[2024-01-25 17:53:50,498] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:53:50,499] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:53:50,500] [INFO] DQC Reference Directory: /var/lib/cwl/stgc83fa675-ac3d-42b9-a062-217937f42de2/dqc_reference
[2024-01-25 17:53:51,747] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:53:51,747] [INFO] Task started: Prodigal
[2024-01-25 17:53:51,748] [INFO] Running command: gunzip -c /var/lib/cwl/stgca3a3bc5-a441-49e2-bccd-ca0919d693d3/GCF_000235445.1_John_igna_ATCC_51276_V1_genomic.fna.gz | prodigal -d GCF_000235445.1_John_igna_ATCC_51276_V1_genomic.fna/cds.fna -a GCF_000235445.1_John_igna_ATCC_51276_V1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:53:56,206] [INFO] Task succeeded: Prodigal
[2024-01-25 17:53:56,206] [INFO] Task started: HMMsearch
[2024-01-25 17:53:56,206] [INFO] Running command: hmmsearch --tblout GCF_000235445.1_John_igna_ATCC_51276_V1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc83fa675-ac3d-42b9-a062-217937f42de2/dqc_reference/reference_markers.hmm GCF_000235445.1_John_igna_ATCC_51276_V1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:53:56,409] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:53:56,411] [INFO] Found 6/6 markers.
[2024-01-25 17:53:56,436] [INFO] Query marker FASTA was written to GCF_000235445.1_John_igna_ATCC_51276_V1_genomic.fna/markers.fasta
[2024-01-25 17:53:56,437] [INFO] Task started: Blastn
[2024-01-25 17:53:56,437] [INFO] Running command: blastn -query GCF_000235445.1_John_igna_ATCC_51276_V1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc83fa675-ac3d-42b9-a062-217937f42de2/dqc_reference/reference_markers.fasta -out GCF_000235445.1_John_igna_ATCC_51276_V1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:53:57,008] [INFO] Task succeeded: Blastn
[2024-01-25 17:53:57,023] [INFO] Selected 21 target genomes.
[2024-01-25 17:53:57,024] [INFO] Target genome list was writen to GCF_000235445.1_John_igna_ATCC_51276_V1_genomic.fna/target_genomes.txt
[2024-01-25 17:53:57,065] [INFO] Task started: fastANI
[2024-01-25 17:53:57,065] [INFO] Running command: fastANI --query /var/lib/cwl/stgca3a3bc5-a441-49e2-bccd-ca0919d693d3/GCF_000235445.1_John_igna_ATCC_51276_V1_genomic.fna.gz --refList GCF_000235445.1_John_igna_ATCC_51276_V1_genomic.fna/target_genomes.txt --output GCF_000235445.1_John_igna_ATCC_51276_V1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:54:08,909] [INFO] Task succeeded: fastANI
[2024-01-25 17:54:08,909] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc83fa675-ac3d-42b9-a062-217937f42de2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:54:08,909] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc83fa675-ac3d-42b9-a062-217937f42de2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:54:08,914] [INFO] Found 3 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:54:08,914] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:54:08,914] [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
Johnsonella ignava	strain=ATCC 51276	GCA_000235445.1	43995	43995	type	True	100.0	873	876	95	conclusive
Lachnoanaerobaculum orale	strain=DSM 24553	GCA_003862485.1	979627	979627	type	True	79.6718	78	876	95	below_threshold
Catonella morbi	strain=ATCC 51271	GCA_000160035.2	43997	43997	type	True	78.8414	50	876	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:54:08,916] [INFO] DFAST Taxonomy check result was written to GCF_000235445.1_John_igna_ATCC_51276_V1_genomic.fna/tc_result.tsv
[2024-01-25 17:54:08,916] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:54:08,916] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:54:08,916] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc83fa675-ac3d-42b9-a062-217937f42de2/dqc_reference/checkm_data
[2024-01-25 17:54:08,917] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:54:08,946] [INFO] Task started: CheckM
[2024-01-25 17:54:08,947] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000235445.1_John_igna_ATCC_51276_V1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000235445.1_John_igna_ATCC_51276_V1_genomic.fna/checkm_input GCF_000235445.1_John_igna_ATCC_51276_V1_genomic.fna/checkm_result
[2024-01-25 17:54:27,469] [INFO] Task succeeded: CheckM
[2024-01-25 17:54:27,471] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:54:27,490] [INFO] ===== Completeness check finished =====
[2024-01-25 17:54:27,490] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:54:27,491] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000235445.1_John_igna_ATCC_51276_V1_genomic.fna/markers.fasta)
[2024-01-25 17:54:27,491] [INFO] Task started: Blastn
[2024-01-25 17:54:27,491] [INFO] Running command: blastn -query GCF_000235445.1_John_igna_ATCC_51276_V1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc83fa675-ac3d-42b9-a062-217937f42de2/dqc_reference/reference_markers_gtdb.fasta -out GCF_000235445.1_John_igna_ATCC_51276_V1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:54:28,432] [INFO] Task succeeded: Blastn
[2024-01-25 17:54:28,435] [INFO] Selected 25 target genomes.
[2024-01-25 17:54:28,435] [INFO] Target genome list was writen to GCF_000235445.1_John_igna_ATCC_51276_V1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:54:28,455] [INFO] Task started: fastANI
[2024-01-25 17:54:28,456] [INFO] Running command: fastANI --query /var/lib/cwl/stgca3a3bc5-a441-49e2-bccd-ca0919d693d3/GCF_000235445.1_John_igna_ATCC_51276_V1_genomic.fna.gz --refList GCF_000235445.1_John_igna_ATCC_51276_V1_genomic.fna/target_genomes_gtdb.txt --output GCF_000235445.1_John_igna_ATCC_51276_V1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:54:42,128] [INFO] Task succeeded: fastANI
[2024-01-25 17:54:42,132] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:54:42,132] [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_000235445.1	s__Johnsonella ignava	100.0	873	876	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Johnsonella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000287675.1	s__Lachnoanaerobaculum sp000287675	79.9925	87	876	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnoanaerobaculum	95.0	96.71	96.71	0.86	0.86	2	-
GCF_003862485.1	s__Lachnoanaerobaculum orale	79.7058	77	876	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnoanaerobaculum	95.0	95.98	95.69	0.85	0.82	6	-
GCF_000160035.2	s__Catonella morbi	78.7674	52	876	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Catonella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:54:42,134] [INFO] GTDB search result was written to GCF_000235445.1_John_igna_ATCC_51276_V1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:54:42,134] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:54:42,136] [INFO] DFAST_QC result json was written to GCF_000235445.1_John_igna_ATCC_51276_V1_genomic.fna/dqc_result.json
[2024-01-25 17:54:42,137] [INFO] DFAST_QC completed!
[2024-01-25 17:54:42,137] [INFO] Total running time: 0h0m52s