[2024-01-24 13:57:43,906] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:57:43,910] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:57:43,910] [INFO] DQC Reference Directory: /var/lib/cwl/stgd3fec7a1-06a1-46b1-9c65-641c68bcfeed/dqc_reference
[2024-01-24 13:57:45,159] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:57:45,160] [INFO] Task started: Prodigal
[2024-01-24 13:57:45,160] [INFO] Running command: gunzip -c /var/lib/cwl/stg9e36d2b5-0eb1-42db-8439-a85a85dfaf7b/GCF_003428625.2_ASM342862v2_genomic.fna.gz | prodigal -d GCF_003428625.2_ASM342862v2_genomic.fna/cds.fna -a GCF_003428625.2_ASM342862v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:57:59,364] [INFO] Task succeeded: Prodigal
[2024-01-24 13:57:59,365] [INFO] Task started: HMMsearch
[2024-01-24 13:57:59,365] [INFO] Running command: hmmsearch --tblout GCF_003428625.2_ASM342862v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd3fec7a1-06a1-46b1-9c65-641c68bcfeed/dqc_reference/reference_markers.hmm GCF_003428625.2_ASM342862v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:57:59,669] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:57:59,670] [INFO] Found 6/6 markers.
[2024-01-24 13:57:59,716] [INFO] Query marker FASTA was written to GCF_003428625.2_ASM342862v2_genomic.fna/markers.fasta
[2024-01-24 13:57:59,716] [INFO] Task started: Blastn
[2024-01-24 13:57:59,716] [INFO] Running command: blastn -query GCF_003428625.2_ASM342862v2_genomic.fna/markers.fasta -db /var/lib/cwl/stgd3fec7a1-06a1-46b1-9c65-641c68bcfeed/dqc_reference/reference_markers.fasta -out GCF_003428625.2_ASM342862v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:00,404] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:00,408] [INFO] Selected 7 target genomes.
[2024-01-24 13:58:00,408] [INFO] Target genome list was writen to GCF_003428625.2_ASM342862v2_genomic.fna/target_genomes.txt
[2024-01-24 13:58:00,424] [INFO] Task started: fastANI
[2024-01-24 13:58:00,424] [INFO] Running command: fastANI --query /var/lib/cwl/stg9e36d2b5-0eb1-42db-8439-a85a85dfaf7b/GCF_003428625.2_ASM342862v2_genomic.fna.gz --refList GCF_003428625.2_ASM342862v2_genomic.fna/target_genomes.txt --output GCF_003428625.2_ASM342862v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:58:07,430] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:07,431] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd3fec7a1-06a1-46b1-9c65-641c68bcfeed/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:58:07,431] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd3fec7a1-06a1-46b1-9c65-641c68bcfeed/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:58:07,438] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:58:07,439] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:58:07,439] [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
Paracidobacterium acidisoli	strain=4G-K13	GCA_003428625.2	2303751	2303751	type	True	100.0	1662	1662	95	conclusive
Silvibacterium dinghuense	strain=CGMCC 1.13007	GCA_014640355.1	1560006	1560006	type	True	78.0415	366	1662	95	below_threshold
Silvibacterium bohemicum	strain=S15	GCA_001006305.1	1577686	1577686	type	True	78.0163	405	1662	95	below_threshold
Silvibacterium dinghuense	strain=DHOF10	GCA_004123295.1	1560006	1560006	type	True	78.0099	368	1662	95	below_threshold
Silvibacterium bohemicum	strain=DSM 103733	GCA_014201455.1	1577686	1577686	type	True	77.9726	399	1662	95	below_threshold
Alloacidobacterium dinghuense	strain=4Y35	GCA_014274465.1	2763107	2763107	type	True	77.6448	262	1662	95	below_threshold
Acidobacterium capsulatum	strain=ATCC 51196	GCA_000022565.1	33075	33075	type	True	77.6152	289	1662	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:58:07,440] [INFO] DFAST Taxonomy check result was written to GCF_003428625.2_ASM342862v2_genomic.fna/tc_result.tsv
[2024-01-24 13:58:07,441] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:58:07,441] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:58:07,441] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd3fec7a1-06a1-46b1-9c65-641c68bcfeed/dqc_reference/checkm_data
[2024-01-24 13:58:07,443] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:58:07,494] [INFO] Task started: CheckM
