[2024-01-25 20:03:05,732] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:03:05,734] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:03:05,734] [INFO] DQC Reference Directory: /var/lib/cwl/stg1978759d-9eb4-49ef-b5e1-eedc9af490a2/dqc_reference
[2024-01-25 20:03:06,871] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:03:06,872] [INFO] Task started: Prodigal
[2024-01-25 20:03:06,872] [INFO] Running command: gunzip -c /var/lib/cwl/stg92d03fa9-ac1c-4679-b4d4-15064a2ca9c9/GCF_000423685.1_ASM42368v1_genomic.fna.gz | prodigal -d GCF_000423685.1_ASM42368v1_genomic.fna/cds.fna -a GCF_000423685.1_ASM42368v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:03:17,137] [INFO] Task succeeded: Prodigal
[2024-01-25 20:03:17,137] [INFO] Task started: HMMsearch
[2024-01-25 20:03:17,137] [INFO] Running command: hmmsearch --tblout GCF_000423685.1_ASM42368v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1978759d-9eb4-49ef-b5e1-eedc9af490a2/dqc_reference/reference_markers.hmm GCF_000423685.1_ASM42368v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:03:17,410] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:03:17,411] [INFO] Found 6/6 markers.
[2024-01-25 20:03:17,453] [INFO] Query marker FASTA was written to GCF_000423685.1_ASM42368v1_genomic.fna/markers.fasta
[2024-01-25 20:03:17,454] [INFO] Task started: Blastn
[2024-01-25 20:03:17,454] [INFO] Running command: blastn -query GCF_000423685.1_ASM42368v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1978759d-9eb4-49ef-b5e1-eedc9af490a2/dqc_reference/reference_markers.fasta -out GCF_000423685.1_ASM42368v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:03:17,982] [INFO] Task succeeded: Blastn
[2024-01-25 20:03:17,985] [INFO] Selected 7 target genomes.
[2024-01-25 20:03:17,985] [INFO] Target genome list was writen to GCF_000423685.1_ASM42368v1_genomic.fna/target_genomes.txt
[2024-01-25 20:03:17,991] [INFO] Task started: fastANI
[2024-01-25 20:03:17,991] [INFO] Running command: fastANI --query /var/lib/cwl/stg92d03fa9-ac1c-4679-b4d4-15064a2ca9c9/GCF_000423685.1_ASM42368v1_genomic.fna.gz --refList GCF_000423685.1_ASM42368v1_genomic.fna/target_genomes.txt --output GCF_000423685.1_ASM42368v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:03:27,104] [INFO] Task succeeded: fastANI
[2024-01-25 20:03:27,104] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1978759d-9eb4-49ef-b5e1-eedc9af490a2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:03:27,105] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1978759d-9eb4-49ef-b5e1-eedc9af490a2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:03:27,111] [INFO] Found 7 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 20:03:27,112] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:03:27,112] [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 ovata	strain=DSM 2662	GCA_000423685.1	2378	2378	type	True	100.0	1676	1683	95	conclusive
Sporomusa ovata	strain=DSM 2662	GCA_000445445.1	2378	2378	type	True	99.9905	1682	1683	95	conclusive
Sporomusa silvacetica	strain=DSM 10669	GCA_002257705.1	55504	55504	type	True	91.278	1085	1683	95	below_threshold
Sporomusa acidovorans	strain=Mol	GCA_900101845.1	112900	112900	type	True	79.5149	586	1683	95	below_threshold
Sporomusa acidovorans	strain=DSM 3132	GCA_002257695.1	112900	112900	type	True	79.4587	591	1683	95	below_threshold
Sporomusa malonica	strain=DSM 5090	GCA_900176355.1	112901	112901	type	True	79.0209	439	1683	95	below_threshold
Sporomusa sphaeroides	strain=DSM 2875	GCA_023660125.1	47679	47679	type	True	78.7664	408	1683	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:03:27,113] [INFO] DFAST Taxonomy check result was written to GCF_000423685.1_ASM42368v1_genomic.fna/tc_result.tsv
[2024-01-25 20:03:27,114] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:03:27,114] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:03:27,114] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1978759d-9eb4-49ef-b5e1-eedc9af490a2/dqc_reference/checkm_data
[2024-01-25 20:03:27,115] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:03:27,165] [INFO] Task started: CheckM
[2024-01-25 20:03:27,166] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000423685.1_ASM42368v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000423685.1_ASM42368v1_genomic.fna/checkm_input GCF_000423685.1_ASM42368v1_genomic.fna/checkm_result
[2024-01-25 20:04:00,301] [INFO] Task succeeded: CheckM
[2024-01-25 20:04:00,302] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:04:00,326] [INFO] ===== Completeness check finished =====
[2024-01-25 20:04:00,326] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:04:00,326] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000423685.1_ASM42368v1_genomic.fna/markers.fasta)
[2024-01-25 20:04:00,327] [INFO] Task started: Blastn
[2024-01-25 20:04:00,327] [INFO] Running command: blastn -query GCF_000423685.1_ASM42368v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1978759d-9eb4-49ef-b5e1-eedc9af490a2/dqc_reference/reference_markers_gtdb.fasta -out GCF_000423685.1_ASM42368v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:04:01,089] [INFO] Task succeeded: Blastn
[2024-01-25 20:04:01,092] [INFO] Selected 7 target genomes.
[2024-01-25 20:04:01,092] [INFO] Target genome list was writen to GCF_000423685.1_ASM42368v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:04:01,103] [INFO] Task started: fastANI
[2024-01-25 20:04:01,103] [INFO] Running command: fastANI --query /var/lib/cwl/stg92d03fa9-ac1c-4679-b4d4-15064a2ca9c9/GCF_000423685.1_ASM42368v1_genomic.fna.gz --refList GCF_000423685.1_ASM42368v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000423685.1_ASM42368v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:04:09,728] [INFO] Task succeeded: fastANI
[2024-01-25 20:04:09,734] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:04:09,734] [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_000445445.1	s__Sporomusa ovata	99.9905	1682	1683	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Sporomusales;f__Sporomusaceae;g__Sporomusa	95.0	99.96	99.93	1.00	0.99	3	conclusive
GCF_007830295.1	s__Sporomusa sp007830295	91.959	1165	1683	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	91.2125	1090	1683	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	84.6026	490	1683	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_900101845.1	s__Sporomusa acidovorans	79.528	583	1683	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Sporomusales;f__Sporomusaceae;g__Sporomusa	95.0	99.98	99.98	0.98	0.98	2	-
GCA_017889705.1	s__Sporomusa sp017889705	79.3025	507	1683	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_900176355.1	s__Sporomusa malonica	79.0148	439	1683	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Sporomusales;f__Sporomusaceae;g__Sporomusa	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:04:09,735] [INFO] GTDB search result was written to GCF_000423685.1_ASM42368v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:04:09,736] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:04:09,738] [INFO] DFAST_QC result json was written to GCF_000423685.1_ASM42368v1_genomic.fna/dqc_result.json
[2024-01-25 20:04:09,738] [INFO] DFAST_QC completed!
[2024-01-25 20:04:09,738] [INFO] Total running time: 0h1m4s