[2024-01-24 13:08:58,397] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:08:58,399] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:08:58,399] [INFO] DQC Reference Directory: /var/lib/cwl/stgff3a1bfa-8cfd-4c3e-a732-7f359ad507a0/dqc_reference
[2024-01-24 13:08:59,639] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:08:59,640] [INFO] Task started: Prodigal
[2024-01-24 13:08:59,640] [INFO] Running command: gunzip -c /var/lib/cwl/stgcad27ea6-3d0b-43c8-85e1-c8c60f7afed9/GCF_001571085.1_ASM157108v1_genomic.fna.gz | prodigal -d GCF_001571085.1_ASM157108v1_genomic.fna/cds.fna -a GCF_001571085.1_ASM157108v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:09:22,515] [INFO] Task succeeded: Prodigal
[2024-01-24 13:09:22,516] [INFO] Task started: HMMsearch
[2024-01-24 13:09:22,516] [INFO] Running command: hmmsearch --tblout GCF_001571085.1_ASM157108v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgff3a1bfa-8cfd-4c3e-a732-7f359ad507a0/dqc_reference/reference_markers.hmm GCF_001571085.1_ASM157108v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:09:22,848] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:09:22,850] [INFO] Found 6/6 markers.
[2024-01-24 13:09:22,908] [INFO] Query marker FASTA was written to GCF_001571085.1_ASM157108v1_genomic.fna/markers.fasta
[2024-01-24 13:09:22,908] [INFO] Task started: Blastn
[2024-01-24 13:09:22,908] [INFO] Running command: blastn -query GCF_001571085.1_ASM157108v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgff3a1bfa-8cfd-4c3e-a732-7f359ad507a0/dqc_reference/reference_markers.fasta -out GCF_001571085.1_ASM157108v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:09:24,024] [INFO] Task succeeded: Blastn
[2024-01-24 13:09:24,028] [INFO] Selected 12 target genomes.
[2024-01-24 13:09:24,028] [INFO] Target genome list was writen to GCF_001571085.1_ASM157108v1_genomic.fna/target_genomes.txt
[2024-01-24 13:09:24,066] [INFO] Task started: fastANI
[2024-01-24 13:09:24,066] [INFO] Running command: fastANI --query /var/lib/cwl/stgcad27ea6-3d0b-43c8-85e1-c8c60f7afed9/GCF_001571085.1_ASM157108v1_genomic.fna.gz --refList GCF_001571085.1_ASM157108v1_genomic.fna/target_genomes.txt --output GCF_001571085.1_ASM157108v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:09:41,806] [INFO] Task succeeded: fastANI
[2024-01-24 13:09:41,806] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgff3a1bfa-8cfd-4c3e-a732-7f359ad507a0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:09:41,807] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgff3a1bfa-8cfd-4c3e-a732-7f359ad507a0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:09:41,817] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:09:41,817] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:09:41,817] [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
Azohydromonas lata	strain=NBRC 102462	GCA_001571085.1	45677	45677	type	True	100.0	2225	2238	95	conclusive
Azohydromonas australica	strain=DSM 1124	GCA_000430725.1	364039	364039	type	True	87.6043	1578	2238	95	below_threshold
Azohydromonas caseinilytica	strain=G-1-1-14	GCA_012927045.1	2728836	2728836	type	True	86.8467	1450	2238	95	below_threshold
Azohydromonas aeria	strain=CFCC 13393	GCA_009760915.1	2590212	2590212	type	True	86.6479	1496	2238	95	below_threshold
Schlegelella thermodepolymerans	strain=DSM 15344	GCA_002933415.1	215580	215580	type	True	80.3884	662	2238	95	below_threshold
Schlegelella thermodepolymerans	strain=DSM 15344	GCA_015476235.1	215580	215580	type	True	80.244	685	2238	95	below_threshold
Ideonella dechloratans	strain=CCUG 30977	GCA_021049305.1	36863	36863	type	True	80.081	716	2238	95	below_threshold
Ideonella benzenivorans	strain=B7	GCA_020387415.1	2831643	2831643	type	True	79.8416	672	2238	95	below_threshold
Sphaerotilus sulfidivorans	strain=D-501	GCA_013426975.1	639200	639200	type	True	79.802	749	2238	95	below_threshold
Hydrogenophaga crocea	strain=BA0156	GCA_011388215.1	2716225	2716225	type	True	79.3271	703	2238	95	below_threshold
Schlegelella brevitalea	strain=DSM 7029	GCA_001017435.1	413882	413882	type	True	78.7545	644	2238	95	below_threshold
