[2024-01-24 15:18:38,679] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:18:38,681] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:18:38,681] [INFO] DQC Reference Directory: /var/lib/cwl/stg5e45377d-1eef-452b-9178-e81ccb0eabfc/dqc_reference
[2024-01-24 15:18:39,984] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:18:39,985] [INFO] Task started: Prodigal
[2024-01-24 15:18:39,985] [INFO] Running command: gunzip -c /var/lib/cwl/stg5e2fa36c-cc1d-4b44-b221-cd71b4ace732/GCF_026684035.1_ASM2668403v1_genomic.fna.gz | prodigal -d GCF_026684035.1_ASM2668403v1_genomic.fna/cds.fna -a GCF_026684035.1_ASM2668403v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:18:47,761] [INFO] Task succeeded: Prodigal
[2024-01-24 15:18:47,761] [INFO] Task started: HMMsearch
[2024-01-24 15:18:47,761] [INFO] Running command: hmmsearch --tblout GCF_026684035.1_ASM2668403v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5e45377d-1eef-452b-9178-e81ccb0eabfc/dqc_reference/reference_markers.hmm GCF_026684035.1_ASM2668403v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:18:48,068] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:18:48,069] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg5e2fa36c-cc1d-4b44-b221-cd71b4ace732/GCF_026684035.1_ASM2668403v1_genomic.fna.gz]
[2024-01-24 15:18:48,093] [INFO] Query marker FASTA was written to GCF_026684035.1_ASM2668403v1_genomic.fna/markers.fasta
[2024-01-24 15:18:48,093] [INFO] Task started: Blastn
[2024-01-24 15:18:48,093] [INFO] Running command: blastn -query GCF_026684035.1_ASM2668403v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5e45377d-1eef-452b-9178-e81ccb0eabfc/dqc_reference/reference_markers.fasta -out GCF_026684035.1_ASM2668403v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:18:49,162] [INFO] Task succeeded: Blastn
[2024-01-24 15:18:49,165] [INFO] Selected 10 target genomes.
[2024-01-24 15:18:49,166] [INFO] Target genome list was writen to GCF_026684035.1_ASM2668403v1_genomic.fna/target_genomes.txt
[2024-01-24 15:18:49,177] [INFO] Task started: fastANI
[2024-01-24 15:18:49,177] [INFO] Running command: fastANI --query /var/lib/cwl/stg5e2fa36c-cc1d-4b44-b221-cd71b4ace732/GCF_026684035.1_ASM2668403v1_genomic.fna.gz --refList GCF_026684035.1_ASM2668403v1_genomic.fna/target_genomes.txt --output GCF_026684035.1_ASM2668403v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:18:55,604] [INFO] Task succeeded: fastANI
[2024-01-24 15:18:55,605] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5e45377d-1eef-452b-9178-e81ccb0eabfc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:18:55,605] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5e45377d-1eef-452b-9178-e81ccb0eabfc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:18:55,630] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 15:18:55,630] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 15:18:55,630] [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
Methanogenium cariaci	strain=JCM 10550	GCA_001315945.1	2197	2197	type	True	81.0238	481	882	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:18:55,632] [INFO] DFAST Taxonomy check result was written to GCF_026684035.1_ASM2668403v1_genomic.fna/tc_result.tsv
[2024-01-24 15:18:55,632] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:18:55,632] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:18:55,633] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5e45377d-1eef-452b-9178-e81ccb0eabfc/dqc_reference/checkm_data
[2024-01-24 15:18:55,639] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:18:55,666] [INFO] Task started: CheckM
[2024-01-24 15:18:55,666] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_026684035.1_ASM2668403v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_026684035.1_ASM2668403v1_genomic.fna/checkm_input GCF_026684035.1_ASM2668403v1_genomic.fna/checkm_result
[2024-01-24 15:19:28,934] [INFO] Task succeeded: CheckM
[2024-01-24 15:19:28,935] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:19:28,954] [INFO] ===== Completeness check finished =====
[2024-01-24 15:19:28,955] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:19:28,956] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_026684035.1_ASM2668403v1_genomic.fna/markers.fasta)
[2024-01-24 15:19:28,956] [INFO] Task started: Blastn
[2024-01-24 15:19:28,956] [INFO] Running command: blastn -query GCF_026684035.1_ASM2668403v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5e45377d-1eef-452b-9178-e81ccb0eabfc/dqc_reference/reference_markers_gtdb.fasta -out GCF_026684035.1_ASM2668403v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:19:29,433] [INFO] Task succeeded: Blastn
[2024-01-24 15:19:29,437] [INFO] Selected 9 target genomes.
[2024-01-24 15:19:29,437] [INFO] Target genome list was writen to GCF_026684035.1_ASM2668403v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:19:29,445] [INFO] Task started: fastANI
[2024-01-24 15:19:29,445] [INFO] Running command: fastANI --query /var/lib/cwl/stg5e2fa36c-cc1d-4b44-b221-cd71b4ace732/GCF_026684035.1_ASM2668403v1_genomic.fna.gz --refList GCF_026684035.1_ASM2668403v1_genomic.fna/target_genomes_gtdb.txt --output GCF_026684035.1_ASM2668403v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:19:33,511] [INFO] Task succeeded: fastANI
[2024-01-24 15:19:33,519] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 15:19:33,519] [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_009914725.1	s__Methanogenium sp009914725	81.8968	430	882	d__Archaea;p__Halobacteriota;c__Methanomicrobia;o__Methanomicrobiales;f__Methanomicrobiaceae;g__Methanogenium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012523385.1	s__Methanogenium sp012523385	79.1353	256	882	d__Archaea;p__Halobacteriota;c__Methanomicrobia;o__Methanomicrobiales;f__Methanomicrobiaceae;g__Methanogenium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011045995.1	s__Methanogenium sp011045995	77.6552	97	882	d__Archaea;p__Halobacteriota;c__Methanomicrobia;o__Methanomicrobiales;f__Methanomicrobiaceae;g__Methanogenium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:19:33,521] [INFO] GTDB search result was written to GCF_026684035.1_ASM2668403v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:19:33,522] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:19:33,524] [INFO] DFAST_QC result json was written to GCF_026684035.1_ASM2668403v1_genomic.fna/dqc_result.json
[2024-01-24 15:19:33,524] [INFO] DFAST_QC completed!
[2024-01-24 15:19:33,524] [INFO] Total running time: 0h0m55s