[2024-01-24 12:40:07,963] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:40:07,965] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:40:07,965] [INFO] DQC Reference Directory: /var/lib/cwl/stgdd59fbda-3fce-4743-9ca5-2a2b0bf352fc/dqc_reference
[2024-01-24 12:40:09,359] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:40:09,360] [INFO] Task started: Prodigal
[2024-01-24 12:40:09,360] [INFO] Running command: gunzip -c /var/lib/cwl/stgdc66be57-cc75-4ef6-88f7-9b17cf95e9fd/GCF_004339725.1_ASM433972v1_genomic.fna.gz | prodigal -d GCF_004339725.1_ASM433972v1_genomic.fna/cds.fna -a GCF_004339725.1_ASM433972v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:40:21,817] [INFO] Task succeeded: Prodigal
[2024-01-24 12:40:21,817] [INFO] Task started: HMMsearch
[2024-01-24 12:40:21,818] [INFO] Running command: hmmsearch --tblout GCF_004339725.1_ASM433972v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdd59fbda-3fce-4743-9ca5-2a2b0bf352fc/dqc_reference/reference_markers.hmm GCF_004339725.1_ASM433972v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:40:22,122] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:40:22,123] [INFO] Found 6/6 markers.
[2024-01-24 12:40:22,161] [INFO] Query marker FASTA was written to GCF_004339725.1_ASM433972v1_genomic.fna/markers.fasta
[2024-01-24 12:40:22,161] [INFO] Task started: Blastn
[2024-01-24 12:40:22,161] [INFO] Running command: blastn -query GCF_004339725.1_ASM433972v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdd59fbda-3fce-4743-9ca5-2a2b0bf352fc/dqc_reference/reference_markers.fasta -out GCF_004339725.1_ASM433972v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:40:22,774] [INFO] Task succeeded: Blastn
[2024-01-24 12:40:22,780] [INFO] Selected 14 target genomes.
[2024-01-24 12:40:22,780] [INFO] Target genome list was writen to GCF_004339725.1_ASM433972v1_genomic.fna/target_genomes.txt
[2024-01-24 12:40:22,790] [INFO] Task started: fastANI
[2024-01-24 12:40:22,790] [INFO] Running command: fastANI --query /var/lib/cwl/stgdc66be57-cc75-4ef6-88f7-9b17cf95e9fd/GCF_004339725.1_ASM433972v1_genomic.fna.gz --refList GCF_004339725.1_ASM433972v1_genomic.fna/target_genomes.txt --output GCF_004339725.1_ASM433972v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:40:34,718] [INFO] Task succeeded: fastANI
[2024-01-24 12:40:34,718] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdd59fbda-3fce-4743-9ca5-2a2b0bf352fc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:40:34,718] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdd59fbda-3fce-4743-9ca5-2a2b0bf352fc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:40:34,728] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:40:34,729] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:40:34,729] [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
Acidipila rosea	strain=DSM 103428	GCA_004339725.1	768535	768535	type	True	100.0	1398	1398	95	conclusive
Silvibacterium dinghuense	strain=DHOF10	GCA_004123295.1	1560006	1560006	type	True	77.5762	261	1398	95	below_threshold
Silvibacterium dinghuense	strain=CGMCC 1.13007	GCA_014640355.1	1560006	1560006	type	True	77.5101	259	1398	95	below_threshold
Silvibacterium bohemicum	strain=DSM 103733	GCA_014201455.1	1577686	1577686	type	True	77.3839	239	1398	95	below_threshold
Acidobacterium capsulatum	strain=ATCC 51196	GCA_000022565.1	33075	33075	type	True	77.3376	203	1398	95	below_threshold
Silvibacterium bohemicum	strain=S15	GCA_001006305.1	1577686	1577686	type	True	77.3284	235	1398	95	below_threshold
Acidisarcina polymorpha	strain=SBC82	GCA_003330725.1	2211140	2211140	type	True	77.3244	132	1398	95	below_threshold
Alloacidobacterium dinghuense	strain=4Y35	GCA_014274465.1	2763107	2763107	type	True	77.2733	192	1398	95	below_threshold
Occallatibacter riparius	strain=DSM 25168	GCA_025264625.1	1002689	1002689	type	True	76.6678	134	1398	95	below_threshold
Pseudacidobacterium ailaaui	strain=PMMR2	GCA_000688455.1	1382359	1382359	type	True	76.4839	141	1398	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:40:34,730] [INFO] DFAST Taxonomy check result was written to GCF_004339725.1_ASM433972v1_genomic.fna/tc_result.tsv
[2024-01-24 12:40:34,731] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:40:34,731] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:40:34,731] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdd59fbda-3fce-4743-9ca5-2a2b0bf352fc/dqc_reference/checkm_data
[2024-01-24 12:40:34,733] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:40:34,781] [INFO] Task started: CheckM
[2024-01-24 12:40:34,782] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004339725.1_ASM433972v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004339725.1_ASM433972v1_genomic.fna/checkm_input GCF_004339725.1_ASM433972v1_genomic.fna/checkm_result
[2024-01-24 12:41:13,247] [INFO] Task succeeded: CheckM
[2024-01-24 12:41:13,248] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:41:13,269] [INFO] ===== Completeness check finished =====
[2024-01-24 12:41:13,269] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:41:13,270] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004339725.1_ASM433972v1_genomic.fna/markers.fasta)
[2024-01-24 12:41:13,270] [INFO] Task started: Blastn
[2024-01-24 12:41:13,270] [INFO] Running command: blastn -query GCF_004339725.1_ASM433972v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdd59fbda-3fce-4743-9ca5-2a2b0bf352fc/dqc_reference/reference_markers_gtdb.fasta -out GCF_004339725.1_ASM433972v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:41:14,151] [INFO] Task succeeded: Blastn
[2024-01-24 12:41:14,156] [INFO] Selected 25 target genomes.
