[2024-01-24 14:30:31,209] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:30:31,211] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:30:31,211] [INFO] DQC Reference Directory: /var/lib/cwl/stg5bc98881-7aaf-4a72-9236-ad98fbcf3ffa/dqc_reference
[2024-01-24 14:30:33,801] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:30:33,806] [INFO] Task started: Prodigal
[2024-01-24 14:30:33,807] [INFO] Running command: gunzip -c /var/lib/cwl/stgaa134497-70c7-42ce-9063-f3c131bf5abc/GCF_003967555.1_ASM396755v1_genomic.fna.gz | prodigal -d GCF_003967555.1_ASM396755v1_genomic.fna/cds.fna -a GCF_003967555.1_ASM396755v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:30:59,815] [INFO] Task succeeded: Prodigal
[2024-01-24 14:30:59,816] [INFO] Task started: HMMsearch
[2024-01-24 14:30:59,816] [INFO] Running command: hmmsearch --tblout GCF_003967555.1_ASM396755v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5bc98881-7aaf-4a72-9236-ad98fbcf3ffa/dqc_reference/reference_markers.hmm GCF_003967555.1_ASM396755v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:31:00,340] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:31:00,341] [INFO] Found 6/6 markers.
[2024-01-24 14:31:00,415] [INFO] Query marker FASTA was written to GCF_003967555.1_ASM396755v1_genomic.fna/markers.fasta
[2024-01-24 14:31:00,415] [INFO] Task started: Blastn
[2024-01-24 14:31:00,416] [INFO] Running command: blastn -query GCF_003967555.1_ASM396755v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5bc98881-7aaf-4a72-9236-ad98fbcf3ffa/dqc_reference/reference_markers.fasta -out GCF_003967555.1_ASM396755v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:31:01,092] [INFO] Task succeeded: Blastn
[2024-01-24 14:31:01,103] [INFO] Selected 7 target genomes.
[2024-01-24 14:31:01,103] [INFO] Target genome list was writen to GCF_003967555.1_ASM396755v1_genomic.fna/target_genomes.txt
[2024-01-24 14:31:01,107] [INFO] Task started: fastANI
[2024-01-24 14:31:01,107] [INFO] Running command: fastANI --query /var/lib/cwl/stgaa134497-70c7-42ce-9063-f3c131bf5abc/GCF_003967555.1_ASM396755v1_genomic.fna.gz --refList GCF_003967555.1_ASM396755v1_genomic.fna/target_genomes.txt --output GCF_003967555.1_ASM396755v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:31:15,871] [INFO] Task succeeded: fastANI
[2024-01-24 14:31:15,871] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5bc98881-7aaf-4a72-9236-ad98fbcf3ffa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:31:15,872] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5bc98881-7aaf-4a72-9236-ad98fbcf3ffa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:31:15,880] [INFO] Found 6 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:31:15,880] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:31:15,880] [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
Dictyobacter kobayashii	strain=Uno11	GCA_003967555.1	2014872	2014872	type	True	100.0	2950	2950	95	conclusive
Dictyobacter formicarum	strain=SOSP1-9	GCA_016587435.1	2778368	2778368	type	True	81.408	1536	2950	95	below_threshold
Dictyobacter aurantiacus	strain=S-27	GCA_003967515.1	1936993	1936993	type	True	80.0014	1286	2950	95	below_threshold
Dictyobacter vulcani	strain=W12	GCA_008974265.1	2607529	2607529	type	True	79.7756	867	2950	95	below_threshold
Dictyobacter alpinus	strain=Uno16	GCA_003967575.1	2014873	2014873	type	True	79.3863	948	2950	95	below_threshold
Dictyobacter arantiisoli	strain=Uno17	GCA_008326305.1	2014874	2014874	type	True	78.4219	499	2950	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:31:15,882] [INFO] DFAST Taxonomy check result was written to GCF_003967555.1_ASM396755v1_genomic.fna/tc_result.tsv
[2024-01-24 14:31:15,883] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:31:15,883] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:31:15,883] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5bc98881-7aaf-4a72-9236-ad98fbcf3ffa/dqc_reference/checkm_data
[2024-01-24 14:31:15,885] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:31:15,971] [INFO] Task started: CheckM
[2024-01-24 14:31:15,972] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003967555.1_ASM396755v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003967555.1_ASM396755v1_genomic.fna/checkm_input GCF_003967555.1_ASM396755v1_genomic.fna/checkm_result
[2024-01-24 14:32:29,694] [INFO] Task succeeded: CheckM
[2024-01-24 14:32:29,698] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 6.94%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:32:29,739] [INFO] ===== Completeness check finished =====
[2024-01-24 14:32:29,739] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:32:29,740] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003967555.1_ASM396755v1_genomic.fna/markers.fasta)
[2024-01-24 14:32:29,740] [INFO] Task started: Blastn
[2024-01-24 14:32:29,740] [INFO] Running command: blastn -query GCF_003967555.1_ASM396755v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5bc98881-7aaf-4a72-9236-ad98fbcf3ffa/dqc_reference/reference_markers_gtdb.fasta -out GCF_003967555.1_ASM396755v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:32:30,534] [INFO] Task succeeded: Blastn
[2024-01-24 14:32:30,538] [INFO] Selected 10 target genomes.
