[2024-01-24 13:13:26,819] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:13:26,823] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:13:26,823] [INFO] DQC Reference Directory: /var/lib/cwl/stg7d305b12-1987-49d6-9723-b2f3860b673d/dqc_reference
[2024-01-24 13:13:28,133] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:13:28,134] [INFO] Task started: Prodigal
[2024-01-24 13:13:28,134] [INFO] Running command: gunzip -c /var/lib/cwl/stge8ef8a4b-baa4-4727-a845-9fe9f835fd46/GCF_014640335.1_ASM1464033v1_genomic.fna.gz | prodigal -d GCF_014640335.1_ASM1464033v1_genomic.fna/cds.fna -a GCF_014640335.1_ASM1464033v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:13:42,661] [INFO] Task succeeded: Prodigal
[2024-01-24 13:13:42,662] [INFO] Task started: HMMsearch
[2024-01-24 13:13:42,662] [INFO] Running command: hmmsearch --tblout GCF_014640335.1_ASM1464033v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7d305b12-1987-49d6-9723-b2f3860b673d/dqc_reference/reference_markers.hmm GCF_014640335.1_ASM1464033v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:13:42,965] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:13:42,966] [INFO] Found 6/6 markers.
[2024-01-24 13:13:43,006] [INFO] Query marker FASTA was written to GCF_014640335.1_ASM1464033v1_genomic.fna/markers.fasta
[2024-01-24 13:13:43,007] [INFO] Task started: Blastn
[2024-01-24 13:13:43,007] [INFO] Running command: blastn -query GCF_014640335.1_ASM1464033v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7d305b12-1987-49d6-9723-b2f3860b673d/dqc_reference/reference_markers.fasta -out GCF_014640335.1_ASM1464033v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:13:43,655] [INFO] Task succeeded: Blastn
[2024-01-24 13:13:43,659] [INFO] Selected 13 target genomes.
[2024-01-24 13:13:43,660] [INFO] Target genome list was writen to GCF_014640335.1_ASM1464033v1_genomic.fna/target_genomes.txt
[2024-01-24 13:13:43,677] [INFO] Task started: fastANI
[2024-01-24 13:13:43,678] [INFO] Running command: fastANI --query /var/lib/cwl/stge8ef8a4b-baa4-4727-a845-9fe9f835fd46/GCF_014640335.1_ASM1464033v1_genomic.fna.gz --refList GCF_014640335.1_ASM1464033v1_genomic.fna/target_genomes.txt --output GCF_014640335.1_ASM1464033v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:13:57,761] [INFO] Task succeeded: fastANI
[2024-01-24 13:13:57,761] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7d305b12-1987-49d6-9723-b2f3860b673d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:13:57,762] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7d305b12-1987-49d6-9723-b2f3860b673d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:13:57,773] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:13:57,773] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:13:57,773] [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 dinghuensis	strain=CGMCC 1.12997	GCA_014640335.1	1560005	1560005	type	True	100.0	1507	1507	95	conclusive
Edaphobacter lichenicola	strain=DSM 104462	GCA_025264645.1	2051959	2051959	suspected-type	True	78.7861	384	1507	95	below_threshold
Edaphobacter aggregans	strain=DSM 19364	GCA_000745965.1	570835	570835	type	True	78.7673	435	1507	95	below_threshold
Edaphobacter flagellatus	strain=HZ411	GCA_025264665.1	1933044	1933044	type	True	78.4859	309	1507	95	below_threshold
Edaphobacter modestus	strain=DSM 18101	GCA_004217555.1	388466	388466	type	True	78.3984	338	1507	95	below_threshold
Edaphobacter acidisoli	strain=CGMCC 1.15447	GCA_014642855.1	2040573	2040573	type	True	78.3038	405	1507	95	below_threshold
Granulicella mallensis	strain=MP5ACTX8	GCA_000178955.2	940614	940614	type	True	78.151	290	1507	95	below_threshold
Granulicella sibirica	strain=AF10	GCA_004115155.1	2479048	2479048	type	True	77.8435	273	1507	95	below_threshold
Granulicella rosea	strain=DSM 18704	GCA_900188085.1	474952	474952	type	True	77.7758	333	1507	95	below_threshold
Granulicella tundricola	strain=MP5ACTX9	GCA_000178975.2	940615	940615	type	True	77.7596	255	1507	95	below_threshold
