[2024-01-24 13:18:44,960] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:18:44,961] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:18:44,962] [INFO] DQC Reference Directory: /var/lib/cwl/stg772cc8c3-81d4-4c13-8875-e95bd6ffd258/dqc_reference
[2024-01-24 13:18:46,292] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:18:46,294] [INFO] Task started: Prodigal
[2024-01-24 13:18:46,295] [INFO] Running command: gunzip -c /var/lib/cwl/stg250aa940-21e9-4eb3-b987-13c64947139f/GCF_025685645.1_ASM2568564v1_genomic.fna.gz | prodigal -d GCF_025685645.1_ASM2568564v1_genomic.fna/cds.fna -a GCF_025685645.1_ASM2568564v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:19:00,468] [INFO] Task succeeded: Prodigal
[2024-01-24 13:19:00,468] [INFO] Task started: HMMsearch
[2024-01-24 13:19:00,468] [INFO] Running command: hmmsearch --tblout GCF_025685645.1_ASM2568564v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg772cc8c3-81d4-4c13-8875-e95bd6ffd258/dqc_reference/reference_markers.hmm GCF_025685645.1_ASM2568564v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:19:00,726] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:19:00,727] [INFO] Found 6/6 markers.
[2024-01-24 13:19:00,767] [INFO] Query marker FASTA was written to GCF_025685645.1_ASM2568564v1_genomic.fna/markers.fasta
[2024-01-24 13:19:00,767] [INFO] Task started: Blastn
[2024-01-24 13:19:00,767] [INFO] Running command: blastn -query GCF_025685645.1_ASM2568564v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg772cc8c3-81d4-4c13-8875-e95bd6ffd258/dqc_reference/reference_markers.fasta -out GCF_025685645.1_ASM2568564v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:01,470] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:01,474] [INFO] Selected 9 target genomes.
[2024-01-24 13:19:01,474] [INFO] Target genome list was writen to GCF_025685645.1_ASM2568564v1_genomic.fna/target_genomes.txt
[2024-01-24 13:19:01,479] [INFO] Task started: fastANI
[2024-01-24 13:19:01,480] [INFO] Running command: fastANI --query /var/lib/cwl/stg250aa940-21e9-4eb3-b987-13c64947139f/GCF_025685645.1_ASM2568564v1_genomic.fna.gz --refList GCF_025685645.1_ASM2568564v1_genomic.fna/target_genomes.txt --output GCF_025685645.1_ASM2568564v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:19:10,341] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:10,342] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg772cc8c3-81d4-4c13-8875-e95bd6ffd258/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:19:10,342] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg772cc8c3-81d4-4c13-8875-e95bd6ffd258/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:19:10,351] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:19:10,351] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:19:10,351] [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 aggregans	strain=DSM 19364	GCA_000745965.1	570835	570835	type	True	80.806	744	1579	95	below_threshold
Edaphobacter modestus	strain=DSM 18101	GCA_004217555.1	388466	388466	type	True	79.2285	515	1579	95	below_threshold
Edaphobacter flagellatus	strain=HZ411	GCA_025264665.1	1933044	1933044	type	True	78.9479	453	1579	95	below_threshold
Edaphobacter dinghuensis	strain=CGMCC 1.12997	GCA_014640335.1	1560005	1560005	type	True	78.8234	398	1579	95	below_threshold
Edaphobacter acidisoli	strain=CGMCC 1.15447	GCA_014642855.1	2040573	2040573	type	True	78.76	397	1579	95	below_threshold
Edaphobacter lichenicola	strain=DSM 104462	GCA_025264645.1	2051959	2051959	suspected-type	True	78.4608	408	1579	95	below_threshold
Granulicella rosea	strain=DSM 18704	GCA_900188085.1	474952	474952	type	True	78.0434	362	1579	95	below_threshold
Bryocella elongata	strain=DSM 22489	GCA_900108185.1	863522	863522	type	True	77.9271	259	1579	95	below_threshold
Terriglobus roseus	strain=DSM 18391	GCA_000265425.1	392734	392734	type	True	77.1966	176	1579	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:19:10,353] [INFO] DFAST Taxonomy check result was written to GCF_025685645.1_ASM2568564v1_genomic.fna/tc_result.tsv
[2024-01-24 13:19:10,353] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:19:10,353] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:19:10,354] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg772cc8c3-81d4-4c13-8875-e95bd6ffd258/dqc_reference/checkm_data
[2024-01-24 13:19:10,355] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:19:10,401] [INFO] Task started: CheckM
[2024-01-24 13:19:10,402] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025685645.1_ASM2568564v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025685645.1_ASM2568564v1_genomic.fna/checkm_input GCF_025685645.1_ASM2568564v1_genomic.fna/checkm_result
[2024-01-24 13:19:51,790] [INFO] Task succeeded: CheckM
[2024-01-24 13:19:51,792] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:19:51,809] [INFO] ===== Completeness check finished =====
[2024-01-24 13:19:51,809] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:19:51,809] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025685645.1_ASM2568564v1_genomic.fna/markers.fasta)
[2024-01-24 13:19:51,809] [INFO] Task started: Blastn
[2024-01-24 13:19:51,810] [INFO] Running command: blastn -query GCF_025685645.1_ASM2568564v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg772cc8c3-81d4-4c13-8875-e95bd6ffd258/dqc_reference/reference_markers_gtdb.fasta -out GCF_025685645.1_ASM2568564v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:52,878] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:52,881] [INFO] Selected 18 target genomes.
[2024-01-24 13:19:52,881] [INFO] Target genome list was writen to GCF_025685645.1_ASM2568564v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:19:52,977] [INFO] Task started: fastANI
[2024-01-24 13:19:52,978] [INFO] Running command: fastANI --query /var/lib/cwl/stg250aa940-21e9-4eb3-b987-13c64947139f/GCF_025685645.1_ASM2568564v1_genomic.fna.gz --refList GCF_025685645.1_ASM2568564v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025685645.1_ASM2568564v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:20:08,430] [INFO] Task succeeded: fastANI
[2024-01-24 13:20:08,443] [INFO] Found 15 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:20:08,443] [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_000745965.1	s__Edaphobacter aggregans	80.8196	744	1579	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Edaphobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003945235.1	s__Edaphobacter aggregans_A	79.6592	603	1579	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Edaphobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018268895.1	s__Edaphobacter sp018268895	79.3449	508	1579	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	79.2249	515	1579	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Edaphobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018449715.1	s__Edaphobacter sp018449715	79.2097	496	1579	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	79.1426	458	1579	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	79.0566	455	1579	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Edaphobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010093025.1	s__Edaphobacter sp010093025	78.4756	377	1579	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Edaphobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000688615.1	s__Edaphobacter sp000688615	78.4545	338	1579	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	78.439	332	1579	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Edaphobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014274685.1	s__Edaphobacter sp014274685	78.0679	346	1579	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Edaphobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014203275.1	s__Granulicella_D aggregans	77.977	300	1579	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_009766105.1	s__Granulicella_A sp009766105	77.8611	244	1579	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_003162875.1	s__Palsa-288 sp003162875	77.2819	287	1579	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_903642265.1	s__Granulicella_D sp903642265	77.1035	183	1579	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Granulicella_D	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:20:08,445] [INFO] GTDB search result was written to GCF_025685645.1_ASM2568564v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:20:08,445] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:20:08,448] [INFO] DFAST_QC result json was written to GCF_025685645.1_ASM2568564v1_genomic.fna/dqc_result.json
[2024-01-24 13:20:08,449] [INFO] DFAST_QC completed!
[2024-01-24 13:20:08,449] [INFO] Total running time: 0h1m23s