[2024-01-24 11:26:10,397] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:26:10,400] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:26:10,400] [INFO] DQC Reference Directory: /var/lib/cwl/stg5ac3afbc-3b78-4e5e-965b-dc0d20f9c2be/dqc_reference
[2024-01-24 11:26:11,666] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:26:11,667] [INFO] Task started: Prodigal
[2024-01-24 11:26:11,667] [INFO] Running command: gunzip -c /var/lib/cwl/stgd8e85ad5-c540-4fb7-bfe0-890c8b6a9767/GCF_025685395.1_ASM2568539v1_genomic.fna.gz | prodigal -d GCF_025685395.1_ASM2568539v1_genomic.fna/cds.fna -a GCF_025685395.1_ASM2568539v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:26:25,159] [INFO] Task succeeded: Prodigal
[2024-01-24 11:26:25,160] [INFO] Task started: HMMsearch
[2024-01-24 11:26:25,160] [INFO] Running command: hmmsearch --tblout GCF_025685395.1_ASM2568539v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5ac3afbc-3b78-4e5e-965b-dc0d20f9c2be/dqc_reference/reference_markers.hmm GCF_025685395.1_ASM2568539v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:26:25,527] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:26:25,528] [INFO] Found 6/6 markers.
[2024-01-24 11:26:25,576] [INFO] Query marker FASTA was written to GCF_025685395.1_ASM2568539v1_genomic.fna/markers.fasta
[2024-01-24 11:26:25,577] [INFO] Task started: Blastn
[2024-01-24 11:26:25,577] [INFO] Running command: blastn -query GCF_025685395.1_ASM2568539v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5ac3afbc-3b78-4e5e-965b-dc0d20f9c2be/dqc_reference/reference_markers.fasta -out GCF_025685395.1_ASM2568539v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:26:26,310] [INFO] Task succeeded: Blastn
[2024-01-24 11:26:26,314] [INFO] Selected 18 target genomes.
[2024-01-24 11:26:26,314] [INFO] Target genome list was writen to GCF_025685395.1_ASM2568539v1_genomic.fna/target_genomes.txt
[2024-01-24 11:26:26,350] [INFO] Task started: fastANI
[2024-01-24 11:26:26,351] [INFO] Running command: fastANI --query /var/lib/cwl/stgd8e85ad5-c540-4fb7-bfe0-890c8b6a9767/GCF_025685395.1_ASM2568539v1_genomic.fna.gz --refList GCF_025685395.1_ASM2568539v1_genomic.fna/target_genomes.txt --output GCF_025685395.1_ASM2568539v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:26:45,152] [INFO] Task succeeded: fastANI
[2024-01-24 11:26:45,152] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5ac3afbc-3b78-4e5e-965b-dc0d20f9c2be/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:26:45,153] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5ac3afbc-3b78-4e5e-965b-dc0d20f9c2be/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:26:45,168] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:26:45,168] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:26:45,168] [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
Bryocella elongata	strain=DSM 22489	GCA_900108185.1	863522	863522	type	True	77.8145	251	1451	95	below_threshold
Granulicella rosea	strain=DSM 18704	GCA_900188085.1	474952	474952	type	True	77.7359	301	1451	95	below_threshold
Granulicella mallensis	strain=MP5ACTX8	GCA_000178955.2	940614	940614	type	True	77.6089	227	1451	95	below_threshold
Terriglobus roseus	strain=DSM 18391	GCA_000265425.1	392734	392734	type	True	77.4937	289	1451	95	below_threshold
Edaphobacter flagellatus	strain=HZ411	GCA_025264665.1	1933044	1933044	type	True	77.4723	244	1451	95	below_threshold
Edaphobacter dinghuensis	strain=CGMCC 1.12997	GCA_014640335.1	1560005	1560005	type	True	77.4424	206	1451	95	below_threshold
Silvibacterium dinghuense	strain=DHOF10	GCA_004123295.1	1560006	1560006	type	True	77.4219	213	1451	95	below_threshold
Edaphobacter aggregans	strain=DSM 19364	GCA_000745965.1	570835	570835	type	True	77.3526	277	1451	95	below_threshold
Granulicella pectinivorans	strain=DSM 21001	GCA_900114625.1	474950	474950	type	True	77.2752	221	1451	95	below_threshold
Edaphobacter modestus	strain=DSM 18101	GCA_004217555.1	388466	388466	type	True	77.2536	217	1451	95	below_threshold
Granulicella tundricola	strain=MP5ACTX9	GCA_000178975.2	940615	940615	type	True	77.2432	191	1451	95	below_threshold
Terriglobus saanensis	strain=SP1PR4	GCA_000179915.2	870903	870903	type	True	77.2399	213	1451	95	below_threshold
Paracidobacterium acidisoli	strain=4G-K13	GCA_003428625.2	2303751	2303751	type	True	77.1582	174	1451	95	below_threshold
Edaphobacter lichenicola	strain=DSM 104462	GCA_025264645.1	2051959	2051959	suspected-type	True	77.1413	166	1451	95	below_threshold
Acidobacterium capsulatum	strain=ATCC 51196	GCA_000022565.1	33075	33075	type	True	77.1246	146	1451	95	below_threshold
Silvibacterium bohemicum	strain=S15	GCA_001006305.1	1577686	1577686	type	True	76.9522	176	1451	95	below_threshold
Alloacidobacterium dinghuense	strain=4Y35	GCA_014274465.1	2763107	2763107	type	True	76.9443	116	1451	95	below_threshold
Silvibacterium bohemicum	strain=DSM 103733	GCA_014201455.1	1577686	1577686	type	True	76.8678	175	1451	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:26:45,170] [INFO] DFAST Taxonomy check result was written to GCF_025685395.1_ASM2568539v1_genomic.fna/tc_result.tsv