Granulicella pectinivorans	strain=DSM 21001	GCA_900114625.1	474950	474950	type	True	77.7376	288	1507	95	below_threshold
Bryocella elongata	strain=DSM 22489	GCA_900108185.1	863522	863522	type	True	77.7073	223	1507	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:13:57,775] [INFO] DFAST Taxonomy check result was written to GCF_014640335.1_ASM1464033v1_genomic.fna/tc_result.tsv
[2024-01-24 13:13:57,775] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:13:57,776] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:13:57,776] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7d305b12-1987-49d6-9723-b2f3860b673d/dqc_reference/checkm_data
[2024-01-24 13:13:57,777] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:13:57,820] [INFO] Task started: CheckM
[2024-01-24 13:13:57,820] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014640335.1_ASM1464033v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014640335.1_ASM1464033v1_genomic.fna/checkm_input GCF_014640335.1_ASM1464033v1_genomic.fna/checkm_result
[2024-01-24 13:14:40,865] [INFO] Task succeeded: CheckM
[2024-01-24 13:14:40,867] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:14:40,888] [INFO] ===== Completeness check finished =====
[2024-01-24 13:14:40,889] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:14:40,889] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014640335.1_ASM1464033v1_genomic.fna/markers.fasta)
[2024-01-24 13:14:40,889] [INFO] Task started: Blastn
[2024-01-24 13:14:40,890] [INFO] Running command: blastn -query GCF_014640335.1_ASM1464033v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7d305b12-1987-49d6-9723-b2f3860b673d/dqc_reference/reference_markers_gtdb.fasta -out GCF_014640335.1_ASM1464033v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:14:41,859] [INFO] Task succeeded: Blastn
[2024-01-24 13:14:41,862] [INFO] Selected 10 target genomes.
[2024-01-24 13:14:41,862] [INFO] Target genome list was writen to GCF_014640335.1_ASM1464033v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:14:41,874] [INFO] Task started: fastANI
[2024-01-24 13:14:41,875] [INFO] Running command: fastANI --query /var/lib/cwl/stge8ef8a4b-baa4-4727-a845-9fe9f835fd46/GCF_014640335.1_ASM1464033v1_genomic.fna.gz --refList GCF_014640335.1_ASM1464033v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014640335.1_ASM1464033v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:14:52,400] [INFO] Task succeeded: fastANI
[2024-01-24 13:14:52,416] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:14:52,417] [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_014640335.1	s__Edaphobacter dinghuensis	100.0	1507	1507	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_009765835.1	s__Edaphobacter sp009765835	85.7624	1062	1507	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	81.4747	655	1507	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	80.9252	644	1507	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	80.522	693	1507	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Edaphobacter	95.0	99.98	99.98	0.99	0.99	2	-
GCF_003751275.1	s__Edaphobacter sp003751275	79.0601	452	1507	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	78.9229	448	1507	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	78.5085	324	1507	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	78.4819	294	1507	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	78.3873	341	1507	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Edaphobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:14:52,425] [INFO] GTDB search result was written to GCF_014640335.1_ASM1464033v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:14:52,427] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:14:52,431] [INFO] DFAST_QC result json was written to GCF_014640335.1_ASM1464033v1_genomic.fna/dqc_result.json
[2024-01-24 13:14:52,431] [INFO] DFAST_QC completed!
[2024-01-24 13:14:52,431] [INFO] Total running time: 0h1m26s