[2024-01-25 19:01:20,896] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:01:20,898] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:01:20,898] [INFO] DQC Reference Directory: /var/lib/cwl/stg455ad065-0bc0-4b5a-b5b3-34b0bd764da7/dqc_reference
[2024-01-25 19:01:22,032] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:01:22,033] [INFO] Task started: Prodigal
[2024-01-25 19:01:22,033] [INFO] Running command: gunzip -c /var/lib/cwl/stg13a469b9-e02f-4708-b4e3-c971a2511ee8/GCF_004115155.1_ASM411515v1_genomic.fna.gz | prodigal -d GCF_004115155.1_ASM411515v1_genomic.fna/cds.fna -a GCF_004115155.1_ASM411515v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:01:37,709] [INFO] Task succeeded: Prodigal
[2024-01-25 19:01:37,710] [INFO] Task started: HMMsearch
[2024-01-25 19:01:37,710] [INFO] Running command: hmmsearch --tblout GCF_004115155.1_ASM411515v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg455ad065-0bc0-4b5a-b5b3-34b0bd764da7/dqc_reference/reference_markers.hmm GCF_004115155.1_ASM411515v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:01:38,087] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:01:38,088] [INFO] Found 6/6 markers.
[2024-01-25 19:01:38,170] [INFO] Query marker FASTA was written to GCF_004115155.1_ASM411515v1_genomic.fna/markers.fasta
[2024-01-25 19:01:38,171] [INFO] Task started: Blastn
[2024-01-25 19:01:38,171] [INFO] Running command: blastn -query GCF_004115155.1_ASM411515v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg455ad065-0bc0-4b5a-b5b3-34b0bd764da7/dqc_reference/reference_markers.fasta -out GCF_004115155.1_ASM411515v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:01:38,763] [INFO] Task succeeded: Blastn
[2024-01-25 19:01:38,766] [INFO] Selected 21 target genomes.
[2024-01-25 19:01:38,766] [INFO] Target genome list was writen to GCF_004115155.1_ASM411515v1_genomic.fna/target_genomes.txt
[2024-01-25 19:01:38,778] [INFO] Task started: fastANI
[2024-01-25 19:01:38,778] [INFO] Running command: fastANI --query /var/lib/cwl/stg13a469b9-e02f-4708-b4e3-c971a2511ee8/GCF_004115155.1_ASM411515v1_genomic.fna.gz --refList GCF_004115155.1_ASM411515v1_genomic.fna/target_genomes.txt --output GCF_004115155.1_ASM411515v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:01:56,565] [INFO] Task succeeded: fastANI
[2024-01-25 19:01:56,566] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg455ad065-0bc0-4b5a-b5b3-34b0bd764da7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:01:56,566] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg455ad065-0bc0-4b5a-b5b3-34b0bd764da7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:01:56,574] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:01:56,574] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:01:56,574] [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 sibirica	strain=AF10	GCA_004115155.1	2479048	2479048	type	True	100.0	2039	2040	95	conclusive
Edaphobacter lichenicola	strain=DSM 104462	GCA_025264645.1	2051959	2051959	suspected-type	True	79.7328	312	2040	95	below_threshold
Granulicella pectinivorans	strain=DSM 21001	GCA_900114625.1	474950	474950	type	True	79.0813	532	2040	95	below_threshold
Granulicella tundricola	strain=MP5ACTX9	GCA_000178975.2	940615	940615	type	True	78.4537	323	2040	95	below_threshold
Granulicella rosea	strain=DSM 18704	GCA_900188085.1	474952	474952	type	True	78.4117	334	2040	95	below_threshold
Edaphobacter aggregans	strain=DSM 19364	GCA_000745965.1	570835	570835	type	True	78.1177	345	2040	95	below_threshold
Edaphobacter dinghuensis	strain=CGMCC 1.12997	GCA_014640335.1	1560005	1560005	type	True	78.0543	270	2040	95	below_threshold
Edaphobacter acidisoli	strain=CGMCC 1.15447	GCA_014642855.1	2040573	2040573	type	True	77.8383	246	2040	95	below_threshold
Edaphobacter modestus	strain=DSM 18101	GCA_004217555.1	388466	388466	type	True	77.744	271	2040	95	below_threshold
Edaphobacter flagellatus	strain=HZ411	GCA_025264665.1	1933044	1933044	type	True	77.72	224	2040	95	below_threshold
Paracidobacterium acidisoli	strain=4G-K13	GCA_003428625.2	2303751	2303751	type	True	76.7684	149	2040	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:01:56,575] [INFO] DFAST Taxonomy check result was written to GCF_004115155.1_ASM411515v1_genomic.fna/tc_result.tsv
[2024-01-25 19:01:56,576] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:01:56,576] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:01:56,576] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg455ad065-0bc0-4b5a-b5b3-34b0bd764da7/dqc_reference/checkm_data
[2024-01-25 19:01:56,577] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:01:56,634] [INFO] Task started: CheckM
[2024-01-25 19:01:56,634] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004115155.1_ASM411515v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004115155.1_ASM411515v1_genomic.fna/checkm_input GCF_004115155.1_ASM411515v1_genomic.fna/checkm_result
