[2024-01-25 18:09:05,645] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:09:05,646] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:09:05,647] [INFO] DQC Reference Directory: /var/lib/cwl/stgbf95b019-2bb0-4a0d-a4d8-051bf42489b3/dqc_reference
[2024-01-25 18:09:06,789] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:09:06,789] [INFO] Task started: Prodigal
[2024-01-25 18:09:06,790] [INFO] Running command: gunzip -c /var/lib/cwl/stg583d4369-9858-458f-9ab5-2390ffef8ee4/GCF_030813495.1_ASM3081349v1_genomic.fna.gz | prodigal -d GCF_030813495.1_ASM3081349v1_genomic.fna/cds.fna -a GCF_030813495.1_ASM3081349v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:09:19,364] [INFO] Task succeeded: Prodigal
[2024-01-25 18:09:19,365] [INFO] Task started: HMMsearch
[2024-01-25 18:09:19,365] [INFO] Running command: hmmsearch --tblout GCF_030813495.1_ASM3081349v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbf95b019-2bb0-4a0d-a4d8-051bf42489b3/dqc_reference/reference_markers.hmm GCF_030813495.1_ASM3081349v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:09:19,621] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:09:19,622] [INFO] Found 6/6 markers.
[2024-01-25 18:09:19,660] [INFO] Query marker FASTA was written to GCF_030813495.1_ASM3081349v1_genomic.fna/markers.fasta
[2024-01-25 18:09:19,661] [INFO] Task started: Blastn
[2024-01-25 18:09:19,661] [INFO] Running command: blastn -query GCF_030813495.1_ASM3081349v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbf95b019-2bb0-4a0d-a4d8-051bf42489b3/dqc_reference/reference_markers.fasta -out GCF_030813495.1_ASM3081349v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:09:20,631] [INFO] Task succeeded: Blastn
[2024-01-25 18:09:20,634] [INFO] Selected 8 target genomes.
[2024-01-25 18:09:20,634] [INFO] Target genome list was writen to GCF_030813495.1_ASM3081349v1_genomic.fna/target_genomes.txt
[2024-01-25 18:09:20,642] [INFO] Task started: fastANI
[2024-01-25 18:09:20,642] [INFO] Running command: fastANI --query /var/lib/cwl/stg583d4369-9858-458f-9ab5-2390ffef8ee4/GCF_030813495.1_ASM3081349v1_genomic.fna.gz --refList GCF_030813495.1_ASM3081349v1_genomic.fna/target_genomes.txt --output GCF_030813495.1_ASM3081349v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:09:30,743] [INFO] Task succeeded: fastANI
[2024-01-25 18:09:30,744] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbf95b019-2bb0-4a0d-a4d8-051bf42489b3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:09:30,744] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbf95b019-2bb0-4a0d-a4d8-051bf42489b3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:09:30,750] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 18:09:30,751] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 18:09:30,751] [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	89.148	1179	1560	95	below_threshold
Ancylobacter aquaticus	strain=DSM 101	GCA_004339465.1	100	100	type	True	87.7761	1135	1560	95	below_threshold
Ancylobacter dichloromethanicus	strain=VKM B-2484	GCA_018390645.1	518825	518825	type	True	87.2679	1123	1560	95	below_threshold
Starkeya koreensis	strain=Jip08	GCA_023016525.1	266121	266121	type	True	85.7459	995	1560	95	below_threshold
Starkeya novella	strain=DSM 506	GCA_000092925.1	921	921	type	True	85.1376	1025	1560	95	below_threshold
Methylobacterium terricola	strain=17Sr1-39	GCA_006151805.1	2583531	2583531	type	True	77.1646	479	1560	95	below_threshold
Methylobacterium cerastii	strain=DSM 23679	GCA_022179125.1	932741	932741	type	True	77.0698	362	1560	95	below_threshold
Methylobacterium crusticola	strain=KCTC 52305	GCA_022179145.1	1697972	1697972	type	True	76.9946	414	1560	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:09:30,753] [INFO] DFAST Taxonomy check result was written to GCF_030813495.1_ASM3081349v1_genomic.fna/tc_result.tsv
[2024-01-25 18:09:30,753] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:09:30,754] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:09:30,754] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbf95b019-2bb0-4a0d-a4d8-051bf42489b3/dqc_reference/checkm_data
[2024-01-25 18:09:30,754] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:09:30,799] [INFO] Task started: CheckM
[2024-01-25 18:09:30,799] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030813495.1_ASM3081349v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030813495.1_ASM3081349v1_genomic.fna/checkm_input GCF_030813495.1_ASM3081349v1_genomic.fna/checkm_result
[2024-01-25 18:10:13,772] [INFO] Task succeeded: CheckM
[2024-01-25 18:10:13,773] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:10:13,789] [INFO] ===== Completeness check finished =====
[2024-01-25 18:10:13,790] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:10:13,790] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030813495.1_ASM3081349v1_genomic.fna/markers.fasta)
[2024-01-25 18:10:13,791] [INFO] Task started: Blastn
[2024-01-25 18:10:13,791] [INFO] Running command: blastn -query GCF_030813495.1_ASM3081349v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbf95b019-2bb0-4a0d-a4d8-051bf42489b3/dqc_reference/reference_markers_gtdb.fasta -out GCF_030813495.1_ASM3081349v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:10:15,775] [INFO] Task succeeded: Blastn
[2024-01-25 18:10:15,778] [INFO] Selected 8 target genomes.
[2024-01-25 18:10:15,778] [INFO] Target genome list was writen to GCF_030813495.1_ASM3081349v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:10:15,785] [INFO] Task started: fastANI
[2024-01-25 18:10:15,785] [INFO] Running command: fastANI --query /var/lib/cwl/stg583d4369-9858-458f-9ab5-2390ffef8ee4/GCF_030813495.1_ASM3081349v1_genomic.fna.gz --refList GCF_030813495.1_ASM3081349v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030813495.1_ASM3081349v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:10:25,605] [INFO] Task succeeded: fastANI
[2024-01-25 18:10:25,612] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 18:10:25,612] [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_900100155.1	s__Ancylobacter rudongensis	89.148	1179	1560	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Ancylobacter	95.0	96.36	96.36	0.88	0.88	2	-
GCA_000378025.1	s__Ancylobacter sp000378025	89.0279	1229	1560	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Ancylobacter	95.0	99.99	99.99	1.00	1.00	2	-
GCF_004339465.1	s__Ancylobacter aquaticus	87.7496	1137	1560	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	87.2727	1123	1560	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	86.0181	984	1560	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Ancylobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017872635.1	s__Starkeya sp017872635	84.9471	992	1560	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Starkeya	95.0	100.00	100.00	1.00	1.00	2	-
GCA_003241485.1	s__Angulomicrobium novellum_A	84.6391	942	1560	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Angulomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018449475.1	s__Angulomicrobium sp018449475	84.4473	944	1560	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Angulomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:10:25,613] [INFO] GTDB search result was written to GCF_030813495.1_ASM3081349v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:10:25,614] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:10:25,616] [INFO] DFAST_QC result json was written to GCF_030813495.1_ASM3081349v1_genomic.fna/dqc_result.json
[2024-01-25 18:10:25,616] [INFO] DFAST_QC completed!
[2024-01-25 18:10:25,616] [INFO] Total running time: 0h1m20s