[2024-01-24 13:58:07,495] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003428625.2_ASM342862v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003428625.2_ASM342862v2_genomic.fna/checkm_input GCF_003428625.2_ASM342862v2_genomic.fna/checkm_result
[2024-01-24 13:58:53,933] [INFO] Task succeeded: CheckM
[2024-01-24 13:58:53,935] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:58:53,949] [INFO] ===== Completeness check finished =====
[2024-01-24 13:58:53,950] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:58:53,950] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003428625.2_ASM342862v2_genomic.fna/markers.fasta)
[2024-01-24 13:58:53,951] [INFO] Task started: Blastn
[2024-01-24 13:58:53,951] [INFO] Running command: blastn -query GCF_003428625.2_ASM342862v2_genomic.fna/markers.fasta -db /var/lib/cwl/stgd3fec7a1-06a1-46b1-9c65-641c68bcfeed/dqc_reference/reference_markers_gtdb.fasta -out GCF_003428625.2_ASM342862v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:55,014] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:55,017] [INFO] Selected 14 target genomes.
[2024-01-24 13:58:55,017] [INFO] Target genome list was writen to GCF_003428625.2_ASM342862v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:58:55,038] [INFO] Task started: fastANI
[2024-01-24 13:58:55,038] [INFO] Running command: fastANI --query /var/lib/cwl/stg9e36d2b5-0eb1-42db-8439-a85a85dfaf7b/GCF_003428625.2_ASM342862v2_genomic.fna.gz --refList GCF_003428625.2_ASM342862v2_genomic.fna/target_genomes_gtdb.txt --output GCF_003428625.2_ASM342862v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:59:07,436] [INFO] Task succeeded: fastANI
[2024-01-24 13:59:07,454] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:59:07,454] [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_003428625.2	s__Palsa-343 sp003428625	100.0	1662	1662	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Palsa-343	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_004123295.1	s__Silvibacterium dinghuense	78.0284	366	1662	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Silvibacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001006305.1	s__Silvibacterium bohemicum	78.0181	406	1662	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Silvibacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCA_011333575.1	s__Acidobacterium capsulatum_A	77.7819	239	1662	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Acidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019234945.1	s__Silvibacterium sp019234945	77.7149	183	1662	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Silvibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014274465.1	s__Acidobacterium_A sp014274465	77.6683	260	1662	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_009765985.1	s__Acidobacterium_A sp009765985	77.6237	283	1662	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_000022565.1	s__Acidobacterium capsulatum	77.5933	291	1662	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Acidobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCA_003166955.1	s__Palsa-343 sp003166955	77.4932	304	1662	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Palsa-343	95.0	99.89	99.89	0.95	0.95	2	-
GCA_013289875.1	s__Silvibacterium sp013289875	77.3485	256	1662	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Silvibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015655315.1	s__Acidobacterium_A sp015655315	77.0221	209	1662	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_003132145.1	s__Palsa-288 sp003132145	76.8957	163	1662	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Palsa-288	95.0	99.75	99.72	0.90	0.88	3	-
GCF_009765785.1	s__UBA5172 sp009765785	76.8253	121	1662	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__UBA5172	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015655585.1	s__Edaphobacter sp015655585	76.6977	137	1662	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 13:59:07,457] [INFO] GTDB search result was written to GCF_003428625.2_ASM342862v2_genomic.fna/result_gtdb.tsv
[2024-01-24 13:59:07,458] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:59:07,461] [INFO] DFAST_QC result json was written to GCF_003428625.2_ASM342862v2_genomic.fna/dqc_result.json
[2024-01-24 13:59:07,462] [INFO] DFAST_QC completed!
[2024-01-24 13:59:07,462] [INFO] Total running time: 0h1m24s