016741895	89.6813	908	1224	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__Gemmatimonadaceae;g__Gemmatimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016742275.1	s__Gemmatimonas sp016742275	80.5242	700	1224	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__Gemmatimonadaceae;g__Gemmatimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000010305.1	s__Gemmatimonas aurantiaca	79.3448	521	1224	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__Gemmatimonadaceae;g__Gemmatimonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000695095.2	s__Gemmatimonas phototrophica	79.1272	523	1224	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__Gemmatimonadaceae;g__Gemmatimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013004105.1	s__Gemmatimonas sp013004105	78.456	462	1224	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__Gemmatimonadaceae;g__Gemmatimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011390885.1	s__JAABRT01 sp011390885	78.2574	380	1224	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__Gemmatimonadaceae;g__JAABRT01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016720905.1	s__Gemmatimonas sp016720905	77.6891	322	1224	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__Gemmatimonadaceae;g__Gemmatimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014377535.1	s__JACMLX01 sp014377535	76.6443	139	1224	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__Gemmatimonadaceae;g__JACMLX01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003152485.1	s__Palsa-1248 sp003152485	76.2469	75	1224	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__Gemmatimonadaceae;g__Palsa-1248	95.0	99.76	99.74	0.95	0.94	3	-
--------------------------------------------------------------------------------
[2023-06-18 22:15:56,425] [INFO] GTDB search result was written to GCA_013822035.1_ASM1382203v1_genomic.fna/result_gtdb.tsv
[2023-06-18 22:15:56,425] [INFO] ===== GTDB Search completed =====
[2023-06-18 22:15:56,430] [INFO] DFAST_QC result json was written to GCA_013822035.1_ASM1382203v1_genomic.fna/dqc_result.json
[2023-06-18 22:15:56,430] [INFO] DFAST_QC completed!
[2023-06-18 22:15:56,430] [INFO] Total running time: 0h1m30s