[2024-01-25 18:41:50,744] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:41:50,747] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:41:50,748] [INFO] DQC Reference Directory: /var/lib/cwl/stg522cef96-9874-4b6e-a4c8-b1f19c8a0dbe/dqc_reference
[2024-01-25 18:41:51,918] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:41:51,919] [INFO] Task started: Prodigal
[2024-01-25 18:41:51,919] [INFO] Running command: gunzip -c /var/lib/cwl/stg193061f2-3120-44e0-8a6f-0a4f4a6adf55/GCF_025685425.1_ASM2568542v1_genomic.fna.gz | prodigal -d GCF_025685425.1_ASM2568542v1_genomic.fna/cds.fna -a GCF_025685425.1_ASM2568542v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:42:07,843] [INFO] Task succeeded: Prodigal
[2024-01-25 18:42:07,844] [INFO] Task started: HMMsearch
[2024-01-25 18:42:07,844] [INFO] Running command: hmmsearch --tblout GCF_025685425.1_ASM2568542v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg522cef96-9874-4b6e-a4c8-b1f19c8a0dbe/dqc_reference/reference_markers.hmm GCF_025685425.1_ASM2568542v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:42:08,103] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:42:08,104] [INFO] Found 6/6 markers.
[2024-01-25 18:42:08,152] [INFO] Query marker FASTA was written to GCF_025685425.1_ASM2568542v1_genomic.fna/markers.fasta
[2024-01-25 18:42:08,152] [INFO] Task started: Blastn
[2024-01-25 18:42:08,153] [INFO] Running command: blastn -query GCF_025685425.1_ASM2568542v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg522cef96-9874-4b6e-a4c8-b1f19c8a0dbe/dqc_reference/reference_markers.fasta -out GCF_025685425.1_ASM2568542v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:42:08,717] [INFO] Task succeeded: Blastn
[2024-01-25 18:42:08,720] [INFO] Selected 19 target genomes.
[2024-01-25 18:42:08,720] [INFO] Target genome list was writen to GCF_025685425.1_ASM2568542v1_genomic.fna/target_genomes.txt
[2024-01-25 18:42:08,725] [INFO] Task started: fastANI
[2024-01-25 18:42:08,725] [INFO] Running command: fastANI --query /var/lib/cwl/stg193061f2-3120-44e0-8a6f-0a4f4a6adf55/GCF_025685425.1_ASM2568542v1_genomic.fna.gz --refList GCF_025685425.1_ASM2568542v1_genomic.fna/target_genomes.txt --output GCF_025685425.1_ASM2568542v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:42:25,303] [INFO] Task succeeded: fastANI
[2024-01-25 18:42:25,303] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg522cef96-9874-4b6e-a4c8-b1f19c8a0dbe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:42:25,303] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg522cef96-9874-4b6e-a4c8-b1f19c8a0dbe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:42:25,313] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 18:42:25,313] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 18:42:25,313] [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
Granulicella mallensis	strain=MP5ACTX8	GCA_000178955.2	940614	940614	type	True	77.5444	200	2010	95	below_threshold
Silvibacterium dinghuense	strain=DHOF10	GCA_004123295.1	1560006	1560006	type	True	77.5072	177	2010	95	below_threshold
Silvibacterium dinghuense	strain=CGMCC 1.13007	GCA_014640355.1	1560006	1560006	type	True	77.5005	180	2010	95	below_threshold
Edaphobacter flagellatus	strain=HZ411	GCA_025264665.1	1933044	1933044	type	True	77.3608	200	2010	95	below_threshold
Edaphobacter acidisoli	strain=CGMCC 1.15447	GCA_014642855.1	2040573	2040573	type	True	77.3379	163	2010	95	below_threshold
Bryocella elongata	strain=DSM 22489	GCA_900108185.1	863522	863522	type	True	77.2974	200	2010	95	below_threshold
Edaphobacter aggregans	strain=DSM 19364	GCA_000745965.1	570835	570835	type	True	77.2097	235	2010	95	below_threshold
Granulicella rosea	strain=DSM 18704	GCA_900188085.1	474952	474952	type	True	77.1633	225	2010	95	below_threshold
Paracidobacterium acidisoli	strain=4G-K13	GCA_003428625.2	2303751	2303751	type	True	77.1124	135	2010	95	below_threshold
Edaphobacter modestus	strain=DSM 18101	GCA_004217555.1	388466	388466	type	True	77.0952	219	2010	95	below_threshold
Terriglobus saanensis	strain=SP1PR4	GCA_000179915.2	870903	870903	type	True	77.0421	175	2010	95	below_threshold
Terriglobus roseus	strain=DSM 18391	GCA_000265425.1	392734	392734	type	True	77.03	202	2010	95	below_threshold
Occallatibacter riparius	strain=DSM 25168	GCA_025264625.1	1002689	1002689	type	True	76.803	120	2010	95	below_threshold
Edaphobacter lichenicola	strain=DSM 104462	GCA_025264645.1	2051959	2051959	suspected-type	True	76.7077	149	2010	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:42:25,314] [INFO] DFAST Taxonomy check result was written to GCF_025685425.1_ASM2568542v1_genomic.fna/tc_result.tsv
[2024-01-25 18:42:25,315] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:42:25,315] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:42:25,315] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg522cef96-9874-4b6e-a4c8-b1f19c8a0dbe/dqc_reference/checkm_data
[2024-01-25 18:42:25,316] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:42:25,376] [INFO] Task started: CheckM
