[2024-01-24 13:45:45,727] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:45:45,730] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:45:45,731] [INFO] DQC Reference Directory: /var/lib/cwl/stg1ab8bccb-bbd9-4caf-8848-f4ca35e88054/dqc_reference
[2024-01-24 13:45:47,096] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:45:47,100] [INFO] Task started: Prodigal
[2024-01-24 13:45:47,100] [INFO] Running command: gunzip -c /var/lib/cwl/stgb174d032-f248-4ddd-94a1-a7bdb2a819c8/GCF_000159415.1_ASM15941v1_genomic.fna.gz | prodigal -d GCF_000159415.1_ASM15941v1_genomic.fna/cds.fna -a GCF_000159415.1_ASM15941v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:45:51,858] [INFO] Task succeeded: Prodigal
[2024-01-24 13:45:51,859] [INFO] Task started: HMMsearch
[2024-01-24 13:45:51,859] [INFO] Running command: hmmsearch --tblout GCF_000159415.1_ASM15941v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1ab8bccb-bbd9-4caf-8848-f4ca35e88054/dqc_reference/reference_markers.hmm GCF_000159415.1_ASM15941v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:45:52,164] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:45:52,165] [INFO] Found 6/6 markers.
[2024-01-24 13:45:52,193] [INFO] Query marker FASTA was written to GCF_000159415.1_ASM15941v1_genomic.fna/markers.fasta
[2024-01-24 13:45:52,193] [INFO] Task started: Blastn
[2024-01-24 13:45:52,193] [INFO] Running command: blastn -query GCF_000159415.1_ASM15941v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1ab8bccb-bbd9-4caf-8848-f4ca35e88054/dqc_reference/reference_markers.fasta -out GCF_000159415.1_ASM15941v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:45:52,791] [INFO] Task succeeded: Blastn
[2024-01-24 13:45:52,795] [INFO] Selected 15 target genomes.
[2024-01-24 13:45:52,795] [INFO] Target genome list was writen to GCF_000159415.1_ASM15941v1_genomic.fna/target_genomes.txt
[2024-01-24 13:45:52,853] [INFO] Task started: fastANI
[2024-01-24 13:45:52,853] [INFO] Running command: fastANI --query /var/lib/cwl/stgb174d032-f248-4ddd-94a1-a7bdb2a819c8/GCF_000159415.1_ASM15941v1_genomic.fna.gz --refList GCF_000159415.1_ASM15941v1_genomic.fna/target_genomes.txt --output GCF_000159415.1_ASM15941v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:45:58,904] [INFO] Task succeeded: fastANI
[2024-01-24 13:45:58,905] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1ab8bccb-bbd9-4caf-8848-f4ca35e88054/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:45:58,905] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1ab8bccb-bbd9-4caf-8848-f4ca35e88054/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:45:58,917] [INFO] Found 14 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:45:58,918] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:45:58,918] [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
Lactobacillus ultunensis	strain=DSM 16047	GCA_000159415.1	227945	227945	type	True	99.9996	722	737	95	conclusive
Lactobacillus ultunensis	strain=DSM 16047	GCA_001436305.1	227945	227945	type	True	99.9136	674	737	95	conclusive
Lactobacillus amylovorus	strain=DSM 20531	GCA_002706375.1	1604	1604	type	True	83.6426	439	737	95	below_threshold
Lactobacillus kitasatonis	strain=DSM 16761	GCA_001434435.1	237446	237446	type	True	83.5992	415	737	95	below_threshold
Lactobacillus amylovorus	strain=DSM 20531	GCA_001433985.1	1604	1604	type	True	83.5075	413	737	95	below_threshold
Lactobacillus kitasatonis	strain=JCM 1039	GCA_000615285.1	237446	237446	type	True	83.4664	420	737	95	below_threshold
Lactobacillus helveticus	strain=CGMCC 1.1877	GCA_001434945.1	1587	1587	type	True	83.3181	334	737	95	below_threshold
Lactobacillus helveticus	strain=JCM 1120	GCA_015698225.1	1587	1587	type	True	83.1685	361	737	95	below_threshold
Lactobacillus helveticus	strain=DSM 20075	GCA_000160855.1	1587	1587	type	True	83.0122	411	737	95	below_threshold
Lactobacillus gallinarum	strain=DSM 10532	GCA_001434975.1	52242	52242	type	True	82.6684	413	737	95	below_threshold
Lactobacillus intestinalis	strain=DSM 6629	GCA_024397795.1	151781	151781	type	True	79.9619	252	737	95	below_threshold
Lactobacillus laiwuensis	strain=F551-2	GCA_019972835.1	2841034	2841034	type	True	77.4971	120	737	95	below_threshold