[2024-01-24 12:41:14,156] [INFO] Target genome list was writen to GCF_004339725.1_ASM433972v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:41:14,206] [INFO] Task started: fastANI
[2024-01-24 12:41:14,207] [INFO] Running command: fastANI --query /var/lib/cwl/stgdc66be57-cc75-4ef6-88f7-9b17cf95e9fd/GCF_004339725.1_ASM433972v1_genomic.fna.gz --refList GCF_004339725.1_ASM433972v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004339725.1_ASM433972v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:41:32,614] [INFO] Task succeeded: fastANI
[2024-01-24 12:41:32,636] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:41:32,636] [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_004339725.1	s__Acidipila rosea	100.0	1398	1398	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Acidipila	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_011333575.1	s__Acidobacterium capsulatum_A	77.3415	175	1398	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Acidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000022565.1	s__Acidobacterium capsulatum	77.3376	203	1398	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Acidobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001006305.1	s__Silvibacterium bohemicum	77.3284	235	1398	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Silvibacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_009765985.1	s__Acidobacterium_A sp009765985	77.3079	220	1398	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Acidobacterium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003330725.1	s__Acidisarcina polymorpha	77.2933	131	1398	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Acidisarcina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014274465.1	s__Acidobacterium_A sp014274465	77.2878	191	1398	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Acidobacterium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013289875.1	s__Silvibacterium sp013289875	77.1983	174	1398	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Silvibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013285705.1	s__Acidobacterium_A sp013285705	77.1607	133	1398	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Acidobacterium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014083945.1	s__UBA5172 sp014083945	77.0677	112	1398	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__UBA5172	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015655315.1	s__Acidobacterium_A sp015655315	76.6832	140	1398	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Acidobacterium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003166955.1	s__Palsa-343 sp003166955	76.5974	185	1398	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Palsa-343	95.0	99.89	99.89	0.95	0.95	2	-
GCF_013410115.1	s__Edaphobacter lichenicola_A	76.5938	118	1398	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Edaphobacter	95.0	98.03	98.03	0.94	0.94	2	-
GCF_000688455.1	s__Acidobacterium_A ailaaui	76.4839	141	1398	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Acidobacterium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903842065.1	s__Terracidiphilus sp903842065	76.4762	101	1398	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Terracidiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003131625.1	s__Palsa-343 sp003131625	76.449	163	1398	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Palsa-343	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016196065.1	s__QIAJ01 sp016196065	76.3896	55	1398	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__SbA1;g__QIAJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003139795.1	s__Terracidiphilus sp003139795	76.3645	131	1398	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Terracidiphilus	95.0	99.74	99.71	0.89	0.87	5	-
GCA_003165075.1	s__Terracidiphilus sp003165075	76.2236	120	1398	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Terracidiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013289685.1	s__Sulfotelmatobacter sp013289685	75.8865	75	1398	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__SbA1;g__Sulfotelmatobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:41:32,638] [INFO] GTDB search result was written to GCF_004339725.1_ASM433972v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:41:32,638] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:41:32,642] [INFO] DFAST_QC result json was written to GCF_004339725.1_ASM433972v1_genomic.fna/dqc_result.json
[2024-01-24 12:41:32,642] [INFO] DFAST_QC completed!
[2024-01-24 12:41:32,642] [INFO] Total running time: 0h1m25s