[2024-01-24 15:10:48,602] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:10:48,607] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:10:48,607] [INFO] DQC Reference Directory: /var/lib/cwl/stg199d88e3-ad7e-4b7e-8f0e-c8e3618261a9/dqc_reference
[2024-01-24 15:10:49,963] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:10:49,964] [INFO] Task started: Prodigal
[2024-01-24 15:10:49,965] [INFO] Running command: gunzip -c /var/lib/cwl/stgf1735e01-90da-4539-9579-70061001bf6e/GCF_900101845.1_IMG-taxon_2622736588_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900101845.1_IMG-taxon_2622736588_annotated_assembly_genomic.fna/cds.fna -a GCF_900101845.1_IMG-taxon_2622736588_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:11:04,912] [INFO] Task succeeded: Prodigal
[2024-01-24 15:11:04,913] [INFO] Task started: HMMsearch
[2024-01-24 15:11:04,913] [INFO] Running command: hmmsearch --tblout GCF_900101845.1_IMG-taxon_2622736588_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg199d88e3-ad7e-4b7e-8f0e-c8e3618261a9/dqc_reference/reference_markers.hmm GCF_900101845.1_IMG-taxon_2622736588_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:11:05,314] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:11:05,315] [INFO] Found 6/6 markers.
[2024-01-24 15:11:05,369] [INFO] Query marker FASTA was written to GCF_900101845.1_IMG-taxon_2622736588_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 15:11:05,370] [INFO] Task started: Blastn
[2024-01-24 15:11:05,370] [INFO] Running command: blastn -query GCF_900101845.1_IMG-taxon_2622736588_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg199d88e3-ad7e-4b7e-8f0e-c8e3618261a9/dqc_reference/reference_markers.fasta -out GCF_900101845.1_IMG-taxon_2622736588_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:11:06,032] [INFO] Task succeeded: Blastn
[2024-01-24 15:11:06,035] [INFO] Selected 7 target genomes.
[2024-01-24 15:11:06,036] [INFO] Target genome list was writen to GCF_900101845.1_IMG-taxon_2622736588_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 15:11:06,039] [INFO] Task started: fastANI
[2024-01-24 15:11:06,039] [INFO] Running command: fastANI --query /var/lib/cwl/stgf1735e01-90da-4539-9579-70061001bf6e/GCF_900101845.1_IMG-taxon_2622736588_annotated_assembly_genomic.fna.gz --refList GCF_900101845.1_IMG-taxon_2622736588_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900101845.1_IMG-taxon_2622736588_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:11:14,473] [INFO] Task succeeded: fastANI
[2024-01-24 15:11:14,473] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg199d88e3-ad7e-4b7e-8f0e-c8e3618261a9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:11:14,474] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg199d88e3-ad7e-4b7e-8f0e-c8e3618261a9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:11:14,485] [INFO] Found 7 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 15:11:14,485] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:11:14,485] [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
Sporomusa acidovorans	strain=Mol	GCA_900101845.1	112900	112900	type	True	100.0	1930	1937	95	conclusive
Sporomusa acidovorans	strain=DSM 3132	GCA_002257695.1	112900	112900	type	True	99.9789	1895	1937	95	conclusive
Sporomusa ovata	strain=DSM 2662	GCA_000445445.1	2378	2378	type	True	79.4305	603	1937	95	below_threshold
Sporomusa ovata	strain=DSM 2662	GCA_000423685.1	2378	2378	type	True	79.3732	604	1937	95	below_threshold
Sporomusa silvacetica	strain=DSM 10669	GCA_002257705.1	55504	55504	type	True	79.1124	612	1937	95	below_threshold
Sporomusa termitida	strain=DSM 4440	GCA_007641255.1	2377	2377	type	True	77.8243	309	1937	95	below_threshold
Propionispora vibrioides	strain=DSM 13305	GCA_900110485.1	112903	112903	type	True	76.5741	75	1937	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:11:14,490] [INFO] DFAST Taxonomy check result was written to GCF_900101845.1_IMG-taxon_2622736588_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 15:11:14,490] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:11:14,491] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:11:14,491] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg199d88e3-ad7e-4b7e-8f0e-c8e3618261a9/dqc_reference/checkm_data
[2024-01-24 15:11:14,493] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:11:14,566] [INFO] Task started: CheckM