Lactobacillus huangpiensis	strain=F306-1	GCA_019972815.1	2799571	2799571	type	True	77.4883	112	737	95	below_threshold
Companilactobacillus kimchii	strain=DSM 13961	GCA_009764365.1	2801452	2801452	type	True	76.3265	53	737	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:45:58,919] [INFO] DFAST Taxonomy check result was written to GCF_000159415.1_ASM15941v1_genomic.fna/tc_result.tsv
[2024-01-24 13:45:58,920] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:45:58,920] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:45:58,920] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1ab8bccb-bbd9-4caf-8848-f4ca35e88054/dqc_reference/checkm_data
[2024-01-24 13:45:58,921] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:45:58,953] [INFO] Task started: CheckM
[2024-01-24 13:45:58,953] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000159415.1_ASM15941v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000159415.1_ASM15941v1_genomic.fna/checkm_input GCF_000159415.1_ASM15941v1_genomic.fna/checkm_result
[2024-01-24 13:46:20,883] [INFO] Task succeeded: CheckM
[2024-01-24 13:46:20,885] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:46:20,904] [INFO] ===== Completeness check finished =====
[2024-01-24 13:46:20,904] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:46:20,904] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000159415.1_ASM15941v1_genomic.fna/markers.fasta)
[2024-01-24 13:46:20,905] [INFO] Task started: Blastn
[2024-01-24 13:46:20,905] [INFO] Running command: blastn -query GCF_000159415.1_ASM15941v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1ab8bccb-bbd9-4caf-8848-f4ca35e88054/dqc_reference/reference_markers_gtdb.fasta -out GCF_000159415.1_ASM15941v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:46:21,696] [INFO] Task succeeded: Blastn
[2024-01-24 13:46:21,699] [INFO] Selected 7 target genomes.
[2024-01-24 13:46:21,700] [INFO] Target genome list was writen to GCF_000159415.1_ASM15941v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:46:21,715] [INFO] Task started: fastANI
[2024-01-24 13:46:21,715] [INFO] Running command: fastANI --query /var/lib/cwl/stgb174d032-f248-4ddd-94a1-a7bdb2a819c8/GCF_000159415.1_ASM15941v1_genomic.fna.gz --refList GCF_000159415.1_ASM15941v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000159415.1_ASM15941v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:46:25,172] [INFO] Task succeeded: fastANI
[2024-01-24 13:46:25,182] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:46:25,183] [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_001436305.1	s__Lactobacillus ultunensis	99.9136	674	737	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	99.98	99.95	0.99	0.98	4	conclusive
GCF_002706375.1	s__Lactobacillus amylovorus	83.6309	439	737	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	97.43	96.81	0.87	0.78	24	-
GCF_000615285.1	s__Lactobacillus kitasatonis	83.4323	422	737	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	98.87	97.76	0.93	0.87	3	-
GCF_000160855.1	s__Lactobacillus helveticus	83.0523	409	737	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	98.35	96.37	0.85	0.75	146	-
GCF_001434975.1	s__Lactobacillus gallinarum	82.6684	413	737	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	98.30	97.84	0.88	0.84	17	-
GCF_001591845.1	s__Lactobacillus acidophilus	82.2808	398	737	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	99.96	99.12	0.99	0.94	59	-
GCF_900103655.1	s__Lactobacillus kefiranofaciens	81.8732	403	737	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	99.62	99.18	0.95	0.85	9	-
--------------------------------------------------------------------------------
[2024-01-24 13:46:25,184] [INFO] GTDB search result was written to GCF_000159415.1_ASM15941v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:46:25,186] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:46:25,200] [INFO] DFAST_QC result json was written to GCF_000159415.1_ASM15941v1_genomic.fna/dqc_result.json
[2024-01-24 13:46:25,201] [INFO] DFAST_QC completed!
[2024-01-24 13:46:25,201] [INFO] Total running time: 0h0m39s