[2023-06-17 11:44:00,089] [INFO] DFAST_QC pipeline started.
[2023-06-17 11:44:00,091] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 11:44:00,091] [INFO] DQC Reference Directory: /var/lib/cwl/stgb025b60a-7336-43df-8d4e-9244f7f1d551/dqc_reference
[2023-06-17 11:44:01,751] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 11:44:01,752] [INFO] Task started: Prodigal
[2023-06-17 11:44:01,752] [INFO] Running command: gunzip -c /var/lib/cwl/stgf28509ee-49a8-4f11-82d7-f1fa7c95c0a5/GCA_028708305.1_ASM2870830v1_genomic.fna.gz | prodigal -d GCA_028708305.1_ASM2870830v1_genomic.fna/cds.fna -a GCA_028708305.1_ASM2870830v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 11:44:04,973] [INFO] Task succeeded: Prodigal
[2023-06-17 11:44:04,974] [INFO] Task started: HMMsearch
[2023-06-17 11:44:04,974] [INFO] Running command: hmmsearch --tblout GCA_028708305.1_ASM2870830v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb025b60a-7336-43df-8d4e-9244f7f1d551/dqc_reference/reference_markers.hmm GCA_028708305.1_ASM2870830v1_genomic.fna/protein.faa > /dev/null
[2023-06-17 11:44:05,191] [INFO] Task succeeded: HMMsearch
[2023-06-17 11:44:05,193] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgf28509ee-49a8-4f11-82d7-f1fa7c95c0a5/GCA_028708305.1_ASM2870830v1_genomic.fna.gz]
[2023-06-17 11:44:05,214] [INFO] Query marker FASTA was written to GCA_028708305.1_ASM2870830v1_genomic.fna/markers.fasta
[2023-06-17 11:44:05,215] [INFO] Task started: Blastn
[2023-06-17 11:44:05,215] [INFO] Running command: blastn -query GCA_028708305.1_ASM2870830v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb025b60a-7336-43df-8d4e-9244f7f1d551/dqc_reference/reference_markers.fasta -out GCA_028708305.1_ASM2870830v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 11:44:05,808] [INFO] Task succeeded: Blastn
[2023-06-17 11:44:05,813] [INFO] Selected 9 target genomes.
[2023-06-17 11:44:05,814] [INFO] Target genome list was writen to GCA_028708305.1_ASM2870830v1_genomic.fna/target_genomes.txt
[2023-06-17 11:44:05,819] [INFO] Task started: fastANI
[2023-06-17 11:44:05,820] [INFO] Running command: fastANI --query /var/lib/cwl/stgf28509ee-49a8-4f11-82d7-f1fa7c95c0a5/GCA_028708305.1_ASM2870830v1_genomic.fna.gz --refList GCA_028708305.1_ASM2870830v1_genomic.fna/target_genomes.txt --output GCA_028708305.1_ASM2870830v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 11:44:09,468] [INFO] Task succeeded: fastANI
[2023-06-17 11:44:09,469] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb025b60a-7336-43df-8d4e-9244f7f1d551/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 11:44:09,469] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb025b60a-7336-43df-8d4e-9244f7f1d551/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 11:44:09,471] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 11:44:09,471] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-17 11:44:09,471] [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
--------------------------------------------------------------------------------
[2023-06-17 11:44:09,473] [INFO] DFAST Taxonomy check result was written to GCA_028708305.1_ASM2870830v1_genomic.fna/tc_result.tsv
[2023-06-17 11:44:09,474] [INFO] ===== Taxonomy check completed =====
[2023-06-17 11:44:09,475] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 11:44:09,475] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb025b60a-7336-43df-8d4e-9244f7f1d551/dqc_reference/checkm_data
[2023-06-17 11:44:09,478] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 11:44:09,498] [INFO] Task started: CheckM
[2023-06-17 11:44:09,499] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_028708305.1_ASM2870830v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_028708305.1_ASM2870830v1_genomic.fna/checkm_input GCA_028708305.1_ASM2870830v1_genomic.fna/checkm_result
[2023-06-17 11:44:26,883] [INFO] Task succeeded: CheckM
[2023-06-17 11:44:26,884] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-17 11:44:26,907] [INFO] ===== Completeness check finished =====
[2023-06-17 11:44:26,907] [INFO] ===== Start GTDB Search =====
[2023-06-17 11:44:26,908] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_028708305.1_ASM2870830v1_genomic.fna/markers.fasta)
[2023-06-17 11:44:26,908] [INFO] Task started: Blastn
[2023-06-17 11:44:26,909] [INFO] Running command: blastn -query GCA_028708305.1_ASM2870830v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb025b60a-7336-43df-8d4e-9244f7f1d551/dqc_reference/reference_markers_gtdb.fasta -out GCA_028708305.1_ASM2870830v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 11:44:27,708] [INFO] Task succeeded: Blastn
[2023-06-17 11:44:27,713] [INFO] Selected 6 target genomes.
[2023-06-17 11:44:27,714] [INFO] Target genome list was writen to GCA_028708305.1_ASM2870830v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 11:44:27,723] [INFO] Task started: fastANI
[2023-06-17 11:44:27,724] [INFO] Running command: fastANI --query /var/lib/cwl/stgf28509ee-49a8-4f11-82d7-f1fa7c95c0a5/GCA_028708305.1_ASM2870830v1_genomic.fna.gz --refList GCA_028708305.1_ASM2870830v1_genomic.fna/target_genomes_gtdb.txt --output GCA_028708305.1_ASM2870830v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 11:44:30,282] [INFO] Task succeeded: fastANI
[2023-06-17 11:44:30,294] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-17 11:44:30,295] [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_012727545.1	s__Syner-03 sp012727545	98.4488	259	422	d__Bacteria;p__Synergistota;c__Synergistia;o__Synergistales;f__Synergistaceae;g__Syner-03	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002428495.1	s__Syner-03 sp002428495	87.632	372	422	d__Bacteria;p__Synergistota;c__Synergistia;o__Synergistales;f__Synergistaceae;g__Syner-03	95.0	99.46	99.46	0.97	0.97	2	-
GCA_002839185.1	s__Syner-03 sp002839185	87.3141	397	422	d__Bacteria;p__Synergistota;c__Synergistia;o__Synergistales;f__Synergistaceae;g__Syner-03	95.0	98.77	98.13	0.94	0.86	5	-
GCA_012513245.1	s__Syner-03 sp012513245	82.4868	288	422	d__Bacteria;p__Synergistota;c__Synergistia;o__Synergistales;f__Synergistaceae;g__Syner-03	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002316795.1	s__Syner-03 sp002316795	81.3771	266	422	d__Bacteria;p__Synergistota;c__Synergistia;o__Synergistales;f__Synergistaceae;g__Syner-03	95.0	99.61	99.43	0.90	0.87	7	-
--------------------------------------------------------------------------------
[2023-06-17 11:44:30,297] [INFO] GTDB search result was written to GCA_028708305.1_ASM2870830v1_genomic.fna/result_gtdb.tsv
[2023-06-17 11:44:30,298] [INFO] ===== GTDB Search completed =====
[2023-06-17 11:44:30,301] [INFO] DFAST_QC result json was written to GCA_028708305.1_ASM2870830v1_genomic.fna/dqc_result.json
[2023-06-17 11:44:30,302] [INFO] DFAST_QC completed!
[2023-06-17 11:44:30,302] [INFO] Total running time: 0h0m30s