[2024-01-24 15:11:14,567] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900101845.1_IMG-taxon_2622736588_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900101845.1_IMG-taxon_2622736588_annotated_assembly_genomic.fna/checkm_input GCF_900101845.1_IMG-taxon_2622736588_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 15:12:00,242] [INFO] Task succeeded: CheckM
[2024-01-24 15:12:00,243] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:12:00,267] [INFO] ===== Completeness check finished =====
[2024-01-24 15:12:00,268] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:12:00,268] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900101845.1_IMG-taxon_2622736588_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 15:12:00,269] [INFO] Task started: Blastn
[2024-01-24 15:12:00,269] [INFO] Running command: blastn -query GCF_900101845.1_IMG-taxon_2622736588_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg199d88e3-ad7e-4b7e-8f0e-c8e3618261a9/dqc_reference/reference_markers_gtdb.fasta -out GCF_900101845.1_IMG-taxon_2622736588_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:12:01,088] [INFO] Task succeeded: Blastn
[2024-01-24 15:12:01,091] [INFO] Selected 13 target genomes.
[2024-01-24 15:12:01,091] [INFO] Target genome list was writen to GCF_900101845.1_IMG-taxon_2622736588_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:12:01,104] [INFO] Task started: fastANI
[2024-01-24 15:12:01,105] [INFO] Running command: fastANI --query /var/lib/cwl/stgf1735e01-90da-4539-9579-70061001bf6e/GCF_900101845.1_IMG-taxon_2622736588_annotated_assembly_genomic.fna.gz --refList GCF_900101845.1_IMG-taxon_2622736588_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900101845.1_IMG-taxon_2622736588_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:12:12,414] [INFO] Task succeeded: fastANI
[2024-01-24 15:12:12,425] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:12:12,425] [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_900101845.1	s__Sporomusa acidovorans	100.0	1930	1937	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Sporomusales;f__Sporomusaceae;g__Sporomusa	95.0	99.98	99.98	0.98	0.98	2	conclusive
GCF_000445445.1	s__Sporomusa ovata	79.4247	606	1937	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Sporomusales;f__Sporomusaceae;g__Sporomusa	95.0	99.96	99.93	1.00	0.99	3	-
GCF_007830295.1	s__Sporomusa sp007830295	79.4102	625	1937	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Sporomusales;f__Sporomusaceae;g__Sporomusa	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002257705.1	s__Sporomusa silvacetica	79.1254	611	1937	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Sporomusales;f__Sporomusaceae;g__Sporomusa	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017889675.1	s__Sporomusa sp017889675	78.7048	326	1937	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Sporomusales;f__Sporomusaceae;g__Sporomusa	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017889705.1	s__Sporomusa sp017889705	78.0249	405	1937	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Sporomusales;f__Sporomusaceae;g__Sporomusa	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007641255.1	s__Sporomusa termitida	77.8033	311	1937	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Sporomusales;f__Sporomusaceae;g__Sporomusa	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900476375.1	s__Lucifera butyrica	77.1692	117	1937	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Sporomusales;f__UPPP01;g__Lucifera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018835585.1	s__Pelorhabdus rhamnosifermentans	77.0613	84	1937	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__UMGS1260;f__UMGS1260;g__Pelorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110485.1	s__Propionispora vibrioides	76.5741	75	1937	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Propionisporales;f__Propionisporaceae;g__Propionispora	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017889625.1	s__CTSoil-081 sp017889625	76.471	52	1937	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Sporomusales;f__UBA7701;g__CTSoil-081	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:12:12,427] [INFO] GTDB search result was written to GCF_900101845.1_IMG-taxon_2622736588_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 15:12:12,428] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:12:12,433] [INFO] DFAST_QC result json was written to GCF_900101845.1_IMG-taxon_2622736588_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 15:12:12,433] [INFO] DFAST_QC completed!
[2024-01-24 15:12:12,433] [INFO] Total running time: 0h1m24s