[2023-06-29 19:52:53,091] [INFO] DFAST_QC pipeline started.
[2023-06-29 19:52:53,098] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 19:52:53,099] [INFO] DQC Reference Directory: /var/lib/cwl/stg709bab9f-8fc7-4ddf-9952-cd56a503a627/dqc_reference
[2023-06-29 19:52:55,501] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 19:52:55,503] [INFO] Task started: Prodigal
[2023-06-29 19:52:55,503] [INFO] Running command: gunzip -c /var/lib/cwl/stgc4d9dd99-4ecb-4583-900d-4cd18ab67c2a/GCA_900764005.1_SRS1596871_53_genomic.fna.gz | prodigal -d GCA_900764005.1_SRS1596871_53_genomic.fna/cds.fna -a GCA_900764005.1_SRS1596871_53_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 19:52:59,278] [INFO] Task succeeded: Prodigal
[2023-06-29 19:52:59,279] [INFO] Task started: HMMsearch
[2023-06-29 19:52:59,279] [INFO] Running command: hmmsearch --tblout GCA_900764005.1_SRS1596871_53_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg709bab9f-8fc7-4ddf-9952-cd56a503a627/dqc_reference/reference_markers.hmm GCA_900764005.1_SRS1596871_53_genomic.fna/protein.faa > /dev/null
[2023-06-29 19:52:59,515] [INFO] Task succeeded: HMMsearch
[2023-06-29 19:52:59,517] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgc4d9dd99-4ecb-4583-900d-4cd18ab67c2a/GCA_900764005.1_SRS1596871_53_genomic.fna.gz]
[2023-06-29 19:52:59,538] [INFO] Query marker FASTA was written to GCA_900764005.1_SRS1596871_53_genomic.fna/markers.fasta
[2023-06-29 19:52:59,539] [INFO] Task started: Blastn
[2023-06-29 19:52:59,539] [INFO] Running command: blastn -query GCA_900764005.1_SRS1596871_53_genomic.fna/markers.fasta -db /var/lib/cwl/stg709bab9f-8fc7-4ddf-9952-cd56a503a627/dqc_reference/reference_markers.fasta -out GCA_900764005.1_SRS1596871_53_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 19:53:00,219] [INFO] Task succeeded: Blastn
[2023-06-29 19:53:00,223] [INFO] Selected 18 target genomes.
[2023-06-29 19:53:00,224] [INFO] Target genome list was writen to GCA_900764005.1_SRS1596871_53_genomic.fna/target_genomes.txt
[2023-06-29 19:53:00,231] [INFO] Task started: fastANI
[2023-06-29 19:53:00,231] [INFO] Running command: fastANI --query /var/lib/cwl/stgc4d9dd99-4ecb-4583-900d-4cd18ab67c2a/GCA_900764005.1_SRS1596871_53_genomic.fna.gz --refList GCA_900764005.1_SRS1596871_53_genomic.fna/target_genomes.txt --output GCA_900764005.1_SRS1596871_53_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 19:53:09,294] [INFO] Task succeeded: fastANI
[2023-06-29 19:53:09,295] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg709bab9f-8fc7-4ddf-9952-cd56a503a627/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 19:53:09,296] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg709bab9f-8fc7-4ddf-9952-cd56a503a627/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 19:53:09,300] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 19:53:09,301] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 19:53:09,301] [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
Roseburia lenta	strain=NSJ-9	GCA_014287435.1	2763061	2763061	type	True	82.5476	241	358	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 19:53:09,303] [INFO] DFAST Taxonomy check result was written to GCA_900764005.1_SRS1596871_53_genomic.fna/tc_result.tsv
[2023-06-29 19:53:09,304] [INFO] ===== Taxonomy check completed =====
[2023-06-29 19:53:09,304] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 19:53:09,304] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg709bab9f-8fc7-4ddf-9952-cd56a503a627/dqc_reference/checkm_data
[2023-06-29 19:53:09,306] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 19:53:09,333] [INFO] Task started: CheckM
[2023-06-29 19:53:09,333] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_900764005.1_SRS1596871_53_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_900764005.1_SRS1596871_53_genomic.fna/checkm_input GCA_900764005.1_SRS1596871_53_genomic.fna/checkm_result
[2023-06-29 19:53:28,219] [INFO] Task succeeded: CheckM
[2023-06-29 19:53:28,221] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 61.98%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 19:53:28,246] [INFO] ===== Completeness check finished =====
[2023-06-29 19:53:28,248] [INFO] ===== Start GTDB Search =====
[2023-06-29 19:53:28,250] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_900764005.1_SRS1596871_53_genomic.fna/markers.fasta)
[2023-06-29 19:53:28,250] [INFO] Task started: Blastn
[2023-06-29 19:53:28,251] [INFO] Running command: blastn -query GCA_900764005.1_SRS1596871_53_genomic.fna/markers.fasta -db /var/lib/cwl/stg709bab9f-8fc7-4ddf-9952-cd56a503a627/dqc_reference/reference_markers_gtdb.fasta -out GCA_900764005.1_SRS1596871_53_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 19:53:29,111] [INFO] Task succeeded: Blastn
[2023-06-29 19:53:29,116] [INFO] Selected 19 target genomes.
[2023-06-29 19:53:29,116] [INFO] Target genome list was writen to GCA_900764005.1_SRS1596871_53_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 19:53:29,148] [INFO] Task started: fastANI
[2023-06-29 19:53:29,148] [INFO] Running command: fastANI --query /var/lib/cwl/stgc4d9dd99-4ecb-4583-900d-4cd18ab67c2a/GCA_900764005.1_SRS1596871_53_genomic.fna.gz --refList GCA_900764005.1_SRS1596871_53_genomic.fna/target_genomes_gtdb.txt --output GCA_900764005.1_SRS1596871_53_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 19:53:37,681] [INFO] Task succeeded: fastANI
[2023-06-29 19:53:37,734] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 19:53:37,735] [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_900546435.1	s__AM51-8 sp900546435	98.3158	316	358	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__AM51-8	95.0	97.06	96.69	0.86	0.85	3	conclusive
GCF_003478275.1	s__AM51-8 sp003478275	82.7653	239	358	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__AM51-8	95.0	99.20	98.90	0.94	0.89	8	-
GCA_900315735.1	s__RUG115 sp900315735	76.9533	50	358	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__RUG115	95.0	99.35	98.93	0.92	0.85	5	-
--------------------------------------------------------------------------------
[2023-06-29 19:53:37,738] [INFO] GTDB search result was written to GCA_900764005.1_SRS1596871_53_genomic.fna/result_gtdb.tsv
[2023-06-29 19:53:37,738] [INFO] ===== GTDB Search completed =====
[2023-06-29 19:53:37,741] [INFO] DFAST_QC result json was written to GCA_900764005.1_SRS1596871_53_genomic.fna/dqc_result.json
[2023-06-29 19:53:37,741] [INFO] DFAST_QC completed!
[2023-06-29 19:53:37,741] [INFO] Total running time: 0h0m45s