[2024-01-25 18:42:25,376] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025685425.1_ASM2568542v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025685425.1_ASM2568542v1_genomic.fna/checkm_input GCF_025685425.1_ASM2568542v1_genomic.fna/checkm_result
[2024-01-25 18:43:12,413] [INFO] Task succeeded: CheckM
[2024-01-25 18:43:12,415] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:43:12,454] [INFO] ===== Completeness check finished =====
[2024-01-25 18:43:12,455] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:43:12,455] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025685425.1_ASM2568542v1_genomic.fna/markers.fasta)
[2024-01-25 18:43:12,455] [INFO] Task started: Blastn
[2024-01-25 18:43:12,455] [INFO] Running command: blastn -query GCF_025685425.1_ASM2568542v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg522cef96-9874-4b6e-a4c8-b1f19c8a0dbe/dqc_reference/reference_markers_gtdb.fasta -out GCF_025685425.1_ASM2568542v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:43:13,370] [INFO] Task succeeded: Blastn
[2024-01-25 18:43:13,373] [INFO] Selected 19 target genomes.
[2024-01-25 18:43:13,373] [INFO] Target genome list was writen to GCF_025685425.1_ASM2568542v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:43:13,386] [INFO] Task started: fastANI
[2024-01-25 18:43:13,386] [INFO] Running command: fastANI --query /var/lib/cwl/stg193061f2-3120-44e0-8a6f-0a4f4a6adf55/GCF_025685425.1_ASM2568542v1_genomic.fna.gz --refList GCF_025685425.1_ASM2568542v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025685425.1_ASM2568542v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:43:30,961] [INFO] Task succeeded: fastANI
[2024-01-25 18:43:30,972] [INFO] Found 17 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 18:43:30,972] [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_008000815.1	s__Terriglobus_A albidus	87.6247	1549	2010	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Terriglobus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013361705.1	s__Terriglobus_A sp013361705	87.4238	1273	2010	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Terriglobus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018268855.1	s__Terriglobus sp018268855	77.5518	160	2010	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Terriglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000421065.1	s__Edaphobacter sp000421065	77.4228	225	2010	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Edaphobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014642855.1	s__Edaphobacter acidisoli	77.3688	161	2010	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Edaphobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102185.1	s__Terriglobus roseus_A	77.3251	162	2010	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Terriglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013410065.1	s__Granulicella_B arctica	77.2849	158	2010	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Granulicella_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000745965.1	s__Edaphobacter aggregans	77.1988	235	2010	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Edaphobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900188085.1	s__Granulicella_C rosea	77.1643	221	2010	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Granulicella_C	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001897435.1	s__Edaphobacter sp001897435	77.1319	205	2010	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Edaphobacter	95.0	99.98	99.98	0.99	0.99	2	-
GCF_003428625.2	s__Palsa-343 sp003428625	77.1124	135	2010	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Palsa-343	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000265425.1	s__Terriglobus roseus	77.03	202	2010	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Terriglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018268775.1	s__Edaphobacter sp018268775	76.9969	215	2010	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Edaphobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900105625.1	s__Terriglobus roseus_B	76.9371	217	2010	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Terriglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015654835.1	s__Terracidiphilus sp015654835	76.174	80	2010	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Terracidiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003151435.1	s__Terracidiphilus sp003151435	76.0984	85	2010	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Terracidiphilus	95.0	99.67	99.67	0.90	0.90	2	-
GCA_003152595.1	s__Palsa-343 sp003152595	75.8874	89	2010	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Palsa-343	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:43:30,973] [INFO] GTDB search result was written to GCF_025685425.1_ASM2568542v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:43:30,975] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:43:30,978] [INFO] DFAST_QC result json was written to GCF_025685425.1_ASM2568542v1_genomic.fna/dqc_result.json
[2024-01-25 18:43:30,978] [INFO] DFAST_QC completed!
[2024-01-25 18:43:30,978] [INFO] Total running time: 0h1m40s