[2024-01-24 13:57:32,142] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:57:32,144] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:57:32,144] [INFO] DQC Reference Directory: /var/lib/cwl/stga0a53363-05e4-470f-a748-243c7958b1be/dqc_reference
[2024-01-24 13:57:33,505] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:57:33,506] [INFO] Task started: Prodigal
[2024-01-24 13:57:33,506] [INFO] Running command: gunzip -c /var/lib/cwl/stgc138a9ef-6000-4c7d-96d7-e64e92f3c365/GCF_025685745.1_ASM2568574v1_genomic.fna.gz | prodigal -d GCF_025685745.1_ASM2568574v1_genomic.fna/cds.fna -a GCF_025685745.1_ASM2568574v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:57:46,648] [INFO] Task succeeded: Prodigal
[2024-01-24 13:57:46,648] [INFO] Task started: HMMsearch
[2024-01-24 13:57:46,649] [INFO] Running command: hmmsearch --tblout GCF_025685745.1_ASM2568574v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga0a53363-05e4-470f-a748-243c7958b1be/dqc_reference/reference_markers.hmm GCF_025685745.1_ASM2568574v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:57:46,920] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:57:46,922] [INFO] Found 6/6 markers.
[2024-01-24 13:57:46,958] [INFO] Query marker FASTA was written to GCF_025685745.1_ASM2568574v1_genomic.fna/markers.fasta
[2024-01-24 13:57:46,959] [INFO] Task started: Blastn
[2024-01-24 13:57:46,959] [INFO] Running command: blastn -query GCF_025685745.1_ASM2568574v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga0a53363-05e4-470f-a748-243c7958b1be/dqc_reference/reference_markers.fasta -out GCF_025685745.1_ASM2568574v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:57:47,599] [INFO] Task succeeded: Blastn
[2024-01-24 13:57:47,612] [INFO] Selected 18 target genomes.
[2024-01-24 13:57:47,612] [INFO] Target genome list was writen to GCF_025685745.1_ASM2568574v1_genomic.fna/target_genomes.txt
[2024-01-24 13:57:47,624] [INFO] Task started: fastANI
[2024-01-24 13:57:47,624] [INFO] Running command: fastANI --query /var/lib/cwl/stgc138a9ef-6000-4c7d-96d7-e64e92f3c365/GCF_025685745.1_ASM2568574v1_genomic.fna.gz --refList GCF_025685745.1_ASM2568574v1_genomic.fna/target_genomes.txt --output GCF_025685745.1_ASM2568574v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:58:02,854] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:02,854] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga0a53363-05e4-470f-a748-243c7958b1be/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:58:02,855] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga0a53363-05e4-470f-a748-243c7958b1be/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:58:02,866] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:58:02,866] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:58:02,867] [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
Edaphobacter acidisoli	strain=CGMCC 1.15447	GCA_014642855.1	2040573	2040573	type	True	99.9969	1392	1395	95	conclusive
Edaphobacter aggregans	strain=DSM 19364	GCA_000745965.1	570835	570835	type	True	79.0877	419	1395	95	below_threshold
Edaphobacter dinghuensis	strain=CGMCC 1.12997	GCA_014640335.1	1560005	1560005	type	True	78.4502	400	1395	95	below_threshold
Edaphobacter flagellatus	strain=HZ411	GCA_025264665.1	1933044	1933044	type	True	78.4454	316	1395	95	below_threshold
Edaphobacter modestus	strain=DSM 18101	GCA_004217555.1	388466	388466	type	True	78.3699	305	1395	95	below_threshold
Granulicella pectinivorans	strain=DSM 21001	GCA_900114625.1	474950	474950	type	True	78.1598	254	1395	95	below_threshold
Granulicella rosea	strain=DSM 18704	GCA_900188085.1	474952	474952	type	True	78.0202	300	1395	95	below_threshold
Granulicella sibirica	strain=AF10	GCA_004115155.1	2479048	2479048	type	True	78.0072	231	1395	95	below_threshold
Bryocella elongata	strain=DSM 22489	GCA_900108185.1	863522	863522	type	True	77.8067	210	1395	95	below_threshold
Paracidobacterium acidisoli	strain=4G-K13	GCA_003428625.2	2303751	2303751	type	True	77.4683	180	1395	95	below_threshold
Silvibacterium bohemicum	strain=S15	GCA_001006305.1	1577686	1577686	type	True	77.3098	146	1395	95	below_threshold
Silvibacterium bohemicum	strain=DSM 103733	GCA_014201455.1	1577686	1577686	type	True	77.3068	143	1395	95	below_threshold
Terriglobus saanensis	strain=SP1PR4	GCA_000179915.2	870903	870903	type	True	76.871	162	1395	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:58:02,868] [INFO] DFAST Taxonomy check result was written to GCF_025685745.1_ASM2568574v1_genomic.fna/tc_result.tsv
[2024-01-24 13:58:02,869] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:58:02,869] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:58:02,869] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga0a53363-05e4-470f-a748-243c7958b1be/dqc_reference/checkm_data
[2024-01-24 13:58:02,870] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:58:02,912] [INFO] Task started: CheckM