[2024-01-24 11:26:45,170] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:26:45,171] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:26:45,171] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5ac3afbc-3b78-4e5e-965b-dc0d20f9c2be/dqc_reference/checkm_data
[2024-01-24 11:26:45,172] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:26:45,217] [INFO] Task started: CheckM
[2024-01-24 11:26:45,217] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025685395.1_ASM2568539v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025685395.1_ASM2568539v1_genomic.fna/checkm_input GCF_025685395.1_ASM2568539v1_genomic.fna/checkm_result
[2024-01-24 11:27:27,314] [INFO] Task succeeded: CheckM
[2024-01-24 11:27:27,315] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:27:27,335] [INFO] ===== Completeness check finished =====
[2024-01-24 11:27:27,336] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:27:27,336] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025685395.1_ASM2568539v1_genomic.fna/markers.fasta)
[2024-01-24 11:27:27,336] [INFO] Task started: Blastn
[2024-01-24 11:27:27,337] [INFO] Running command: blastn -query GCF_025685395.1_ASM2568539v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5ac3afbc-3b78-4e5e-965b-dc0d20f9c2be/dqc_reference/reference_markers_gtdb.fasta -out GCF_025685395.1_ASM2568539v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:27:28,290] [INFO] Task succeeded: Blastn
[2024-01-24 11:27:28,294] [INFO] Selected 18 target genomes.
[2024-01-24 11:27:28,294] [INFO] Target genome list was writen to GCF_025685395.1_ASM2568539v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:27:28,328] [INFO] Task started: fastANI
[2024-01-24 11:27:28,328] [INFO] Running command: fastANI --query /var/lib/cwl/stgd8e85ad5-c540-4fb7-bfe0-890c8b6a9767/GCF_025685395.1_ASM2568539v1_genomic.fna.gz --refList GCF_025685395.1_ASM2568539v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025685395.1_ASM2568539v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:27:43,003] [INFO] Task succeeded: fastANI
[2024-01-24 11:27:43,021] [INFO] Found 17 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 11:27:43,022] [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_008000815.1	s__Terriglobus_A albidus	79.9534	797	1451	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Terriglobus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013361705.1	s__Terriglobus_A sp013361705	79.8281	641	1451	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Terriglobus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900108185.1	s__Bryocella elongata	77.8145	251	1451	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Bryocella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102185.1	s__Terriglobus roseus_A	77.5688	203	1451	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Terriglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000265425.1	s__Terriglobus roseus	77.5039	290	1451	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Terriglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018268895.1	s__Edaphobacter sp018268895	77.4865	243	1451	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Edaphobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900105625.1	s__Terriglobus roseus_B	77.4464	260	1451	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Terriglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014274685.1	s__Edaphobacter sp014274685	77.3542	153	1451	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	77.3481	303	1451	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	77.3424	278	1451	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Edaphobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018268855.1	s__Terriglobus sp018268855	77.3395	188	1451	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Terriglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000688615.1	s__Edaphobacter sp000688615	77.2815	175	1451	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Edaphobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018449545.1	s__Edaphobacter sp018449545	77.2105	207	1451	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Edaphobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000022565.1	s__Acidobacterium capsulatum	77.0717	149	1451	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Acidobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCA_011333575.1	s__Acidobacterium capsulatum_A	77.0097	143	1451	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Acidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001006305.1	s__Silvibacterium bohemicum	76.9386	177	1451	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Silvibacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCA_903932385.1	s__CAIZGA01 sp903932385	75.757	69	1451	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__CAIZGA01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:27:43,024] [INFO] GTDB search result was written to GCF_025685395.1_ASM2568539v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:27:43,025] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:27:43,030] [INFO] DFAST_QC result json was written to GCF_025685395.1_ASM2568539v1_genomic.fna/dqc_result.json
[2024-01-24 11:27:43,030] [INFO] DFAST_QC completed!
[2024-01-24 11:27:43,030] [INFO] Total running time: 0h1m33s