[2024-01-25 19:32:36,137] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:32:36,138] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:32:36,139] [INFO] DQC Reference Directory: /var/lib/cwl/stgabd85f69-c905-4024-ac5c-604208c362c5/dqc_reference
[2024-01-25 19:32:37,241] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:32:37,242] [INFO] Task started: Prodigal
[2024-01-25 19:32:37,242] [INFO] Running command: gunzip -c /var/lib/cwl/stg8c9e3a5a-81a2-4270-a23d-83b7e0d5a913/GCF_002257705.1_ASM225770v1_genomic.fna.gz | prodigal -d GCF_002257705.1_ASM225770v1_genomic.fna/cds.fna -a GCF_002257705.1_ASM225770v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:32:48,813] [INFO] Task succeeded: Prodigal
[2024-01-25 19:32:48,813] [INFO] Task started: HMMsearch
[2024-01-25 19:32:48,813] [INFO] Running command: hmmsearch --tblout GCF_002257705.1_ASM225770v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgabd85f69-c905-4024-ac5c-604208c362c5/dqc_reference/reference_markers.hmm GCF_002257705.1_ASM225770v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:32:49,129] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:32:49,130] [INFO] Found 6/6 markers.
[2024-01-25 19:32:49,179] [INFO] Query marker FASTA was written to GCF_002257705.1_ASM225770v1_genomic.fna/markers.fasta
[2024-01-25 19:32:49,179] [INFO] Task started: Blastn
[2024-01-25 19:32:49,180] [INFO] Running command: blastn -query GCF_002257705.1_ASM225770v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgabd85f69-c905-4024-ac5c-604208c362c5/dqc_reference/reference_markers.fasta -out GCF_002257705.1_ASM225770v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:32:49,720] [INFO] Task succeeded: Blastn
[2024-01-25 19:32:49,723] [INFO] Selected 10 target genomes.
[2024-01-25 19:32:49,724] [INFO] Target genome list was writen to GCF_002257705.1_ASM225770v1_genomic.fna/target_genomes.txt
[2024-01-25 19:32:49,730] [INFO] Task started: fastANI
[2024-01-25 19:32:49,730] [INFO] Running command: fastANI --query /var/lib/cwl/stg8c9e3a5a-81a2-4270-a23d-83b7e0d5a913/GCF_002257705.1_ASM225770v1_genomic.fna.gz --refList GCF_002257705.1_ASM225770v1_genomic.fna/target_genomes.txt --output GCF_002257705.1_ASM225770v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:33:00,688] [INFO] Task succeeded: fastANI
[2024-01-25 19:33:00,689] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgabd85f69-c905-4024-ac5c-604208c362c5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:33:00,689] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgabd85f69-c905-4024-ac5c-604208c362c5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:33:00,696] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:33:00,696] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:33:00,696] [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 silvacetica	strain=DSM 10669	GCA_002257705.1	55504	55504	type	True	100.0	1891	1901	95	conclusive
Sporomusa ovata	strain=DSM 2662	GCA_000445445.1	2378	2378	type	True	91.1514	1105	1901	95	below_threshold
Sporomusa ovata	strain=DSM 2662	GCA_000423685.1	2378	2378	type	True	91.084	1081	1901	95	below_threshold
Sporomusa malonica	strain=DSM 5090	GCA_900176355.1	112901	112901	type	True	79.3278	539	1901	95	below_threshold
Sporomusa acidovorans	strain=Mol	GCA_900101845.1	112900	112900	type	True	79.1692	609	1901	95	below_threshold
Sporomusa acidovorans	strain=DSM 3132	GCA_002257695.1	112900	112900	type	True	79.1417	605	1901	95	below_threshold
Sporomusa sphaeroides	strain=DSM 2875	GCA_001941975.1	47679	47679	type	True	78.4697	427	1901	95	below_threshold
Sporomusa sphaeroides	strain=DSM 2875	GCA_023660125.1	47679	47679	type	True	78.412	409	1901	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:33:00,697] [INFO] DFAST Taxonomy check result was written to GCF_002257705.1_ASM225770v1_genomic.fna/tc_result.tsv
[2024-01-25 19:33:00,698] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:33:00,698] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:33:00,698] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgabd85f69-c905-4024-ac5c-604208c362c5/dqc_reference/checkm_data
[2024-01-25 19:33:00,699] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:33:00,756] [INFO] Task started: CheckM
[2024-01-25 19:33:00,756] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002257705.1_ASM225770v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002257705.1_ASM225770v1_genomic.fna/checkm_input GCF_002257705.1_ASM225770v1_genomic.fna/checkm_result
[2024-01-25 19:33:37,299] [INFO] Task succeeded: CheckM
[2024-01-25 19:33:37,301] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 8.33%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:33:37,324] [INFO] ===== Completeness check finished =====
[2024-01-25 19:33:37,324] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:33:37,326] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002257705.1_ASM225770v1_genomic.fna/markers.fasta)
[2024-01-25 19:33:37,326] [INFO] Task started: Blastn
[2024-01-25 19:33:37,326] [INFO] Running command: blastn -query GCF_002257705.1_ASM225770v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgabd85f69-c905-4024-ac5c-604208c362c5/dqc_reference/reference_markers_gtdb.fasta -out GCF_002257705.1_ASM225770v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:33:38,046] [INFO] Task succeeded: Blastn
[2024-01-25 19:33:38,049] [INFO] Selected 8 target genomes.
[2024-01-25 19:33:38,049] [INFO] Target genome list was writen to GCF_002257705.1_ASM225770v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:33:38,053] [INFO] Task started: fastANI
[2024-01-25 19:33:38,053] [INFO] Running command: fastANI --query /var/lib/cwl/stg8c9e3a5a-81a2-4270-a23d-83b7e0d5a913/GCF_002257705.1_ASM225770v1_genomic.fna.gz --refList GCF_002257705.1_ASM225770v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002257705.1_ASM225770v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:33:48,150] [INFO] Task succeeded: fastANI
[2024-01-25 19:33:48,156] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:33:48,156] [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_002257705.1	s__Sporomusa silvacetica	100.0	1891	1901	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Sporomusales;f__Sporomusaceae;g__Sporomusa	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_007830295.1	s__Sporomusa sp007830295	92.5303	1322	1901	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_000445445.1	s__Sporomusa ovata	91.1655	1103	1901	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Sporomusales;f__Sporomusaceae;g__Sporomusa	95.0	99.96	99.93	1.00	0.99	3	-
GCA_017889675.1	s__Sporomusa sp017889675	85.9769	509	1901	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	79.5789	598	1901	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	79.3243	536	1901	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	79.1518	612	1901	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Sporomusales;f__Sporomusaceae;g__Sporomusa	95.0	99.98	99.98	0.98	0.98	2	-
GCF_001941975.1	s__Sporomusa sphaeroides	78.4722	423	1901	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Sporomusales;f__Sporomusaceae;g__Sporomusa	95.0	98.27	97.38	0.92	0.86	4	-
--------------------------------------------------------------------------------
[2024-01-25 19:33:48,158] [INFO] GTDB search result was written to GCF_002257705.1_ASM225770v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:33:48,159] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:33:48,161] [INFO] DFAST_QC result json was written to GCF_002257705.1_ASM225770v1_genomic.fna/dqc_result.json
[2024-01-25 19:33:48,161] [INFO] DFAST_QC completed!
[2024-01-25 19:33:48,161] [INFO] Total running time: 0h1m12s