[2023-06-18 10:35:46,123] [INFO] DFAST_QC pipeline started.
[2023-06-18 10:35:46,127] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 10:35:46,127] [INFO] DQC Reference Directory: /var/lib/cwl/stgfcbeecac-24e7-467e-a09c-ae4f4687d7cb/dqc_reference
[2023-06-18 10:35:47,591] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 10:35:47,592] [INFO] Task started: Prodigal
[2023-06-18 10:35:47,592] [INFO] Running command: gunzip -c /var/lib/cwl/stg605e25e5-ec66-4051-baf1-1e107543bf66/GCA_018435415.1_SL1_genomic.fna.gz | prodigal -d GCA_018435415.1_SL1_genomic.fna/cds.fna -a GCA_018435415.1_SL1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 10:35:55,542] [INFO] Task succeeded: Prodigal
[2023-06-18 10:35:55,542] [INFO] Task started: HMMsearch
[2023-06-18 10:35:55,542] [INFO] Running command: hmmsearch --tblout GCA_018435415.1_SL1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfcbeecac-24e7-467e-a09c-ae4f4687d7cb/dqc_reference/reference_markers.hmm GCA_018435415.1_SL1_genomic.fna/protein.faa > /dev/null
[2023-06-18 10:35:55,870] [INFO] Task succeeded: HMMsearch
[2023-06-18 10:35:55,873] [INFO] Found 6/6 markers.
[2023-06-18 10:35:55,928] [INFO] Query marker FASTA was written to GCA_018435415.1_SL1_genomic.fna/markers.fasta
[2023-06-18 10:35:55,929] [INFO] Task started: Blastn
[2023-06-18 10:35:55,929] [INFO] Running command: blastn -query GCA_018435415.1_SL1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfcbeecac-24e7-467e-a09c-ae4f4687d7cb/dqc_reference/reference_markers.fasta -out GCA_018435415.1_SL1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 10:35:56,564] [INFO] Task succeeded: Blastn
[2023-06-18 10:35:56,570] [INFO] Selected 11 target genomes.
[2023-06-18 10:35:56,571] [INFO] Target genome list was writen to GCA_018435415.1_SL1_genomic.fna/target_genomes.txt
[2023-06-18 10:35:56,576] [INFO] Task started: fastANI
[2023-06-18 10:35:56,576] [INFO] Running command: fastANI --query /var/lib/cwl/stg605e25e5-ec66-4051-baf1-1e107543bf66/GCA_018435415.1_SL1_genomic.fna.gz --refList GCA_018435415.1_SL1_genomic.fna/target_genomes.txt --output GCA_018435415.1_SL1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 10:36:03,614] [INFO] Task succeeded: fastANI
[2023-06-18 10:36:03,614] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfcbeecac-24e7-467e-a09c-ae4f4687d7cb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 10:36:03,614] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfcbeecac-24e7-467e-a09c-ae4f4687d7cb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 10:36:03,619] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-18 10:36:03,619] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-18 10:36:03,619] [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
Mesotoga prima	strain=MesG1.Ag.4.2	GCA_000147715.3	1184387	1184387	type	True	79.4682	120	968	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-18 10:36:03,623] [INFO] DFAST Taxonomy check result was written to GCA_018435415.1_SL1_genomic.fna/tc_result.tsv
[2023-06-18 10:36:03,626] [INFO] ===== Taxonomy check completed =====
[2023-06-18 10:36:03,626] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 10:36:03,626] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfcbeecac-24e7-467e-a09c-ae4f4687d7cb/dqc_reference/checkm_data
[2023-06-18 10:36:03,628] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 10:36:03,671] [INFO] Task started: CheckM
[2023-06-18 10:36:03,671] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018435415.1_SL1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018435415.1_SL1_genomic.fna/checkm_input GCA_018435415.1_SL1_genomic.fna/checkm_result
[2023-06-18 10:36:33,574] [INFO] Task succeeded: CheckM
[2023-06-18 10:36:33,575] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 8.80%
Strain heterogeneity: 66.67%
--------------------------------------------------------------------------------
[2023-06-18 10:36:33,613] [INFO] ===== Completeness check finished =====
[2023-06-18 10:36:33,613] [INFO] ===== Start GTDB Search =====
[2023-06-18 10:36:33,614] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018435415.1_SL1_genomic.fna/markers.fasta)
[2023-06-18 10:36:33,614] [INFO] Task started: Blastn
[2023-06-18 10:36:33,614] [INFO] Running command: blastn -query GCA_018435415.1_SL1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfcbeecac-24e7-467e-a09c-ae4f4687d7cb/dqc_reference/reference_markers_gtdb.fasta -out GCA_018435415.1_SL1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 10:36:34,352] [INFO] Task succeeded: Blastn
[2023-06-18 10:36:34,361] [INFO] Selected 18 target genomes.