[2024-01-25 19:02:41,268] [INFO] Task succeeded: CheckM
[2024-01-25 19:02:41,269] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:02:41,286] [INFO] ===== Completeness check finished =====
[2024-01-25 19:02:41,286] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:02:41,287] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004115155.1_ASM411515v1_genomic.fna/markers.fasta)
[2024-01-25 19:02:41,287] [INFO] Task started: Blastn
[2024-01-25 19:02:41,287] [INFO] Running command: blastn -query GCF_004115155.1_ASM411515v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg455ad065-0bc0-4b5a-b5b3-34b0bd764da7/dqc_reference/reference_markers_gtdb.fasta -out GCF_004115155.1_ASM411515v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:02:42,183] [INFO] Task succeeded: Blastn
[2024-01-25 19:02:42,186] [INFO] Selected 24 target genomes.
[2024-01-25 19:02:42,186] [INFO] Target genome list was writen to GCF_004115155.1_ASM411515v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:02:42,207] [INFO] Task started: fastANI
[2024-01-25 19:02:42,207] [INFO] Running command: fastANI --query /var/lib/cwl/stg13a469b9-e02f-4708-b4e3-c971a2511ee8/GCF_004115155.1_ASM411515v1_genomic.fna.gz --refList GCF_004115155.1_ASM411515v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004115155.1_ASM411515v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:03:03,401] [INFO] Task succeeded: fastANI
[2024-01-25 19:03:03,414] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:03:03,414] [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_004115155.1	s__Granulicella_C sibirica	100.0	2038	2040	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Granulicella_C	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_009765825.1	s__Edaphobacter sp009765825	79.1298	341	2040	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Edaphobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114625.1	s__Granulicella_C pectinivorans	79.0717	534	2040	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_014203275.1	s__Granulicella_D aggregans	79.0289	409	2040	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_013410065.1	s__Granulicella_B arctica	78.4627	286	2040	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_014201315.1	s__Edaphobacter lichenicola_B	78.4358	339	2040	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	78.3813	327	2040	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Edaphobacter	95.0	98.03	98.03	0.94	0.94	2	-
GCF_018449545.1	s__Edaphobacter sp018449545	78.3628	346	2040	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Edaphobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014201335.1	s__Edaphobacter lichenicola_E	78.3374	284	2040	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	78.2929	276	2040	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	78.1248	243	2040	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Edaphobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013410875.1	s__Edaphobacter lichenicola_C	78.0756	330	2040	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Edaphobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014640335.1	s__Edaphobacter dinghuensis	78.0543	270	2040	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Edaphobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009914315.1	s__Granulicella_C sp009914315	78.0255	330	2040	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_004217555.1	s__Edaphobacter modestus	77.7448	271	2040	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	77.735	248	2040	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Edaphobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001897435.1	s__Edaphobacter sp001897435	77.7289	297	2040	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Edaphobacter	95.0	99.98	99.98	0.99	0.99	2	-
GCA_015655585.1	s__Edaphobacter sp015655585	77.7208	219	2040	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	77.3912	123	2040	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Terriglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903642235.1	s__CAHJWL01 sp903642235	77.2104	200	2040	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__CAHJWL01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009781125.1	s__Edaphobacter sp009781125	76.3418	89	2040	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Edaphobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:03:03,419] [INFO] GTDB search result was written to GCF_004115155.1_ASM411515v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:03:03,419] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:03:03,423] [INFO] DFAST_QC result json was written to GCF_004115155.1_ASM411515v1_genomic.fna/dqc_result.json
[2024-01-25 19:03:03,423] [INFO] DFAST_QC completed!
[2024-01-25 19:03:03,423] [INFO] Total running time: 0h1m43s