[2024-01-24 12:44:43,960] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:44:43,961] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:44:43,961] [INFO] DQC Reference Directory: /var/lib/cwl/stg357073e8-ffe4-4ca2-a0f1-282d8b5923a3/dqc_reference
[2024-01-24 12:44:45,432] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:44:45,435] [INFO] Task started: Prodigal
[2024-01-24 12:44:45,436] [INFO] Running command: gunzip -c /var/lib/cwl/stg398fe41f-ee67-4116-8048-63c89f2172da/GCF_016587375.1_ASM1658737v1_genomic.fna.gz | prodigal -d GCF_016587375.1_ASM1658737v1_genomic.fna/cds.fna -a GCF_016587375.1_ASM1658737v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:45:22,356] [INFO] Task succeeded: Prodigal
[2024-01-24 12:45:22,356] [INFO] Task started: HMMsearch
[2024-01-24 12:45:22,356] [INFO] Running command: hmmsearch --tblout GCF_016587375.1_ASM1658737v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg357073e8-ffe4-4ca2-a0f1-282d8b5923a3/dqc_reference/reference_markers.hmm GCF_016587375.1_ASM1658737v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:45:22,817] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:45:22,818] [INFO] Found 6/6 markers.
[2024-01-24 12:45:22,904] [INFO] Query marker FASTA was written to GCF_016587375.1_ASM1658737v1_genomic.fna/markers.fasta
[2024-01-24 12:45:22,905] [INFO] Task started: Blastn
[2024-01-24 12:45:22,905] [INFO] Running command: blastn -query GCF_016587375.1_ASM1658737v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg357073e8-ffe4-4ca2-a0f1-282d8b5923a3/dqc_reference/reference_markers.fasta -out GCF_016587375.1_ASM1658737v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:45:23,548] [INFO] Task succeeded: Blastn
[2024-01-24 12:45:23,553] [INFO] Selected 20 target genomes.
[2024-01-24 12:45:23,554] [INFO] Target genome list was writen to GCF_016587375.1_ASM1658737v1_genomic.fna/target_genomes.txt
[2024-01-24 12:45:23,582] [INFO] Task started: fastANI
[2024-01-24 12:45:23,582] [INFO] Running command: fastANI --query /var/lib/cwl/stg398fe41f-ee67-4116-8048-63c89f2172da/GCF_016587375.1_ASM1658737v1_genomic.fna.gz --refList GCF_016587375.1_ASM1658737v1_genomic.fna/target_genomes.txt --output GCF_016587375.1_ASM1658737v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:45:51,372] [INFO] Task succeeded: fastANI
[2024-01-24 12:45:51,372] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg357073e8-ffe4-4ca2-a0f1-282d8b5923a3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:45:51,372] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg357073e8-ffe4-4ca2-a0f1-282d8b5923a3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:45:51,381] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:45:51,381] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:45:51,381] [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
Ktedonobacter robiniae	strain=SOSP1-30	GCA_016587375.1	2778365	2778365	type	True	100.0	3568	3568	95	conclusive
Ktedonobacter racemifer	strain=SOSP1-21	GCA_000178855.1	363277	363277	type	True	92.1565	2623	3568	95	below_threshold
Ktedonospora formicarum	strain=SOSP1-1	GCA_016587355.1	2778364	2778364	type	True	79.8309	921	3568	95	below_threshold
Reticulibacter mediterranei	strain=150040	GCA_016587455.1	2778369	2778369	type	True	78.6618	383	3568	95	below_threshold
Dictyobacter arantiisoli	strain=Uno17	GCA_008326305.1	2014874	2014874	type	True	78.3951	202	3568	95	below_threshold
Tengunoibacter tsumagoiensis	strain=Uno3	GCA_003967535.1	2014871	2014871	type	True	78.1911	196	3568	95	below_threshold
Dictyobacter kobayashii	strain=Uno11	GCA_003967555.1	2014872	2014872	type	True	78.0824	244	3568	95	below_threshold
Dictyobacter vulcani	strain=W12	GCA_008974265.1	2607529	2607529	type	True	77.9435	210	3568	95	below_threshold
Dictyobacter aurantiacus	strain=S-27	GCA_003967515.1	1936993	1936993	type	True	77.4016	285	3568	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:45:51,383] [INFO] DFAST Taxonomy check result was written to GCF_016587375.1_ASM1658737v1_genomic.fna/tc_result.tsv
[2024-01-24 12:45:51,383] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:45:51,384] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:45:51,384] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg357073e8-ffe4-4ca2-a0f1-282d8b5923a3/dqc_reference/checkm_data
[2024-01-24 12:45:51,386] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:45:51,482] [INFO] Task started: CheckM
[2024-01-24 12:45:51,482] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016587375.1_ASM1658737v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016587375.1_ASM1658737v1_genomic.fna/checkm_input GCF_016587375.1_ASM1658737v1_genomic.fna/checkm_result
[2024-01-24 12:47:28,297] [INFO] Task succeeded: CheckM
[2024-01-24 12:47:28,298] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 6.48%
Strain heterogeneity: 83.33%
--------------------------------------------------------------------------------
[2024-01-24 12:47:28,332] [INFO] ===== Completeness check finished =====
[2024-01-24 12:47:28,333] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:47:28,333] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016587375.1_ASM1658737v1_genomic.fna/markers.fasta)
[2024-01-24 12:47:28,334] [INFO] Task started: Blastn
[2024-01-24 12:47:28,334] [INFO] Running command: blastn -query GCF_016587375.1_ASM1658737v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg357073e8-ffe4-4ca2-a0f1-282d8b5923a3/dqc_reference/reference_markers_gtdb.fasta -out GCF_016587375.1_ASM1658737v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:47:29,312] [INFO] Task succeeded: Blastn
[2024-01-24 12:47:29,315] [INFO] Selected 15 target genomes.
