[2024-01-24 15:10:54,277] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:10:54,279] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:10:54,280] [INFO] DQC Reference Directory: /var/lib/cwl/stg746fbd6c-17fd-4262-9094-811b8f4a9d27/dqc_reference
[2024-01-24 15:10:56,637] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:10:56,639] [INFO] Task started: Prodigal
[2024-01-24 15:10:56,639] [INFO] Running command: gunzip -c /var/lib/cwl/stg9be33637-54fe-4016-8e2b-ef24815bc475/GCF_014647255.1_ASM1464725v1_genomic.fna.gz | prodigal -d GCF_014647255.1_ASM1464725v1_genomic.fna/cds.fna -a GCF_014647255.1_ASM1464725v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:11:07,203] [INFO] Task succeeded: Prodigal
[2024-01-24 15:11:07,203] [INFO] Task started: HMMsearch
[2024-01-24 15:11:07,203] [INFO] Running command: hmmsearch --tblout GCF_014647255.1_ASM1464725v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg746fbd6c-17fd-4262-9094-811b8f4a9d27/dqc_reference/reference_markers.hmm GCF_014647255.1_ASM1464725v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:11:07,478] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:11:07,479] [INFO] Found 6/6 markers.
[2024-01-24 15:11:07,506] [INFO] Query marker FASTA was written to GCF_014647255.1_ASM1464725v1_genomic.fna/markers.fasta
[2024-01-24 15:11:07,507] [INFO] Task started: Blastn
[2024-01-24 15:11:07,507] [INFO] Running command: blastn -query GCF_014647255.1_ASM1464725v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg746fbd6c-17fd-4262-9094-811b8f4a9d27/dqc_reference/reference_markers.fasta -out GCF_014647255.1_ASM1464725v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:11:08,374] [INFO] Task succeeded: Blastn
[2024-01-24 15:11:08,378] [INFO] Selected 25 target genomes.
[2024-01-24 15:11:08,379] [INFO] Target genome list was writen to GCF_014647255.1_ASM1464725v1_genomic.fna/target_genomes.txt
[2024-01-24 15:11:08,390] [INFO] Task started: fastANI
[2024-01-24 15:11:08,390] [INFO] Running command: fastANI --query /var/lib/cwl/stg9be33637-54fe-4016-8e2b-ef24815bc475/GCF_014647255.1_ASM1464725v1_genomic.fna.gz --refList GCF_014647255.1_ASM1464725v1_genomic.fna/target_genomes.txt --output GCF_014647255.1_ASM1464725v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:11:24,252] [INFO] Task succeeded: fastANI
[2024-01-24 15:11:24,253] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg746fbd6c-17fd-4262-9094-811b8f4a9d27/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:11:24,253] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg746fbd6c-17fd-4262-9094-811b8f4a9d27/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:11:24,260] [INFO] Found 2 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 15:11:24,260] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 15:11:24,261] [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
Iodidimonas muriae	strain=JCM 17843	GCA_014647255.1	261467	261467	type	True	100.0	989	990	95	inconclusive
Iodidimonas gelatinilytica	strain=Hi-2	GCA_008579125.1	1236966	1236966	type	True	95.8828	861	990	95	inconclusive
--------------------------------------------------------------------------------
[2024-01-24 15:11:24,262] [INFO] DFAST Taxonomy check result was written to GCF_014647255.1_ASM1464725v1_genomic.fna/tc_result.tsv
[2024-01-24 15:11:24,263] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:11:24,263] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:11:24,263] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg746fbd6c-17fd-4262-9094-811b8f4a9d27/dqc_reference/checkm_data
[2024-01-24 15:11:24,264] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:11:24,297] [INFO] Task started: CheckM
[2024-01-24 15:11:24,297] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014647255.1_ASM1464725v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014647255.1_ASM1464725v1_genomic.fna/checkm_input GCF_014647255.1_ASM1464725v1_genomic.fna/checkm_result
[2024-01-24 15:11:59,041] [INFO] Task succeeded: CheckM
[2024-01-24 15:11:59,043] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:11:59,065] [INFO] ===== Completeness check finished =====
[2024-01-24 15:11:59,065] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:11:59,066] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014647255.1_ASM1464725v1_genomic.fna/markers.fasta)
[2024-01-24 15:11:59,066] [INFO] Task started: Blastn
[2024-01-24 15:11:59,067] [INFO] Running command: blastn -query GCF_014647255.1_ASM1464725v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg746fbd6c-17fd-4262-9094-811b8f4a9d27/dqc_reference/reference_markers_gtdb.fasta -out GCF_014647255.1_ASM1464725v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:12:00,267] [INFO] Task succeeded: Blastn
[2024-01-24 15:12:00,271] [INFO] Selected 24 target genomes.
[2024-01-24 15:12:00,271] [INFO] Target genome list was writen to GCF_014647255.1_ASM1464725v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:12:00,290] [INFO] Task started: fastANI
[2024-01-24 15:12:00,290] [INFO] Running command: fastANI --query /var/lib/cwl/stg9be33637-54fe-4016-8e2b-ef24815bc475/GCF_014647255.1_ASM1464725v1_genomic.fna.gz --refList GCF_014647255.1_ASM1464725v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014647255.1_ASM1464725v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:12:13,531] [INFO] Task succeeded: fastANI
[2024-01-24 15:12:13,540] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:12:13,540] [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_014647255.1	s__Iodidimonas muriae	100.0	989	990	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Rhodothalassiaceae;g__Iodidimonas	95.0	97.25	95.88	0.95	0.93	4	conclusive
GCA_000710935.1	s__Iodidimonas sp000710935	78.625	427	990	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Rhodothalassiaceae;g__Iodidimonas	95.0	99.95	99.95	0.98	0.98	2	-
GCF_005849285.1	s__Luteithermobacter gelatinilyticus	75.6144	50	990	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Emcibacteraceae;g__Luteithermobacter	95.0	99.04	99.04	0.96	0.96	2	-
GCA_003577275.1	s__PRO5 sp003577275	75.4845	54	990	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__J090;g__PRO5	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:12:13,542] [INFO] GTDB search result was written to GCF_014647255.1_ASM1464725v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:12:13,542] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:12:13,545] [INFO] DFAST_QC result json was written to GCF_014647255.1_ASM1464725v1_genomic.fna/dqc_result.json
[2024-01-24 15:12:13,545] [INFO] DFAST_QC completed!
[2024-01-24 15:12:13,545] [INFO] Total running time: 0h1m19s