[2024-01-24 13:17:05,709] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:17:05,711] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:17:05,712] [INFO] DQC Reference Directory: /var/lib/cwl/stga16aac04-8290-4dce-bbcf-92840e8ea1e7/dqc_reference
[2024-01-24 13:17:07,111] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:17:07,112] [INFO] Task started: Prodigal
[2024-01-24 13:17:07,112] [INFO] Running command: gunzip -c /var/lib/cwl/stgc510e3b5-2dca-48b2-b581-12626ae5598d/GCF_000808015.1_pear-SPAdes-1.0_genomic.fna.gz | prodigal -d GCF_000808015.1_pear-SPAdes-1.0_genomic.fna/cds.fna -a GCF_000808015.1_pear-SPAdes-1.0_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:17:13,324] [INFO] Task succeeded: Prodigal
[2024-01-24 13:17:13,325] [INFO] Task started: HMMsearch
[2024-01-24 13:17:13,325] [INFO] Running command: hmmsearch --tblout GCF_000808015.1_pear-SPAdes-1.0_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga16aac04-8290-4dce-bbcf-92840e8ea1e7/dqc_reference/reference_markers.hmm GCF_000808015.1_pear-SPAdes-1.0_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:17:13,620] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:17:13,621] [INFO] Found 6/6 markers.
[2024-01-24 13:17:13,658] [INFO] Query marker FASTA was written to GCF_000808015.1_pear-SPAdes-1.0_genomic.fna/markers.fasta
[2024-01-24 13:17:13,658] [INFO] Task started: Blastn
[2024-01-24 13:17:13,658] [INFO] Running command: blastn -query GCF_000808015.1_pear-SPAdes-1.0_genomic.fna/markers.fasta -db /var/lib/cwl/stga16aac04-8290-4dce-bbcf-92840e8ea1e7/dqc_reference/reference_markers.fasta -out GCF_000808015.1_pear-SPAdes-1.0_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:17:14,271] [INFO] Task succeeded: Blastn
[2024-01-24 13:17:14,274] [INFO] Selected 5 target genomes.
[2024-01-24 13:17:14,274] [INFO] Target genome list was writen to GCF_000808015.1_pear-SPAdes-1.0_genomic.fna/target_genomes.txt
[2024-01-24 13:17:14,277] [INFO] Task started: fastANI
[2024-01-24 13:17:14,277] [INFO] Running command: fastANI --query /var/lib/cwl/stgc510e3b5-2dca-48b2-b581-12626ae5598d/GCF_000808015.1_pear-SPAdes-1.0_genomic.fna.gz --refList GCF_000808015.1_pear-SPAdes-1.0_genomic.fna/target_genomes.txt --output GCF_000808015.1_pear-SPAdes-1.0_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:17:19,173] [INFO] Task succeeded: fastANI
[2024-01-24 13:17:19,173] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga16aac04-8290-4dce-bbcf-92840e8ea1e7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:17:19,173] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga16aac04-8290-4dce-bbcf-92840e8ea1e7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:17:19,179] [INFO] Found 5 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:17:19,179] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:17:19,179] [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
Terrisporobacter othiniensis	strain=08-306576	GCA_000808015.1	1577792	1577792	type	True	100.0	1242	1246	95	conclusive
Terrisporobacter mayombei	strain=DSM 6539	GCA_020748465.1	1541	1541	type	True	87.4311	901	1246	95	below_threshold
Terrisporobacter glycolicus	strain=DSM 1288	GCA_000439105.1	36841	36841	suspected-type	True	87.1544	925	1246	95	below_threshold
Terrisporobacter glycolicus	strain=ATCC 14880	GCA_000373865.1	36841	36841	suspected-type	True	87.1009	922	1246	95	below_threshold
Terrisporobacter petrolearius	strain=LAM0A37	GCA_020748185.1	1460447	1460447	type	True	86.7586	853	1246	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:17:19,181] [INFO] DFAST Taxonomy check result was written to GCF_000808015.1_pear-SPAdes-1.0_genomic.fna/tc_result.tsv
