[2024-01-24 13:40:35,026] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:35,030] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:35,031] [INFO] DQC Reference Directory: /var/lib/cwl/stgbd271570-641b-4bd9-b378-3ed00a32549b/dqc_reference
[2024-01-24 13:40:36,457] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:36,458] [INFO] Task started: Prodigal
[2024-01-24 13:40:36,458] [INFO] Running command: gunzip -c /var/lib/cwl/stg0b8d8c7d-6467-4ff3-a8eb-ded07ea49016/GCF_900199435.1_PRJEB21892_genomic.fna.gz | prodigal -d GCF_900199435.1_PRJEB21892_genomic.fna/cds.fna -a GCF_900199435.1_PRJEB21892_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:40:45,306] [INFO] Task succeeded: Prodigal
[2024-01-24 13:40:45,306] [INFO] Task started: HMMsearch
[2024-01-24 13:40:45,307] [INFO] Running command: hmmsearch --tblout GCF_900199435.1_PRJEB21892_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbd271570-641b-4bd9-b378-3ed00a32549b/dqc_reference/reference_markers.hmm GCF_900199435.1_PRJEB21892_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:40:45,701] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:40:45,703] [INFO] Found 6/6 markers.
[2024-01-24 13:40:45,737] [INFO] Query marker FASTA was written to GCF_900199435.1_PRJEB21892_genomic.fna/markers.fasta
[2024-01-24 13:40:45,737] [INFO] Task started: Blastn
[2024-01-24 13:40:45,738] [INFO] Running command: blastn -query GCF_900199435.1_PRJEB21892_genomic.fna/markers.fasta -db /var/lib/cwl/stgbd271570-641b-4bd9-b378-3ed00a32549b/dqc_reference/reference_markers.fasta -out GCF_900199435.1_PRJEB21892_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:40:46,416] [INFO] Task succeeded: Blastn
[2024-01-24 13:40:46,422] [INFO] Selected 19 target genomes.
[2024-01-24 13:40:46,423] [INFO] Target genome list was writen to GCF_900199435.1_PRJEB21892_genomic.fna/target_genomes.txt
[2024-01-24 13:40:46,431] [INFO] Task started: fastANI
[2024-01-24 13:40:46,431] [INFO] Running command: fastANI --query /var/lib/cwl/stg0b8d8c7d-6467-4ff3-a8eb-ded07ea49016/GCF_900199435.1_PRJEB21892_genomic.fna.gz --refList GCF_900199435.1_PRJEB21892_genomic.fna/target_genomes.txt --output GCF_900199435.1_PRJEB21892_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:40:56,030] [INFO] Task succeeded: fastANI
[2024-01-24 13:40:56,030] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbd271570-641b-4bd9-b378-3ed00a32549b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:40:56,031] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbd271570-641b-4bd9-b378-3ed00a32549b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:40:56,036] [INFO] Found 3 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:40:56,036] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:40:56,036] [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
Pygmaiobacter massiliensis	strain=Marseille-P3336	GCA_900199435.1	1917873	1917873	type	True	100.0	933	933	95	conclusive
Ruthenibacterium lactatiformans	strain=585-1	GCA_000949455.1	1550024	1550024	suspected-type	True	76.821	50	933	95	below_threshold
Fournierella massiliensis	strain=DSM 100451	GCA_004345265.1	1650663	1650663	type	True	76.4959	53	933	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:40:56,038] [INFO] DFAST Taxonomy check result was written to GCF_900199435.1_PRJEB21892_genomic.fna/tc_result.tsv
[2024-01-24 13:40:56,039] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:40:56,039] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:40:56,039] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbd271570-641b-4bd9-b378-3ed00a32549b/dqc_reference/checkm_data
[2024-01-24 13:40:56,040] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:40:56,069] [INFO] Task started: CheckM
[2024-01-24 13:40:56,070] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900199435.1_PRJEB21892_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900199435.1_PRJEB21892_genomic.fna/checkm_input GCF_900199435.1_PRJEB21892_genomic.fna/checkm_result
[2024-01-24 13:41:27,172] [INFO] Task succeeded: CheckM
[2024-01-24 13:41:27,173] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:41:27,203] [INFO] ===== Completeness check finished =====
[2024-01-24 13:41:27,204] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:41:27,204] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900199435.1_PRJEB21892_genomic.fna/markers.fasta)
[2024-01-24 13:41:27,205] [INFO] Task started: Blastn
[2024-01-24 13:41:27,205] [INFO] Running command: blastn -query GCF_900199435.1_PRJEB21892_genomic.fna/markers.fasta -db /var/lib/cwl/stgbd271570-641b-4bd9-b378-3ed00a32549b/dqc_reference/reference_markers_gtdb.fasta -out GCF_900199435.1_PRJEB21892_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:28,120] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:28,123] [INFO] Selected 25 target genomes.
[2024-01-24 13:41:28,124] [INFO] Target genome list was writen to GCF_900199435.1_PRJEB21892_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:41:28,182] [INFO] Task started: fastANI
[2024-01-24 13:41:28,182] [INFO] Running command: fastANI --query /var/lib/cwl/stg0b8d8c7d-6467-4ff3-a8eb-ded07ea49016/GCF_900199435.1_PRJEB21892_genomic.fna.gz --refList GCF_900199435.1_PRJEB21892_genomic.fna/target_genomes_gtdb.txt --output GCF_900199435.1_PRJEB21892_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:41:38,933] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:38,938] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:41:38,939] [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_900199435.1	s__Pygmaiobacter massiliensis	100.0	932	933	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Pygmaiobacter	95.0	97.38	97.07	0.92	0.89	3	conclusive
GCF_014287275.1	s__Pygmaiobacter sp014287275	77.2517	79	933	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Pygmaiobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000949455.1	s__Ruthenibacterium lactatiformans	76.821	50	933	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruthenibacterium	95.0	98.75	98.24	0.81	0.72	47	-
GCA_004555405.1	s__Gemmiger sp004555405	76.2845	51	933	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Gemmiger	95.0	97.36	97.23	0.85	0.84	4	-
--------------------------------------------------------------------------------
[2024-01-24 13:41:38,940] [INFO] GTDB search result was written to GCF_900199435.1_PRJEB21892_genomic.fna/result_gtdb.tsv
[2024-01-24 13:41:38,940] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:41:38,942] [INFO] DFAST_QC result json was written to GCF_900199435.1_PRJEB21892_genomic.fna/dqc_result.json
[2024-01-24 13:41:38,943] [INFO] DFAST_QC completed!
[2024-01-24 13:41:38,943] [INFO] Total running time: 0h1m4s