[2024-01-25 19:59:05,930] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:59:05,931] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:59:05,932] [INFO] DQC Reference Directory: /var/lib/cwl/stgc883f02d-39d7-40ef-b387-dbdc7cd07119/dqc_reference
[2024-01-25 19:59:07,145] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:59:07,146] [INFO] Task started: Prodigal
[2024-01-25 19:59:07,146] [INFO] Running command: gunzip -c /var/lib/cwl/stg7c0736ab-0275-4c37-ad53-357dd56feb88/GCF_030813595.1_ASM3081359v1_genomic.fna.gz | prodigal -d GCF_030813595.1_ASM3081359v1_genomic.fna/cds.fna -a GCF_030813595.1_ASM3081359v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:59:21,079] [INFO] Task succeeded: Prodigal
[2024-01-25 19:59:21,080] [INFO] Task started: HMMsearch
[2024-01-25 19:59:21,080] [INFO] Running command: hmmsearch --tblout GCF_030813595.1_ASM3081359v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc883f02d-39d7-40ef-b387-dbdc7cd07119/dqc_reference/reference_markers.hmm GCF_030813595.1_ASM3081359v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:59:21,369] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:59:21,370] [INFO] Found 6/6 markers.
[2024-01-25 19:59:21,426] [INFO] Query marker FASTA was written to GCF_030813595.1_ASM3081359v1_genomic.fna/markers.fasta
[2024-01-25 19:59:21,426] [INFO] Task started: Blastn
[2024-01-25 19:59:21,426] [INFO] Running command: blastn -query GCF_030813595.1_ASM3081359v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc883f02d-39d7-40ef-b387-dbdc7cd07119/dqc_reference/reference_markers.fasta -out GCF_030813595.1_ASM3081359v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:59:22,409] [INFO] Task succeeded: Blastn
[2024-01-25 19:59:22,411] [INFO] Selected 8 target genomes.
[2024-01-25 19:59:22,412] [INFO] Target genome list was writen to GCF_030813595.1_ASM3081359v1_genomic.fna/target_genomes.txt
[2024-01-25 19:59:22,413] [INFO] Task started: fastANI
[2024-01-25 19:59:22,413] [INFO] Running command: fastANI --query /var/lib/cwl/stg7c0736ab-0275-4c37-ad53-357dd56feb88/GCF_030813595.1_ASM3081359v1_genomic.fna.gz --refList GCF_030813595.1_ASM3081359v1_genomic.fna/target_genomes.txt --output GCF_030813595.1_ASM3081359v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:59:32,246] [INFO] Task succeeded: fastANI
[2024-01-25 19:59:32,246] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc883f02d-39d7-40ef-b387-dbdc7cd07119/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:59:32,247] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc883f02d-39d7-40ef-b387-dbdc7cd07119/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:59:32,253] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 19:59:32,253] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 19:59:32,253] [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
Ancylobacter rudongensis	strain=CGMCC 1.1761	GCA_900100155.1	177413	177413	type	True	92.2305	1335	1661	95	below_threshold
Ancylobacter aquaticus	strain=DSM 101	GCA_004339465.1	100	100	type	True	90.2427	1276	1661	95	below_threshold
Ancylobacter dichloromethanicus	strain=VKM B-2484	GCA_018390645.1	518825	518825	type	True	88.2768	1194	1661	95	below_threshold
Starkeya koreensis	strain=Jip08	GCA_023016525.1	266121	266121	type	True	85.6501	1032	1661	95	below_threshold
Starkeya novella	strain=DSM 506	GCA_000092925.1	921	921	type	True	85.0749	1069	1661	95	below_threshold
Xanthobacter oligotrophicus	strain=29k	GCA_008364685.1	2607286	2607286	type	True	78.7294	570	1661	95	below_threshold
Methylobacterium oryzihabitans	strain=TER-1	GCA_004004555.2	2499852	2499852	type	True	77.499	495	1661	95	below_threshold
Methylobacterium terricola	strain=17Sr1-39	GCA_006151805.1	2583531	2583531	type	True	77.4032	490	1661	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:59:32,254] [INFO] DFAST Taxonomy check result was written to GCF_030813595.1_ASM3081359v1_genomic.fna/tc_result.tsv
[2024-01-25 19:59:32,255] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:59:32,255] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:59:32,255] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc883f02d-39d7-40ef-b387-dbdc7cd07119/dqc_reference/checkm_data
[2024-01-25 19:59:32,256] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:59:32,303] [INFO] Task started: CheckM
[2024-01-25 19:59:32,304] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030813595.1_ASM3081359v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030813595.1_ASM3081359v1_genomic.fna/checkm_input GCF_030813595.1_ASM3081359v1_genomic.fna/checkm_result
[2024-01-25 20:00:19,167] [INFO] Task succeeded: CheckM
[2024-01-25 20:00:19,168] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:00:19,184] [INFO] ===== Completeness check finished =====
[2024-01-25 20:00:19,184] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:00:19,185] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030813595.1_ASM3081359v1_genomic.fna/markers.fasta)
[2024-01-25 20:00:19,185] [INFO] Task started: Blastn
[2024-01-25 20:00:19,185] [INFO] Running command: blastn -query GCF_030813595.1_ASM3081359v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc883f02d-39d7-40ef-b387-dbdc7cd07119/dqc_reference/reference_markers_gtdb.fasta -out GCF_030813595.1_ASM3081359v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:00:21,318] [INFO] Task succeeded: Blastn
[2024-01-25 20:00:21,324] [INFO] Selected 7 target genomes.
[2024-01-25 20:00:21,324] [INFO] Target genome list was writen to GCF_030813595.1_ASM3081359v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:00:21,325] [INFO] Task started: fastANI
[2024-01-25 20:00:21,325] [INFO] Running command: fastANI --query /var/lib/cwl/stg7c0736ab-0275-4c37-ad53-357dd56feb88/GCF_030813595.1_ASM3081359v1_genomic.fna.gz --refList GCF_030813595.1_ASM3081359v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030813595.1_ASM3081359v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:00:29,996] [INFO] Task succeeded: fastANI
[2024-01-25 20:00:30,001] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 20:00:30,001] [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
GCA_000378025.1	s__Ancylobacter sp000378025	93.8644	1434	1661	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Ancylobacter	95.0	99.99	99.99	1.00	1.00	2	-
GCF_900100155.1	s__Ancylobacter rudongensis	92.2305	1335	1661	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Ancylobacter	95.0	96.36	96.36	0.88	0.88	2	-
GCF_004339465.1	s__Ancylobacter aquaticus	90.2547	1275	1661	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Ancylobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018390645.1	s__Ancylobacter dichloromethanicus	88.277	1194	1661	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Ancylobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009223885.1	s__Ancylobacter sp009223885	86.1266	1014	1661	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Ancylobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007559435.1	s__Starkeya sp007559435	84.9673	983	1661	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Starkeya	95.0	98.55	98.55	0.95	0.95	2	-
GCF_017872635.1	s__Starkeya sp017872635	84.939	1036	1661	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Starkeya	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-25 20:00:30,003] [INFO] GTDB search result was written to GCF_030813595.1_ASM3081359v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:00:30,003] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:00:30,005] [INFO] DFAST_QC result json was written to GCF_030813595.1_ASM3081359v1_genomic.fna/dqc_result.json
[2024-01-25 20:00:30,005] [INFO] DFAST_QC completed!
[2024-01-25 20:00:30,005] [INFO] Total running time: 0h1m24s