[2024-01-24 12:47:29,316] [INFO] Target genome list was writen to GCF_016587375.1_ASM1658737v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:47:29,326] [INFO] Task started: fastANI
[2024-01-24 12:47:29,327] [INFO] Running command: fastANI --query /var/lib/cwl/stg398fe41f-ee67-4116-8048-63c89f2172da/GCF_016587375.1_ASM1658737v1_genomic.fna.gz --refList GCF_016587375.1_ASM1658737v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016587375.1_ASM1658737v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:47:55,395] [INFO] Task succeeded: fastANI
[2024-01-24 12:47:55,405] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:47:55,405] [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_016587375.1	s__Ktedonobacter sp016587375	100.0	3567	3568	d__Bacteria;p__Chloroflexota;c__Ktedonobacteria;o__Ktedonobacterales;f__Ktedonobacteraceae;g__Ktedonobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_016587415.1	s__Ktedonobacter sp016587415	94.6498	2711	3568	d__Bacteria;p__Chloroflexota;c__Ktedonobacteria;o__Ktedonobacterales;f__Ktedonobacteraceae;g__Ktedonobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000178855.1	s__Ktedonobacter racemifer	92.146	2625	3568	d__Bacteria;p__Chloroflexota;c__Ktedonobacteria;o__Ktedonobacterales;f__Ktedonobacteraceae;g__Ktedonobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016587355.1	s__Ktedonobacter sp016587355	79.8112	917	3568	d__Bacteria;p__Chloroflexota;c__Ktedonobacteria;o__Ktedonobacterales;f__Ktedonobacteraceae;g__Ktedonobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008326305.1	s__Dictyobacter sp008326305	78.3948	202	3568	d__Bacteria;p__Chloroflexota;c__Ktedonobacteria;o__Ktedonobacterales;f__Ktedonobacteraceae;g__Dictyobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003967535.1	s__Tengunoibacter tsumagoiensis	78.309	197	3568	d__Bacteria;p__Chloroflexota;c__Ktedonobacteria;o__Ktedonobacterales;f__Ktedonobacteraceae;g__Tengunoibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008974265.1	s__Dictyobacter vulcani	77.8395	207	3568	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	77.3948	288	3568	d__Bacteria;p__Chloroflexota;c__Ktedonobacteria;o__Ktedonobacterales;f__Ktedonobacteraceae;g__Dictyobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902810755.1	s__CADDYT01 sp902810755	76.2704	144	3568	d__Bacteria;p__Chloroflexota;c__Ktedonobacteria;o__Ktedonobacterales;f__Ktedonobacteraceae;g__CADDYT01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011389075.1	s__DTNP01 sp011389075	75.9384	125	3568	d__Bacteria;p__Chloroflexota;c__Ktedonobacteria;o__Ktedonobacterales;f__Ktedonobacteraceae;g__DTNP01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:47:55,408] [INFO] GTDB search result was written to GCF_016587375.1_ASM1658737v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:47:55,408] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:47:55,412] [INFO] DFAST_QC result json was written to GCF_016587375.1_ASM1658737v1_genomic.fna/dqc_result.json
[2024-01-24 12:47:55,413] [INFO] DFAST_QC completed!
[2024-01-24 12:47:55,413] [INFO] Total running time: 0h3m11s