[2024-01-24 11:52:49,798] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:52:49,800] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:52:49,801] [INFO] DQC Reference Directory: /var/lib/cwl/stg7e7ed582-b5d0-4ef5-9859-86272af6fdca/dqc_reference
[2024-01-24 11:52:51,007] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:52:51,008] [INFO] Task started: Prodigal
[2024-01-24 11:52:51,008] [INFO] Running command: gunzip -c /var/lib/cwl/stg16652e6f-da5d-41d4-b271-ed22fc8ceb66/GCF_015732175.1_ASM1573217v1_genomic.fna.gz | prodigal -d GCF_015732175.1_ASM1573217v1_genomic.fna/cds.fna -a GCF_015732175.1_ASM1573217v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:52:57,100] [INFO] Task succeeded: Prodigal
[2024-01-24 11:52:57,101] [INFO] Task started: HMMsearch
[2024-01-24 11:52:57,101] [INFO] Running command: hmmsearch --tblout GCF_015732175.1_ASM1573217v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7e7ed582-b5d0-4ef5-9859-86272af6fdca/dqc_reference/reference_markers.hmm GCF_015732175.1_ASM1573217v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:52:57,336] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:52:57,338] [INFO] Found 6/6 markers.
[2024-01-24 11:52:57,362] [INFO] Query marker FASTA was written to GCF_015732175.1_ASM1573217v1_genomic.fna/markers.fasta
[2024-01-24 11:52:57,362] [INFO] Task started: Blastn
[2024-01-24 11:52:57,362] [INFO] Running command: blastn -query GCF_015732175.1_ASM1573217v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7e7ed582-b5d0-4ef5-9859-86272af6fdca/dqc_reference/reference_markers.fasta -out GCF_015732175.1_ASM1573217v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:52:57,935] [INFO] Task succeeded: Blastn
[2024-01-24 11:52:57,938] [INFO] Selected 12 target genomes.
[2024-01-24 11:52:57,938] [INFO] Target genome list was writen to GCF_015732175.1_ASM1573217v1_genomic.fna/target_genomes.txt
[2024-01-24 11:52:57,944] [INFO] Task started: fastANI
[2024-01-24 11:52:57,944] [INFO] Running command: fastANI --query /var/lib/cwl/stg16652e6f-da5d-41d4-b271-ed22fc8ceb66/GCF_015732175.1_ASM1573217v1_genomic.fna.gz --refList GCF_015732175.1_ASM1573217v1_genomic.fna/target_genomes.txt --output GCF_015732175.1_ASM1573217v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:53:04,373] [INFO] Task succeeded: fastANI
[2024-01-24 11:53:04,374] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7e7ed582-b5d0-4ef5-9859-86272af6fdca/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:53:04,374] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7e7ed582-b5d0-4ef5-9859-86272af6fdca/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:53:04,382] [INFO] Found 5 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:53:04,382] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:53:04,382] [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
Pectinatus cerevisiiphilus	strain=MB134	GCA_015732175.1	86956	86956	type	True	100.0	905	906	95	conclusive
Pectinatus cerevisiiphilus	strain=DSM 20467	GCA_004341685.1	86956	86956	type	True	99.9281	850	906	95	conclusive
Pectinatus sottacetonis	strain=MB620	GCA_015732155.1	1002795	1002795	type	True	78.6425	224	906	95	below_threshold
Pectinatus frisingensis	strain=MB174	GCA_015732285.1	865	865	type	True	77.8393	206	906	95	below_threshold
Propionispira raffinosivorans	strain=DSM 20765	GCA_000381065.1	86959	86959	type	True	76.4413	52	906	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:53:04,384] [INFO] DFAST Taxonomy check result was written to GCF_015732175.1_ASM1573217v1_genomic.fna/tc_result.tsv
[2024-01-24 11:53:04,384] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:53:04,384] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:53:04,385] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7e7ed582-b5d0-4ef5-9859-86272af6fdca/dqc_reference/checkm_data
[2024-01-24 11:53:04,385] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:53:04,412] [INFO] Task started: CheckM
[2024-01-24 11:53:04,412] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_015732175.1_ASM1573217v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_015732175.1_ASM1573217v1_genomic.fna/checkm_input GCF_015732175.1_ASM1573217v1_genomic.fna/checkm_result
[2024-01-24 11:53:28,364] [INFO] Task succeeded: CheckM
[2024-01-24 11:53:28,365] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:53:28,387] [INFO] ===== Completeness check finished =====
[2024-01-24 11:53:28,388] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:53:28,388] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_015732175.1_ASM1573217v1_genomic.fna/markers.fasta)
[2024-01-24 11:53:28,389] [INFO] Task started: Blastn
[2024-01-24 11:53:28,389] [INFO] Running command: blastn -query GCF_015732175.1_ASM1573217v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7e7ed582-b5d0-4ef5-9859-86272af6fdca/dqc_reference/reference_markers_gtdb.fasta -out GCF_015732175.1_ASM1573217v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:53:29,185] [INFO] Task succeeded: Blastn
[2024-01-24 11:53:29,189] [INFO] Selected 15 target genomes.
[2024-01-24 11:53:29,189] [INFO] Target genome list was writen to GCF_015732175.1_ASM1573217v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:53:29,199] [INFO] Task started: fastANI
[2024-01-24 11:53:29,199] [INFO] Running command: fastANI --query /var/lib/cwl/stg16652e6f-da5d-41d4-b271-ed22fc8ceb66/GCF_015732175.1_ASM1573217v1_genomic.fna.gz --refList GCF_015732175.1_ASM1573217v1_genomic.fna/target_genomes_gtdb.txt --output GCF_015732175.1_ASM1573217v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:53:36,651] [INFO] Task succeeded: fastANI
[2024-01-24 11:53:36,661] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:53:36,661] [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_004341685.1	s__Pectinatus cerevisiiphilus	99.9011	851	906	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Pectinatus	95.0	99.98	99.98	0.99	0.99	2	conclusive
GCF_015732185.1	s__Pectinatus haikarae	79.565	429	906	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Pectinatus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015732155.1	s__Pectinatus sottacetonis	78.629	221	906	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Pectinatus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015732285.1	s__Pectinatus frisingensis	77.8559	205	906	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Pectinatus	95.0	98.00	97.22	0.85	0.81	9	-
GCF_000381065.1	s__Propionispira raffinosivorans	76.4413	52	906	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Propionispira	96.4486	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:53:36,663] [INFO] GTDB search result was written to GCF_015732175.1_ASM1573217v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:53:36,663] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:53:36,666] [INFO] DFAST_QC result json was written to GCF_015732175.1_ASM1573217v1_genomic.fna/dqc_result.json
[2024-01-24 11:53:36,666] [INFO] DFAST_QC completed!
[2024-01-24 11:53:36,667] [INFO] Total running time: 0h0m47s