[2024-01-24 13:17:19,181] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:17:19,182] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:17:19,182] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga16aac04-8290-4dce-bbcf-92840e8ea1e7/dqc_reference/checkm_data
[2024-01-24 13:17:19,183] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:17:19,222] [INFO] Task started: CheckM
[2024-01-24 13:17:19,222] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000808015.1_pear-SPAdes-1.0_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000808015.1_pear-SPAdes-1.0_genomic.fna/checkm_input GCF_000808015.1_pear-SPAdes-1.0_genomic.fna/checkm_result
[2024-01-24 13:17:44,943] [INFO] Task succeeded: CheckM
[2024-01-24 13:17:44,944] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:17:44,964] [INFO] ===== Completeness check finished =====
[2024-01-24 13:17:44,964] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:17:44,965] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000808015.1_pear-SPAdes-1.0_genomic.fna/markers.fasta)
[2024-01-24 13:17:44,965] [INFO] Task started: Blastn
[2024-01-24 13:17:44,965] [INFO] Running command: blastn -query GCF_000808015.1_pear-SPAdes-1.0_genomic.fna/markers.fasta -db /var/lib/cwl/stga16aac04-8290-4dce-bbcf-92840e8ea1e7/dqc_reference/reference_markers_gtdb.fasta -out GCF_000808015.1_pear-SPAdes-1.0_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:17:45,697] [INFO] Task succeeded: Blastn
[2024-01-24 13:17:45,701] [INFO] Selected 7 target genomes.
[2024-01-24 13:17:45,701] [INFO] Target genome list was writen to GCF_000808015.1_pear-SPAdes-1.0_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:17:45,710] [INFO] Task started: fastANI
[2024-01-24 13:17:45,710] [INFO] Running command: fastANI --query /var/lib/cwl/stgc510e3b5-2dca-48b2-b581-12626ae5598d/GCF_000808015.1_pear-SPAdes-1.0_genomic.fna.gz --refList GCF_000808015.1_pear-SPAdes-1.0_genomic.fna/target_genomes_gtdb.txt --output GCF_000808015.1_pear-SPAdes-1.0_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:17:51,667] [INFO] Task succeeded: fastANI
[2024-01-24 13:17:51,674] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:17:51,674] [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_000808015.1	s__Terrisporobacter othiniensis	100.0	1242	1246	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Terrisporobacter	95.0	99.48	99.45	0.91	0.90	3	conclusive
GCA_902363255.1	s__Terrisporobacter sp902363255	88.0026	946	1246	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Terrisporobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000439105.1	s__Terrisporobacter glycolicus	87.1791	923	1246	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Terrisporobacter	95.0	99.67	99.35	0.98	0.96	3	-
GCF_900114105.1	s__Terrisporobacter glycolicus_A	86.7225	873	1246	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Terrisporobacter	95.0	98.29	98.07	0.91	0.91	3	-
GCF_014333445.1	s__Terrisporobacter mayombei	83.2138	323	1246	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Terrisporobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900557165.1	s__Terrisporobacter sp900557165	83.0546	488	1246	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Terrisporobacter	95.0	99.06	99.06	0.78	0.78	2	-
GCA_017888745.1	s__Terrisporobacter sp017888745	82.4817	543	1246	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Terrisporobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:17:51,676] [INFO] GTDB search result was written to GCF_000808015.1_pear-SPAdes-1.0_genomic.fna/result_gtdb.tsv
[2024-01-24 13:17:51,676] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:17:51,679] [INFO] DFAST_QC result json was written to GCF_000808015.1_pear-SPAdes-1.0_genomic.fna/dqc_result.json
[2024-01-24 13:17:51,679] [INFO] DFAST_QC completed!
[2024-01-24 13:17:51,679] [INFO] Total running time: 0h0m46s