[2024-01-24 13:57:12,262] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:57:12,263] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:57:12,263] [INFO] DQC Reference Directory: /var/lib/cwl/stgdd740066-0c82-44ec-ab7b-968b127979fa/dqc_reference
[2024-01-24 13:57:13,497] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:57:13,498] [INFO] Task started: Prodigal
[2024-01-24 13:57:13,498] [INFO] Running command: gunzip -c /var/lib/cwl/stg4981ae90-22b9-4c6f-9024-77ca7ea271ae/GCF_025685565.1_ASM2568556v1_genomic.fna.gz | prodigal -d GCF_025685565.1_ASM2568556v1_genomic.fna/cds.fna -a GCF_025685565.1_ASM2568556v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:57:30,057] [INFO] Task succeeded: Prodigal
[2024-01-24 13:57:30,057] [INFO] Task started: HMMsearch
[2024-01-24 13:57:30,057] [INFO] Running command: hmmsearch --tblout GCF_025685565.1_ASM2568556v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdd740066-0c82-44ec-ab7b-968b127979fa/dqc_reference/reference_markers.hmm GCF_025685565.1_ASM2568556v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:57:30,372] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:57:30,374] [INFO] Found 6/6 markers.
[2024-01-24 13:57:30,421] [INFO] Query marker FASTA was written to GCF_025685565.1_ASM2568556v1_genomic.fna/markers.fasta
[2024-01-24 13:57:30,422] [INFO] Task started: Blastn
[2024-01-24 13:57:30,422] [INFO] Running command: blastn -query GCF_025685565.1_ASM2568556v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdd740066-0c82-44ec-ab7b-968b127979fa/dqc_reference/reference_markers.fasta -out GCF_025685565.1_ASM2568556v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:57:31,035] [INFO] Task succeeded: Blastn
[2024-01-24 13:57:31,039] [INFO] Selected 12 target genomes.
[2024-01-24 13:57:31,039] [INFO] Target genome list was writen to GCF_025685565.1_ASM2568556v1_genomic.fna/target_genomes.txt
[2024-01-24 13:57:31,043] [INFO] Task started: fastANI
[2024-01-24 13:57:31,044] [INFO] Running command: fastANI --query /var/lib/cwl/stg4981ae90-22b9-4c6f-9024-77ca7ea271ae/GCF_025685565.1_ASM2568556v1_genomic.fna.gz --refList GCF_025685565.1_ASM2568556v1_genomic.fna/target_genomes.txt --output GCF_025685565.1_ASM2568556v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:57:42,865] [INFO] Task succeeded: fastANI
[2024-01-24 13:57:42,866] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdd740066-0c82-44ec-ab7b-968b127979fa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:57:42,866] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdd740066-0c82-44ec-ab7b-968b127979fa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:57:42,877] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:57:42,877] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:57:42,877] [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 pectinivorans	strain=DSM 21001	GCA_900114625.1	474950	474950	type	True	78.1286	399	1908	95	below_threshold
Granulicella rosea	strain=DSM 18704	GCA_900188085.1	474952	474952	type	True	78.1153	435	1908	95	below_threshold
Edaphobacter dinghuensis	strain=CGMCC 1.12997	GCA_014640335.1	1560005	1560005	type	True	78.0266	311	1908	95	below_threshold
Edaphobacter lichenicola	strain=DSM 104462	GCA_025264645.1	2051959	2051959	suspected-type	True	77.9519	302	1908	95	below_threshold
Edaphobacter aggregans	strain=DSM 19364	GCA_000745965.1	570835	570835	type	True	77.9311	383	1908	95	below_threshold
Granulicella sibirica	strain=AF10	GCA_004115155.1	2479048	2479048	type	True	77.8947	355	1908	95	below_threshold
Edaphobacter acidisoli	strain=CGMCC 1.15447	GCA_014642855.1	2040573	2040573	type	True	77.8916	281	1908	95	below_threshold
Granulicella tundricola	strain=MP5ACTX9	GCA_000178975.2	940615	940615	type	True	77.8341	323	1908	95	below_threshold
Edaphobacter modestus	strain=DSM 18101	GCA_004217555.1	388466	388466	type	True	77.5989	271	1908	95	below_threshold
Granulicella mallensis	strain=MP5ACTX8	GCA_000178955.2	940614	940614	type	True	77.4976	298	1908	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:57:42,879] [INFO] DFAST Taxonomy check result was written to GCF_025685565.1_ASM2568556v1_genomic.fna/tc_result.tsv
[2024-01-24 13:57:42,880] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:57:42,880] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:57:42,880] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdd740066-0c82-44ec-ab7b-968b127979fa/dqc_reference/checkm_data
[2024-01-24 13:57:42,882] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:57:42,940] [INFO] Task started: CheckM
[2024-01-24 13:57:42,941] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025685565.1_ASM2568556v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025685565.1_ASM2568556v1_genomic.fna/checkm_input GCF_025685565.1_ASM2568556v1_genomic.fna/checkm_result
[2024-01-24 13:58:33,636] [INFO] Task succeeded: CheckM
[2024-01-24 13:58:33,637] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:58:33,659] [INFO] ===== Completeness check finished =====
[2024-01-24 13:58:33,659] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:58:33,660] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025685565.1_ASM2568556v1_genomic.fna/markers.fasta)
[2024-01-24 13:58:33,660] [INFO] Task started: Blastn
[2024-01-24 13:58:33,660] [INFO] Running command: blastn -query GCF_025685565.1_ASM2568556v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdd740066-0c82-44ec-ab7b-968b127979fa/dqc_reference/reference_markers_gtdb.fasta -out GCF_025685565.1_ASM2568556v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:34,547] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:34,552] [INFO] Selected 25 target genomes.
