[2023-06-30 18:10:22,924] [INFO] DFAST_QC pipeline started.
[2023-06-30 18:10:22,931] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 18:10:22,931] [INFO] DQC Reference Directory: /var/lib/cwl/stgfb2285b8-bd93-405d-aafe-c9c689d9ed06/dqc_reference
[2023-06-30 18:10:24,161] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 18:10:24,162] [INFO] Task started: Prodigal
[2023-06-30 18:10:24,162] [INFO] Running command: gunzip -c /var/lib/cwl/stgf6f83c2c-434a-4272-963c-de6a30cb774e/GCA_900752575.1_ERS235623_78_genomic.fna.gz | prodigal -d GCA_900752575.1_ERS235623_78_genomic.fna/cds.fna -a GCA_900752575.1_ERS235623_78_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 18:10:28,350] [INFO] Task succeeded: Prodigal
[2023-06-30 18:10:28,350] [INFO] Task started: HMMsearch
[2023-06-30 18:10:28,350] [INFO] Running command: hmmsearch --tblout GCA_900752575.1_ERS235623_78_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfb2285b8-bd93-405d-aafe-c9c689d9ed06/dqc_reference/reference_markers.hmm GCA_900752575.1_ERS235623_78_genomic.fna/protein.faa > /dev/null
[2023-06-30 18:10:28,578] [INFO] Task succeeded: HMMsearch
[2023-06-30 18:10:28,580] [INFO] Found 6/6 markers.
[2023-06-30 18:10:28,605] [INFO] Query marker FASTA was written to GCA_900752575.1_ERS235623_78_genomic.fna/markers.fasta
[2023-06-30 18:10:28,605] [INFO] Task started: Blastn
[2023-06-30 18:10:28,605] [INFO] Running command: blastn -query GCA_900752575.1_ERS235623_78_genomic.fna/markers.fasta -db /var/lib/cwl/stgfb2285b8-bd93-405d-aafe-c9c689d9ed06/dqc_reference/reference_markers.fasta -out GCA_900752575.1_ERS235623_78_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 18:10:29,237] [INFO] Task succeeded: Blastn
[2023-06-30 18:10:29,242] [INFO] Selected 17 target genomes.
[2023-06-30 18:10:29,242] [INFO] Target genome list was writen to GCA_900752575.1_ERS235623_78_genomic.fna/target_genomes.txt
[2023-06-30 18:10:29,246] [INFO] Task started: fastANI
[2023-06-30 18:10:29,247] [INFO] Running command: fastANI --query /var/lib/cwl/stgf6f83c2c-434a-4272-963c-de6a30cb774e/GCA_900752575.1_ERS235623_78_genomic.fna.gz --refList GCA_900752575.1_ERS235623_78_genomic.fna/target_genomes.txt --output GCA_900752575.1_ERS235623_78_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 18:10:38,978] [INFO] Task succeeded: fastANI
[2023-06-30 18:10:38,979] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfb2285b8-bd93-405d-aafe-c9c689d9ed06/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 18:10:38,979] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfb2285b8-bd93-405d-aafe-c9c689d9ed06/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 18:10:38,985] [INFO] Found 1 fastANI hits (1 hits with ANI > threshold)
[2023-06-30 18:10:38,985] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-30 18:10:38,985] [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
Ruminococcus bromii	strain=ATCC 27255	GCA_002834225.1	40518	40518	suspected-type	True	98.3755	545	569	95	conclusive
--------------------------------------------------------------------------------
[2023-06-30 18:10:38,988] [INFO] DFAST Taxonomy check result was written to GCA_900752575.1_ERS235623_78_genomic.fna/tc_result.tsv
[2023-06-30 18:10:38,988] [INFO] ===== Taxonomy check completed =====
[2023-06-30 18:10:38,988] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 18:10:38,989] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfb2285b8-bd93-405d-aafe-c9c689d9ed06/dqc_reference/checkm_data
[2023-06-30 18:10:38,990] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 18:10:39,013] [INFO] Task started: CheckM
[2023-06-30 18:10:39,014] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_900752575.1_ERS235623_78_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_900752575.1_ERS235623_78_genomic.fna/checkm_input GCA_900752575.1_ERS235623_78_genomic.fna/checkm_result
[2023-06-30 18:10:59,532] [INFO] Task succeeded: CheckM
[2023-06-30 18:10:59,533] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 18:10:59,554] [INFO] ===== Completeness check finished =====
[2023-06-30 18:10:59,555] [INFO] ===== Start GTDB Search =====
[2023-06-30 18:10:59,555] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_900752575.1_ERS235623_78_genomic.fna/markers.fasta)
[2023-06-30 18:10:59,555] [INFO] Task started: Blastn
[2023-06-30 18:10:59,556] [INFO] Running command: blastn -query GCA_900752575.1_ERS235623_78_genomic.fna/markers.fasta -db /var/lib/cwl/stgfb2285b8-bd93-405d-aafe-c9c689d9ed06/dqc_reference/reference_markers_gtdb.fasta -out GCA_900752575.1_ERS235623_78_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 18:11:00,609] [INFO] Task succeeded: Blastn
[2023-06-30 18:11:00,613] [INFO] Selected 6 target genomes.
[2023-06-30 18:11:00,613] [INFO] Target genome list was writen to GCA_900752575.1_ERS235623_78_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 18:11:00,618] [INFO] Task started: fastANI
[2023-06-30 18:11:00,619] [INFO] Running command: fastANI --query /var/lib/cwl/stgf6f83c2c-434a-4272-963c-de6a30cb774e/GCA_900752575.1_ERS235623_78_genomic.fna.gz --refList GCA_900752575.1_ERS235623_78_genomic.fna/target_genomes_gtdb.txt --output GCA_900752575.1_ERS235623_78_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 18:11:03,476] [INFO] Task succeeded: fastANI
[2023-06-30 18:11:03,487] [INFO] Found 6 fastANI hits (3 hits with ANI > circumscription radius)
[2023-06-30 18:11:03,488] [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_002834225.1	s__Ruminococcus_E bromii	98.3755	545	569	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E	95.0	98.59	98.08	0.94	0.90	6	inconclusive
GCF_002834235.1	s__Ruminococcus_E bromii_B	95.0497	510	569	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E	95.0	97.64	96.93	0.86	0.80	74	inconclusive
GCA_905215855.1	s__Ruminococcus_E sp905215855	95.0045	486	569	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E	95.0	97.72	97.72	0.86	0.84	4	inconclusive
GCA_902771755.1	s__Ruminococcus_E sp902771755	91.2386	392	569	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902766775.1	s__Ruminococcus_E sp902766775	89.9788	371	569	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910585865.1	s__Ruminococcus_E sp910585865	78.868	200	569	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 18:11:03,490] [INFO] GTDB search result was written to GCA_900752575.1_ERS235623_78_genomic.fna/result_gtdb.tsv
[2023-06-30 18:11:03,491] [INFO] ===== GTDB Search completed =====
[2023-06-30 18:11:03,495] [INFO] DFAST_QC result json was written to GCA_900752575.1_ERS235623_78_genomic.fna/dqc_result.json
[2023-06-30 18:11:03,495] [INFO] DFAST_QC completed!
[2023-06-30 18:11:03,496] [INFO] Total running time: 0h0m41s