[2024-01-24 14:32:30,538] [INFO] Target genome list was writen to GCF_003967555.1_ASM396755v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:32:30,548] [INFO] Task started: fastANI
[2024-01-24 14:32:30,549] [INFO] Running command: fastANI --query /var/lib/cwl/stgaa134497-70c7-42ce-9063-f3c131bf5abc/GCF_003967555.1_ASM396755v1_genomic.fna.gz --refList GCF_003967555.1_ASM396755v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003967555.1_ASM396755v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:32:49,115] [INFO] Task succeeded: fastANI
[2024-01-24 14:32:49,123] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:32:49,124] [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_003967555.1	s__Dictyobacter kobayashii	100.0	2950	2950	d__Bacteria;p__Chloroflexota;c__Ktedonobacteria;o__Ktedonobacterales;f__Ktedonobacteraceae;g__Dictyobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_016587435.1	s__Dictyobacter sp016587435	81.4054	1539	2950	d__Bacteria;p__Chloroflexota;c__Ktedonobacteria;o__Ktedonobacterales;f__Ktedonobacteraceae;g__Dictyobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003967515.1	s__Dictyobacter aurantiacus	80.0007	1289	2950	d__Bacteria;p__Chloroflexota;c__Ktedonobacteria;o__Ktedonobacterales;f__Ktedonobacteraceae;g__Dictyobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008974265.1	s__Dictyobacter vulcani	79.781	868	2950	d__Bacteria;p__Chloroflexota;c__Ktedonobacteria;o__Ktedonobacterales;f__Ktedonobacteraceae;g__Dictyobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008326305.1	s__Dictyobacter sp008326305	78.376	505	2950	d__Bacteria;p__Chloroflexota;c__Ktedonobacteria;o__Ktedonobacterales;f__Ktedonobacteraceae;g__Dictyobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015099395.1	s__Dictyobacter sp015099395	78.2216	343	2950	d__Bacteria;p__Chloroflexota;c__Ktedonobacteria;o__Ktedonobacterales;f__Ktedonobacteraceae;g__Dictyobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000178855.1	s__Ktedonobacter racemifer	78.0338	266	2950	d__Bacteria;p__Chloroflexota;c__Ktedonobacteria;o__Ktedonobacterales;f__Ktedonobacteraceae;g__Ktedonobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005881495.1	s__UBA11361 sp005881495	76.811	83	2950	d__Bacteria;p__Chloroflexota;c__Ktedonobacteria;o__Ktedonobacterales;f__Ktedonobacteraceae;g__UBA11361	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:32:49,131] [INFO] GTDB search result was written to GCF_003967555.1_ASM396755v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:32:49,131] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:32:49,136] [INFO] DFAST_QC result json was written to GCF_003967555.1_ASM396755v1_genomic.fna/dqc_result.json
[2024-01-24 14:32:49,136] [INFO] DFAST_QC completed!
[2024-01-24 14:32:49,136] [INFO] Total running time: 0h2m18s