[2024-01-24 13:58:34,552] [INFO] Target genome list was writen to GCF_025685565.1_ASM2568556v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:58:34,595] [INFO] Task started: fastANI
[2024-01-24 13:58:34,596] [INFO] Running command: fastANI --query /var/lib/cwl/stg4981ae90-22b9-4c6f-9024-77ca7ea271ae/GCF_025685565.1_ASM2568556v1_genomic.fna.gz --refList GCF_025685565.1_ASM2568556v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025685565.1_ASM2568556v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:58:59,080] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:59,099] [INFO] Found 24 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:58:59,099] [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_014203275.1	s__Granulicella_D aggregans	85.4357	1398	1908	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Granulicella_D	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903642265.1	s__Granulicella_D sp903642265	78.3812	410	1908	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Granulicella_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018449545.1	s__Edaphobacter sp018449545	78.31	357	1908	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Edaphobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003633965.1	s__Edaphobacter dinghuensis_A	78.2746	240	1908	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Edaphobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013410115.1	s__Edaphobacter lichenicola_A	78.2644	300	1908	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Edaphobacter	95.0	98.03	98.03	0.94	0.94	2	-
GCF_009914315.1	s__Granulicella_C sp009914315	78.2555	346	1908	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Granulicella_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013410875.1	s__Edaphobacter lichenicola_C	78.1494	295	1908	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	78.1359	432	1908	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Granulicella_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009765825.1	s__Edaphobacter sp009765825	78.1102	364	1908	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Edaphobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009765835.1	s__Edaphobacter sp009765835	78.0241	330	1908	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Edaphobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002197545.1	s__Edaphobacter sp002197545	77.9256	244	1908	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Edaphobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000421065.1	s__Edaphobacter sp000421065	77.9154	311	1908	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	77.8944	280	1908	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Edaphobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004115155.1	s__Granulicella_C sibirica	77.8496	359	1908	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Granulicella_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000178975.2	s__Granulicella_C tundricola	77.8448	322	1908	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Granulicella_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014201315.1	s__Edaphobacter lichenicola_B	77.8445	324	1908	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Edaphobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018268775.1	s__Edaphobacter sp018268775	77.7974	293	1908	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Edaphobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014201375.1	s__Edaphobacter lichenicola_D	77.7211	340	1908	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Edaphobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000178955.2	s__Granulicella_A mallensis	77.4981	298	1908	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Granulicella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003133205.1	s__Palsa-288 sp003133205	77.3335	277	1908	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Palsa-288	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003162875.1	s__Palsa-288 sp003162875	77.246	262	1908	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Palsa-288	95.0	99.28	99.01	0.85	0.82	10	-
GCA_000620725.1	s__Terracidiphilus sp000620725	76.815	116	1908	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Terracidiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000014005.1	s__Koribacter versatilis_A	76.7143	81	1908	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Koribacteraceae;g__Koribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013289875.1	s__Silvibacterium sp013289875	76.4066	108	1908	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Silvibacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:58:59,103] [INFO] GTDB search result was written to GCF_025685565.1_ASM2568556v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:58:59,104] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:58:59,111] [INFO] DFAST_QC result json was written to GCF_025685565.1_ASM2568556v1_genomic.fna/dqc_result.json
[2024-01-24 13:58:59,111] [INFO] DFAST_QC completed!
[2024-01-24 13:58:59,111] [INFO] Total running time: 0h1m47s