[2024-01-25 18:12:20,522] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:12:20,523] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:12:20,523] [INFO] DQC Reference Directory: /var/lib/cwl/stg09c87d45-5d09-45a1-a8ee-1362513485a1/dqc_reference
[2024-01-25 18:12:21,737] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:12:21,738] [INFO] Task started: Prodigal
[2024-01-25 18:12:21,739] [INFO] Running command: gunzip -c /var/lib/cwl/stge0f2d178-470a-476a-ae43-c5c433b6385d/GCF_000271485.2_Pelosinus_fermentans_DSM_17108_v1.1_genomic.fna.gz | prodigal -d GCF_000271485.2_Pelosinus_fermentans_DSM_17108_v1.1_genomic.fna/cds.fna -a GCF_000271485.2_Pelosinus_fermentans_DSM_17108_v1.1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:12:31,430] [INFO] Task succeeded: Prodigal
[2024-01-25 18:12:31,431] [INFO] Task started: HMMsearch
[2024-01-25 18:12:31,431] [INFO] Running command: hmmsearch --tblout GCF_000271485.2_Pelosinus_fermentans_DSM_17108_v1.1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg09c87d45-5d09-45a1-a8ee-1362513485a1/dqc_reference/reference_markers.hmm GCF_000271485.2_Pelosinus_fermentans_DSM_17108_v1.1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:12:31,683] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:12:31,684] [INFO] Found 6/6 markers.
[2024-01-25 18:12:31,723] [INFO] Query marker FASTA was written to GCF_000271485.2_Pelosinus_fermentans_DSM_17108_v1.1_genomic.fna/markers.fasta
[2024-01-25 18:12:31,724] [INFO] Task started: Blastn
[2024-01-25 18:12:31,724] [INFO] Running command: blastn -query GCF_000271485.2_Pelosinus_fermentans_DSM_17108_v1.1_genomic.fna/markers.fasta -db /var/lib/cwl/stg09c87d45-5d09-45a1-a8ee-1362513485a1/dqc_reference/reference_markers.fasta -out GCF_000271485.2_Pelosinus_fermentans_DSM_17108_v1.1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:12:32,254] [INFO] Task succeeded: Blastn
[2024-01-25 18:12:32,257] [INFO] Selected 13 target genomes.
[2024-01-25 18:12:32,257] [INFO] Target genome list was writen to GCF_000271485.2_Pelosinus_fermentans_DSM_17108_v1.1_genomic.fna/target_genomes.txt
[2024-01-25 18:12:32,295] [INFO] Task started: fastANI
[2024-01-25 18:12:32,295] [INFO] Running command: fastANI --query /var/lib/cwl/stge0f2d178-470a-476a-ae43-c5c433b6385d/GCF_000271485.2_Pelosinus_fermentans_DSM_17108_v1.1_genomic.fna.gz --refList GCF_000271485.2_Pelosinus_fermentans_DSM_17108_v1.1_genomic.fna/target_genomes.txt --output GCF_000271485.2_Pelosinus_fermentans_DSM_17108_v1.1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:12:42,168] [INFO] Task succeeded: fastANI
[2024-01-25 18:12:42,168] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg09c87d45-5d09-45a1-a8ee-1362513485a1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:12:42,168] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg09c87d45-5d09-45a1-a8ee-1362513485a1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:12:42,173] [INFO] Found 3 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:12:42,173] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:12:42,173] [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
Pelosinus fermentans	strain=R7	GCA_000271485.2	365349	365349	type	True	100.0	1674	1675	95	conclusive
Pelosinus propionicus	strain=DSM 13327	GCA_900114615.1	380084	380084	type	True	88.6034	1227	1675	95	below_threshold
Massilibacillus massiliensis	strain=Marseille-P2411	GCA_900086705.1	1806837	1806837	type	True	77.9254	94	1675	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:12:42,174] [INFO] DFAST Taxonomy check result was written to GCF_000271485.2_Pelosinus_fermentans_DSM_17108_v1.1_genomic.fna/tc_result.tsv
[2024-01-25 18:12:42,174] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:12:42,175] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:12:42,175] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg09c87d45-5d09-45a1-a8ee-1362513485a1/dqc_reference/checkm_data
