[2024-01-24 11:26:38,979] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:26:38,980] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:26:38,981] [INFO] DQC Reference Directory: /var/lib/cwl/stg4ce02ee1-d654-43f9-b007-c7645484472e/dqc_reference
[2024-01-24 11:26:40,308] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:26:40,309] [INFO] Task started: Prodigal
[2024-01-24 11:26:40,309] [INFO] Running command: gunzip -c /var/lib/cwl/stg2f2031bb-8605-486b-bac3-76ffb34a4118/GCF_014672715.2_ASM1467271v2_genomic.fna.gz | prodigal -d GCF_014672715.2_ASM1467271v2_genomic.fna/cds.fna -a GCF_014672715.2_ASM1467271v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:26:45,812] [INFO] Task succeeded: Prodigal
[2024-01-24 11:26:45,813] [INFO] Task started: HMMsearch
[2024-01-24 11:26:45,813] [INFO] Running command: hmmsearch --tblout GCF_014672715.2_ASM1467271v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4ce02ee1-d654-43f9-b007-c7645484472e/dqc_reference/reference_markers.hmm GCF_014672715.2_ASM1467271v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:26:46,037] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:26:46,039] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg2f2031bb-8605-486b-bac3-76ffb34a4118/GCF_014672715.2_ASM1467271v2_genomic.fna.gz]
[2024-01-24 11:26:46,064] [INFO] Query marker FASTA was written to GCF_014672715.2_ASM1467271v2_genomic.fna/markers.fasta
[2024-01-24 11:26:46,064] [INFO] Task started: Blastn
[2024-01-24 11:26:46,065] [INFO] Running command: blastn -query GCF_014672715.2_ASM1467271v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg4ce02ee1-d654-43f9-b007-c7645484472e/dqc_reference/reference_markers.fasta -out GCF_014672715.2_ASM1467271v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:26:46,656] [INFO] Task succeeded: Blastn
[2024-01-24 11:26:46,659] [INFO] Selected 13 target genomes.
[2024-01-24 11:26:46,660] [INFO] Target genome list was writen to GCF_014672715.2_ASM1467271v2_genomic.fna/target_genomes.txt
[2024-01-24 11:26:46,672] [INFO] Task started: fastANI
[2024-01-24 11:26:46,672] [INFO] Running command: fastANI --query /var/lib/cwl/stg2f2031bb-8605-486b-bac3-76ffb34a4118/GCF_014672715.2_ASM1467271v2_genomic.fna.gz --refList GCF_014672715.2_ASM1467271v2_genomic.fna/target_genomes.txt --output GCF_014672715.2_ASM1467271v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:26:53,652] [INFO] Task succeeded: fastANI
[2024-01-24 11:26:53,653] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4ce02ee1-d654-43f9-b007-c7645484472e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:26:53,654] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4ce02ee1-d654-43f9-b007-c7645484472e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:26:53,662] [INFO] Found 4 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:26:53,663] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:26:53,663] [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
Candidatus Dehalogenimonas etheniformans	strain=GP	GCA_014672715.2	1536648	1536648	type	True	100.0	689	689	95	conclusive
Candidatus Dehalogenimonas etheniformans	strain=GP	GCA_002878295.2	1536648	1536648	type	True	99.9605	663	689	95	conclusive
Dehalogenimonas formicexedens	strain=NSZ-14	GCA_001953175.1	1839801	1839801	type	True	81.3018	375	689	95	below_threshold
Dehalogenimonas alkenigignens	strain=IP3-3	GCA_001466665.1	1217799	1217799	type	True	77.9079	143	689	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:26:53,664] [INFO] DFAST Taxonomy check result was written to GCF_014672715.2_ASM1467271v2_genomic.fna/tc_result.tsv
[2024-01-24 11:26:53,665] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:26:53,665] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:26:53,665] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4ce02ee1-d654-43f9-b007-c7645484472e/dqc_reference/checkm_data
[2024-01-24 11:26:53,666] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:26:53,692] [INFO] Task started: CheckM
[2024-01-24 11:26:53,693] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014672715.2_ASM1467271v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014672715.2_ASM1467271v2_genomic.fna/checkm_input GCF_014672715.2_ASM1467271v2_genomic.fna/checkm_result
[2024-01-24 11:27:16,510] [INFO] Task succeeded: CheckM
[2024-01-24 11:27:16,511] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:27:16,530] [INFO] ===== Completeness check finished =====
[2024-01-24 11:27:16,530] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:27:16,531] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014672715.2_ASM1467271v2_genomic.fna/markers.fasta)
[2024-01-24 11:27:16,531] [INFO] Task started: Blastn
[2024-01-24 11:27:16,532] [INFO] Running command: blastn -query GCF_014672715.2_ASM1467271v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg4ce02ee1-d654-43f9-b007-c7645484472e/dqc_reference/reference_markers_gtdb.fasta -out GCF_014672715.2_ASM1467271v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:27:17,305] [INFO] Task succeeded: Blastn
[2024-01-24 11:27:17,309] [INFO] Selected 16 target genomes.
[2024-01-24 11:27:17,310] [INFO] Target genome list was writen to GCF_014672715.2_ASM1467271v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:27:17,327] [INFO] Task started: fastANI
[2024-01-24 11:27:17,327] [INFO] Running command: fastANI --query /var/lib/cwl/stg2f2031bb-8605-486b-bac3-76ffb34a4118/GCF_014672715.2_ASM1467271v2_genomic.fna.gz --refList GCF_014672715.2_ASM1467271v2_genomic.fna/target_genomes_gtdb.txt --output GCF_014672715.2_ASM1467271v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:27:24,086] [INFO] Task succeeded: fastANI
[2024-01-24 11:27:24,094] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:27:24,094] [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_014672715.2	s__Dehalogenimonas sp002878295	100.0	689	689	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__Dehalococcoidales;f__Dehalococcoidaceae;g__Dehalogenimonas	95.0	99.99	99.99	1.00	1.00	2	conclusive
GCF_001953175.1	s__Dehalogenimonas formicexedens	81.2999	374	689	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__Dehalococcoidales;f__Dehalococcoidaceae;g__Dehalogenimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001005265.1	s__Dehalogenimonas sp001005265	78.8128	69	689	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__Dehalococcoidales;f__Dehalococcoidaceae;g__Dehalogenimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001466665.1	s__Dehalogenimonas alkenigignens	77.8999	144	689	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__Dehalococcoidales;f__Dehalococcoidaceae;g__Dehalogenimonas	95.0	99.11	99.11	0.94	0.94	2	-
GCF_000143165.1	s__Dehalogenimonas lykanthroporepellens	77.2544	68	689	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__Dehalococcoidales;f__Dehalococcoidaceae;g__Dehalogenimonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:27:24,096] [INFO] GTDB search result was written to GCF_014672715.2_ASM1467271v2_genomic.fna/result_gtdb.tsv
[2024-01-24 11:27:24,097] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:27:24,099] [INFO] DFAST_QC result json was written to GCF_014672715.2_ASM1467271v2_genomic.fna/dqc_result.json
[2024-01-24 11:27:24,099] [INFO] DFAST_QC completed!
[2024-01-24 11:27:24,099] [INFO] Total running time: 0h0m45s