Acidovorax valerianellae	strain=DSM 16619	GCA_900102625.1	187868	187868	type	True	78.2911	574	2238	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:09:41,819] [INFO] DFAST Taxonomy check result was written to GCF_001571085.1_ASM157108v1_genomic.fna/tc_result.tsv
[2024-01-24 13:09:41,819] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:09:41,820] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:09:41,820] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgff3a1bfa-8cfd-4c3e-a732-7f359ad507a0/dqc_reference/checkm_data
[2024-01-24 13:09:41,821] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:09:41,892] [INFO] Task started: CheckM
[2024-01-24 13:09:41,892] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001571085.1_ASM157108v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001571085.1_ASM157108v1_genomic.fna/checkm_input GCF_001571085.1_ASM157108v1_genomic.fna/checkm_result
[2024-01-24 13:11:06,382] [INFO] Task succeeded: CheckM
[2024-01-24 13:11:06,384] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:11:06,408] [INFO] ===== Completeness check finished =====
[2024-01-24 13:11:06,408] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:11:06,409] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001571085.1_ASM157108v1_genomic.fna/markers.fasta)
[2024-01-24 13:11:06,409] [INFO] Task started: Blastn
[2024-01-24 13:11:06,409] [INFO] Running command: blastn -query GCF_001571085.1_ASM157108v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgff3a1bfa-8cfd-4c3e-a732-7f359ad507a0/dqc_reference/reference_markers_gtdb.fasta -out GCF_001571085.1_ASM157108v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:11:08,750] [INFO] Task succeeded: Blastn
[2024-01-24 13:11:08,753] [INFO] Selected 8 target genomes.
[2024-01-24 13:11:08,754] [INFO] Target genome list was writen to GCF_001571085.1_ASM157108v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:11:09,426] [INFO] Task started: fastANI
[2024-01-24 13:11:09,427] [INFO] Running command: fastANI --query /var/lib/cwl/stgcad27ea6-3d0b-43c8-85e1-c8c60f7afed9/GCF_001571085.1_ASM157108v1_genomic.fna.gz --refList GCF_001571085.1_ASM157108v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001571085.1_ASM157108v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:11:25,255] [INFO] Task succeeded: fastANI
[2024-01-24 13:11:25,265] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:11:25,266] [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_001571085.1	s__Azohydromonas lata	100.0	2225	2238	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Azohydromonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000430725.1	s__Azohydromonas australica	87.591	1580	2238	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Azohydromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012927045.1	s__Azohydromonas caseinilytica	86.8277	1452	2238	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Azohydromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009760915.1	s__Azohydromonas aeria	86.6164	1501	2238	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Azohydromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014873965.1	s__VBDL01 sp014873965	80.5839	885	2238	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__VBDL01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000969605.1	s__Aquincola tertiaricarbonis	80.2259	947	2238	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquincola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003569765.1	s__Aquabacterium_B tepidiphilum	80.081	859	2238	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquabacterium_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017992055.1	s__Aquabacterium_A sp017992055	79.7018	887	2238	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquabacterium_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:11:25,267] [INFO] GTDB search result was written to GCF_001571085.1_ASM157108v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:11:25,268] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:11:25,272] [INFO] DFAST_QC result json was written to GCF_001571085.1_ASM157108v1_genomic.fna/dqc_result.json
[2024-01-24 13:11:25,272] [INFO] DFAST_QC completed!
[2024-01-24 13:11:25,272] [INFO] Total running time: 0h2m27s