[2024-01-24 15:02:23,185] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:02:23,187] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:02:23,187] [INFO] DQC Reference Directory: /var/lib/cwl/stg5158f1d7-ea0e-46b6-a609-b99d531569d0/dqc_reference
[2024-01-24 15:02:24,423] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:02:24,424] [INFO] Task started: Prodigal
[2024-01-24 15:02:24,425] [INFO] Running command: gunzip -c /var/lib/cwl/stg8516ed24-5134-4622-8ec6-93b11d911f19/GCF_011634775.1_ASM1163477v1_genomic.fna.gz | prodigal -d GCF_011634775.1_ASM1163477v1_genomic.fna/cds.fna -a GCF_011634775.1_ASM1163477v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:02:51,856] [INFO] Task succeeded: Prodigal
[2024-01-24 15:02:51,857] [INFO] Task started: HMMsearch
[2024-01-24 15:02:51,857] [INFO] Running command: hmmsearch --tblout GCF_011634775.1_ASM1163477v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5158f1d7-ea0e-46b6-a609-b99d531569d0/dqc_reference/reference_markers.hmm GCF_011634775.1_ASM1163477v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:02:52,252] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:02:52,253] [INFO] Found 6/6 markers.
[2024-01-24 15:02:52,321] [INFO] Query marker FASTA was written to GCF_011634775.1_ASM1163477v1_genomic.fna/markers.fasta
[2024-01-24 15:02:52,321] [INFO] Task started: Blastn
[2024-01-24 15:02:52,321] [INFO] Running command: blastn -query GCF_011634775.1_ASM1163477v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5158f1d7-ea0e-46b6-a609-b99d531569d0/dqc_reference/reference_markers.fasta -out GCF_011634775.1_ASM1163477v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:02:52,988] [INFO] Task succeeded: Blastn
[2024-01-24 15:02:52,991] [INFO] Selected 22 target genomes.
[2024-01-24 15:02:52,992] [INFO] Target genome list was writen to GCF_011634775.1_ASM1163477v1_genomic.fna/target_genomes.txt
[2024-01-24 15:02:53,008] [INFO] Task started: fastANI
[2024-01-24 15:02:53,008] [INFO] Running command: fastANI --query /var/lib/cwl/stg8516ed24-5134-4622-8ec6-93b11d911f19/GCF_011634775.1_ASM1163477v1_genomic.fna.gz --refList GCF_011634775.1_ASM1163477v1_genomic.fna/target_genomes.txt --output GCF_011634775.1_ASM1163477v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:03:13,097] [INFO] Task succeeded: fastANI
[2024-01-24 15:03:13,098] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5158f1d7-ea0e-46b6-a609-b99d531569d0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:03:13,098] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5158f1d7-ea0e-46b6-a609-b99d531569d0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:03:13,102] [INFO] Found 2 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:03:13,103] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:03:13,103] [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
Thalassoroseus pseudoceratinae	strain=JC658	GCA_011634775.1	2713176	2713176	type	True	100.0	2442	2443	95	conclusive
Gimesia panareensis	strain=Enr10	GCA_007748155.1	2527978	2527978	type	True	76.1213	51	2443	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:03:13,104] [INFO] DFAST Taxonomy check result was written to GCF_011634775.1_ASM1163477v1_genomic.fna/tc_result.tsv
[2024-01-24 15:03:13,104] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:03:13,104] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:03:13,105] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5158f1d7-ea0e-46b6-a609-b99d531569d0/dqc_reference/checkm_data
[2024-01-24 15:03:13,106] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:03:13,236] [INFO] Task started: CheckM
[2024-01-24 15:03:13,237] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_011634775.1_ASM1163477v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_011634775.1_ASM1163477v1_genomic.fna/checkm_input GCF_011634775.1_ASM1163477v1_genomic.fna/checkm_result
[2024-01-24 15:04:39,609] [INFO] Task succeeded: CheckM
[2024-01-24 15:04:39,610] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:04:39,633] [INFO] ===== Completeness check finished =====
[2024-01-24 15:04:39,633] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:04:39,634] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_011634775.1_ASM1163477v1_genomic.fna/markers.fasta)
[2024-01-24 15:04:39,634] [INFO] Task started: Blastn
[2024-01-24 15:04:39,634] [INFO] Running command: blastn -query GCF_011634775.1_ASM1163477v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5158f1d7-ea0e-46b6-a609-b99d531569d0/dqc_reference/reference_markers_gtdb.fasta -out GCF_011634775.1_ASM1163477v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:04:40,440] [INFO] Task succeeded: Blastn
[2024-01-24 15:04:40,443] [INFO] Selected 26 target genomes.
[2024-01-24 15:04:40,443] [INFO] Target genome list was writen to GCF_011634775.1_ASM1163477v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:04:40,465] [INFO] Task started: fastANI
[2024-01-24 15:04:40,465] [INFO] Running command: fastANI --query /var/lib/cwl/stg8516ed24-5134-4622-8ec6-93b11d911f19/GCF_011634775.1_ASM1163477v1_genomic.fna.gz --refList GCF_011634775.1_ASM1163477v1_genomic.fna/target_genomes_gtdb.txt --output GCF_011634775.1_ASM1163477v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:05:04,472] [INFO] Task succeeded: fastANI
[2024-01-24 15:05:04,480] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:05:04,480] [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_011634775.1	s__JC658 sp011634775	100.0	2442	2443	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__JC658	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_007748155.1	s__Gimesia panareensis	76.1213	51	2443	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Gimesia	95.0	96.61	95.86	0.91	0.90	3	-
GCA_903840265.1	s__Schlesneria sp903840265	74.9702	52	2443	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Schlesneria	95.0	99.98	99.98	0.97	0.97	3	-
--------------------------------------------------------------------------------
[2024-01-24 15:05:04,483] [INFO] GTDB search result was written to GCF_011634775.1_ASM1163477v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:05:04,484] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:05:04,486] [INFO] DFAST_QC result json was written to GCF_011634775.1_ASM1163477v1_genomic.fna/dqc_result.json
[2024-01-24 15:05:04,487] [INFO] DFAST_QC completed!
[2024-01-24 15:05:04,487] [INFO] Total running time: 0h2m41s