[2024-01-24 13:58:02,912] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025685745.1_ASM2568574v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025685745.1_ASM2568574v1_genomic.fna/checkm_input GCF_025685745.1_ASM2568574v1_genomic.fna/checkm_result
[2024-01-24 13:58:43,868] [INFO] Task succeeded: CheckM
[2024-01-24 13:58:43,869] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:58:43,886] [INFO] ===== Completeness check finished =====
[2024-01-24 13:58:43,886] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:58:43,886] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025685745.1_ASM2568574v1_genomic.fna/markers.fasta)
[2024-01-24 13:58:43,887] [INFO] Task started: Blastn
[2024-01-24 13:58:43,887] [INFO] Running command: blastn -query GCF_025685745.1_ASM2568574v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga0a53363-05e4-470f-a748-243c7958b1be/dqc_reference/reference_markers_gtdb.fasta -out GCF_025685745.1_ASM2568574v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:44,813] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:44,817] [INFO] Selected 22 target genomes.
[2024-01-24 13:58:44,817] [INFO] Target genome list was writen to GCF_025685745.1_ASM2568574v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:58:44,867] [INFO] Task started: fastANI
[2024-01-24 13:58:44,868] [INFO] Running command: fastANI --query /var/lib/cwl/stgc138a9ef-6000-4c7d-96d7-e64e92f3c365/GCF_025685745.1_ASM2568574v1_genomic.fna.gz --refList GCF_025685745.1_ASM2568574v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025685745.1_ASM2568574v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:59:04,930] [INFO] Task succeeded: fastANI
[2024-01-24 13:59:04,948] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:59:04,948] [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_014642855.1	s__Edaphobacter acidisoli	99.9969	1392	1395	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Edaphobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_009765825.1	s__Edaphobacter sp009765825	79.1733	371	1395	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Edaphobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000745965.1	s__Edaphobacter aggregans	79.0881	418	1395	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Edaphobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003751275.1	s__Edaphobacter sp003751275	79.0801	405	1395	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Edaphobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014201315.1	s__Edaphobacter lichenicola_B	79.0285	390	1395	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	78.8786	359	1395	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Edaphobacter	95.0	98.03	98.03	0.94	0.94	2	-
GCA_002197545.1	s__Edaphobacter sp002197545	78.8611	336	1395	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	78.8543	371	1395	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	78.7698	328	1395	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	78.6379	329	1395	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Edaphobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015655585.1	s__Edaphobacter sp015655585	78.633	277	1395	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	78.5854	412	1395	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Edaphobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009766095.1	s__Edaphobacter sp009766095	78.4808	349	1395	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	78.4516	393	1395	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Edaphobacter	95.0	99.98	99.98	0.99	0.99	2	-
GCA_018268895.1	s__Edaphobacter sp018268895	78.4406	353	1395	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	78.4303	402	1395	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Edaphobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004217555.1	s__Edaphobacter modestus	78.3699	305	1395	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	78.1737	253	1395	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_014274685.1	s__Edaphobacter sp014274685	78.0403	228	1395	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Edaphobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003133205.1	s__Palsa-288 sp003133205	77.8657	277	1395	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Palsa-288	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009765785.1	s__UBA5172 sp009765785	77.647	190	1395	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__UBA5172	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003151155.1	s__Koribacter sp003151155	76.2674	57	1395	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Koribacteraceae;g__Koribacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:59:04,950] [INFO] GTDB search result was written to GCF_025685745.1_ASM2568574v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:59:04,950] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:59:04,954] [INFO] DFAST_QC result json was written to GCF_025685745.1_ASM2568574v1_genomic.fna/dqc_result.json
[2024-01-24 13:59:04,954] [INFO] DFAST_QC completed!
[2024-01-24 13:59:04,954] [INFO] Total running time: 0h1m33s