[2024-01-25 18:12:42,176] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:12:42,237] [INFO] Task started: CheckM
[2024-01-25 18:12:42,237] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000271485.2_Pelosinus_fermentans_DSM_17108_v1.1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000271485.2_Pelosinus_fermentans_DSM_17108_v1.1_genomic.fna/checkm_input GCF_000271485.2_Pelosinus_fermentans_DSM_17108_v1.1_genomic.fna/checkm_result
[2024-01-25 18:13:15,141] [INFO] Task succeeded: CheckM
[2024-01-25 18:13:15,142] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:13:15,159] [INFO] ===== Completeness check finished =====
[2024-01-25 18:13:15,159] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:13:15,160] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000271485.2_Pelosinus_fermentans_DSM_17108_v1.1_genomic.fna/markers.fasta)
[2024-01-25 18:13:15,160] [INFO] Task started: Blastn
[2024-01-25 18:13:15,160] [INFO] Running command: blastn -query GCF_000271485.2_Pelosinus_fermentans_DSM_17108_v1.1_genomic.fna/markers.fasta -db /var/lib/cwl/stg09c87d45-5d09-45a1-a8ee-1362513485a1/dqc_reference/reference_markers_gtdb.fasta -out GCF_000271485.2_Pelosinus_fermentans_DSM_17108_v1.1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:13:15,891] [INFO] Task succeeded: Blastn
[2024-01-25 18:13:15,894] [INFO] Selected 6 target genomes.
[2024-01-25 18:13:15,895] [INFO] Target genome list was writen to GCF_000271485.2_Pelosinus_fermentans_DSM_17108_v1.1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:13:15,903] [INFO] Task started: fastANI
[2024-01-25 18:13:15,903] [INFO] Running command: fastANI --query /var/lib/cwl/stge0f2d178-470a-476a-ae43-c5c433b6385d/GCF_000271485.2_Pelosinus_fermentans_DSM_17108_v1.1_genomic.fna.gz --refList GCF_000271485.2_Pelosinus_fermentans_DSM_17108_v1.1_genomic.fna/target_genomes_gtdb.txt --output GCF_000271485.2_Pelosinus_fermentans_DSM_17108_v1.1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:13:23,856] [INFO] Task succeeded: fastANI
[2024-01-25 18:13:23,862] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:13:23,862] [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_000271485.2	s__Pelosinus fermentans	100.0	1673	1675	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Propionisporales;f__Propionisporaceae;g__Pelosinus	95.0	99.65	99.40	0.97	0.95	5	conclusive
GCA_002434245.1	s__Pelosinus fermentans_B	94.6259	1178	1675	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Propionisporales;f__Propionisporaceae;g__Pelosinus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000271665.2	s__Pelosinus fermentans_A	93.4751	1325	1675	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Propionisporales;f__Propionisporaceae;g__Pelosinus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114615.1	s__Pelosinus propionicus	88.601	1227	1675	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Propionisporales;f__Propionisporaceae;g__Pelosinus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000725345.1	s__Pelosinus sp000725345	80.1958	619	1675	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Propionisporales;f__Propionisporaceae;g__Pelosinus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017889585.1	s__CTSoil-075 sp017889585	77.8459	296	1675	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Propionisporales;f__Propionisporaceae;g__CTSoil-075	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:13:23,864] [INFO] GTDB search result was written to GCF_000271485.2_Pelosinus_fermentans_DSM_17108_v1.1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:13:23,864] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:13:23,866] [INFO] DFAST_QC result json was written to GCF_000271485.2_Pelosinus_fermentans_DSM_17108_v1.1_genomic.fna/dqc_result.json
[2024-01-25 18:13:23,867] [INFO] DFAST_QC completed!
[2024-01-25 18:13:23,867] [INFO] Total running time: 0h1m3s