[2023-06-18 10:36:34,361] [INFO] Target genome list was writen to GCA_018435415.1_SL1_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 10:36:34,403] [INFO] Task started: fastANI
[2023-06-18 10:36:34,403] [INFO] Running command: fastANI --query /var/lib/cwl/stg605e25e5-ec66-4051-baf1-1e107543bf66/GCA_018435415.1_SL1_genomic.fna.gz --refList GCA_018435415.1_SL1_genomic.fna/target_genomes_gtdb.txt --output GCA_018435415.1_SL1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 10:36:43,073] [INFO] Task succeeded: fastANI
[2023-06-18 10:36:43,086] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-18 10:36:43,087] [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_002305955.1	s__Mesotoga sp002305955	99.501	662	968	d__Bacteria;p__Thermotogota;c__Thermotogae;o__Petrotogales;f__Kosmotogaceae;g__Mesotoga	95.0	99.56	99.32	0.86	0.77	7	conclusive
GCF_900157305.1	s__Mesotoga infera_B	89.3958	701	968	d__Bacteria;p__Thermotogota;c__Thermotogae;o__Petrotogales;f__Kosmotogaceae;g__Mesotoga	95.0	98.81	98.51	0.92	0.74	9	-
GCF_003664995.1	s__Mesotoga sp003664995	80.3439	139	968	d__Bacteria;p__Thermotogota;c__Thermotogae;o__Petrotogales;f__Kosmotogaceae;g__Mesotoga	95.0	98.98	98.98	0.91	0.91	2	-
GCF_000147715.2	s__Mesotoga prima	79.4682	120	968	d__Bacteria;p__Thermotogota;c__Thermotogae;o__Petrotogales;f__Kosmotogaceae;g__Mesotoga	95.0	97.16	96.75	0.87	0.85	6	-
GCF_002752635.1	s__Mesotoga sp002752635	78.8125	120	968	d__Bacteria;p__Thermotogota;c__Thermotogae;o__Petrotogales;f__Kosmotogaceae;g__Mesotoga	95.0	98.07	97.29	0.90	0.81	15	-
GCA_011045915.1	s__Mesotoga infera_D	78.5067	112	968	d__Bacteria;p__Thermotogota;c__Thermotogae;o__Petrotogales;f__Kosmotogaceae;g__Mesotoga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016933635.1	s__Mesotoga sp016933635	78.3767	65	968	d__Bacteria;p__Thermotogota;c__Thermotogae;o__Petrotogales;f__Kosmotogaceae;g__Mesotoga	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-18 10:36:43,089] [INFO] GTDB search result was written to GCA_018435415.1_SL1_genomic.fna/result_gtdb.tsv
[2023-06-18 10:36:43,093] [INFO] ===== GTDB Search completed =====
[2023-06-18 10:36:43,101] [INFO] DFAST_QC result json was written to GCA_018435415.1_SL1_genomic.fna/dqc_result.json
[2023-06-18 10:36:43,101] [INFO] DFAST_QC completed!
[2023-06-18 10:36:43,101] [INFO] Total running time: 0h0m57s