[2024-01-24 15:10:19,842] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:10:19,844] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:10:19,844] [INFO] DQC Reference Directory: /var/lib/cwl/stg7201f354-8f64-472d-ae38-14f89e8d6cdb/dqc_reference
[2024-01-24 15:10:22,719] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:10:22,720] [INFO] Task started: Prodigal
[2024-01-24 15:10:22,720] [INFO] Running command: gunzip -c /var/lib/cwl/stg20fa1a5f-f5b2-46d6-95e5-1a4897c9d498/GCF_900141835.1_IMG-taxon_2585428088_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900141835.1_IMG-taxon_2585428088_annotated_assembly_genomic.fna/cds.fna -a GCF_900141835.1_IMG-taxon_2585428088_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:10:32,905] [INFO] Task succeeded: Prodigal
[2024-01-24 15:10:32,906] [INFO] Task started: HMMsearch
[2024-01-24 15:10:32,906] [INFO] Running command: hmmsearch --tblout GCF_900141835.1_IMG-taxon_2585428088_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7201f354-8f64-472d-ae38-14f89e8d6cdb/dqc_reference/reference_markers.hmm GCF_900141835.1_IMG-taxon_2585428088_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:10:33,186] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:10:33,188] [INFO] Found 6/6 markers.
[2024-01-24 15:10:33,231] [INFO] Query marker FASTA was written to GCF_900141835.1_IMG-taxon_2585428088_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 15:10:33,231] [INFO] Task started: Blastn
[2024-01-24 15:10:33,231] [INFO] Running command: blastn -query GCF_900141835.1_IMG-taxon_2585428088_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg7201f354-8f64-472d-ae38-14f89e8d6cdb/dqc_reference/reference_markers.fasta -out GCF_900141835.1_IMG-taxon_2585428088_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:10:33,825] [INFO] Task succeeded: Blastn
[2024-01-24 15:10:33,828] [INFO] Selected 17 target genomes.
[2024-01-24 15:10:33,828] [INFO] Target genome list was writen to GCF_900141835.1_IMG-taxon_2585428088_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 15:10:33,867] [INFO] Task started: fastANI
[2024-01-24 15:10:33,867] [INFO] Running command: fastANI --query /var/lib/cwl/stg20fa1a5f-f5b2-46d6-95e5-1a4897c9d498/GCF_900141835.1_IMG-taxon_2585428088_annotated_assembly_genomic.fna.gz --refList GCF_900141835.1_IMG-taxon_2585428088_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900141835.1_IMG-taxon_2585428088_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:10:44,454] [INFO] Task succeeded: fastANI
[2024-01-24 15:10:44,455] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7201f354-8f64-472d-ae38-14f89e8d6cdb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:10:44,455] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7201f354-8f64-472d-ae38-14f89e8d6cdb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:10:44,460] [INFO] Found 3 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:10:44,460] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:10:44,460] [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
Propionispora hippei	strain=DSM 15287	GCA_900141835.1	209080	209080	type	True	100.0	1341	1346	95	conclusive
Propionispora vibrioides	strain=DSM 13305	GCA_900110485.1	112903	112903	type	True	93.3391	1144	1346	95	below_threshold
Methylomusa anaerophila	strain=MMFC1	GCA_003966895.1	1930071	1930071	type	True	76.7043	64	1346	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:10:44,462] [INFO] DFAST Taxonomy check result was written to GCF_900141835.1_IMG-taxon_2585428088_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 15:10:44,462] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:10:44,463] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:10:44,463] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7201f354-8f64-472d-ae38-14f89e8d6cdb/dqc_reference/checkm_data
[2024-01-24 15:10:44,464] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:10:44,503] [INFO] Task started: CheckM
[2024-01-24 15:10:44,503] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900141835.1_IMG-taxon_2585428088_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900141835.1_IMG-taxon_2585428088_annotated_assembly_genomic.fna/checkm_input GCF_900141835.1_IMG-taxon_2585428088_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 15:11:20,251] [INFO] Task succeeded: CheckM
[2024-01-24 15:11:20,252] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:11:20,272] [INFO] ===== Completeness check finished =====
[2024-01-24 15:11:20,272] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:11:20,272] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900141835.1_IMG-taxon_2585428088_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 15:11:20,273] [INFO] Task started: Blastn
[2024-01-24 15:11:20,273] [INFO] Running command: blastn -query GCF_900141835.1_IMG-taxon_2585428088_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg7201f354-8f64-472d-ae38-14f89e8d6cdb/dqc_reference/reference_markers_gtdb.fasta -out GCF_900141835.1_IMG-taxon_2585428088_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:11:21,190] [INFO] Task succeeded: Blastn
[2024-01-24 15:11:21,194] [INFO] Selected 17 target genomes.
[2024-01-24 15:11:21,194] [INFO] Target genome list was writen to GCF_900141835.1_IMG-taxon_2585428088_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:11:21,230] [INFO] Task started: fastANI
[2024-01-24 15:11:21,230] [INFO] Running command: fastANI --query /var/lib/cwl/stg20fa1a5f-f5b2-46d6-95e5-1a4897c9d498/GCF_900141835.1_IMG-taxon_2585428088_annotated_assembly_genomic.fna.gz --refList GCF_900141835.1_IMG-taxon_2585428088_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900141835.1_IMG-taxon_2585428088_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:11:31,248] [INFO] Task succeeded: fastANI
[2024-01-24 15:11:31,254] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:11:31,255] [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_900141835.1	s__Propionispora hippei	100.0	1341	1346	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Propionisporales;f__Propionisporaceae;g__Propionispora	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900110485.1	s__Propionispora vibrioides	93.3391	1144	1346	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_003990955.1	s__Dendrosporobacter sp003990955	76.9057	83	1346	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__DSM-1736;f__Dendrosporobacteraceae;g__Dendrosporobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCA_002337925.1	s__Anaerospora sp002337925	76.7689	55	1346	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Sporomusales;f__Thermosinaceae;g__Anaerospora	95.0	98.38	98.05	0.87	0.84	4	-
GCF_003966895.1	s__Methylomusa anaerophila	76.7447	64	1346	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Sporomusales;f__Sporomusaceae;g__Methylomusa	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:11:31,256] [INFO] GTDB search result was written to GCF_900141835.1_IMG-taxon_2585428088_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 15:11:31,257] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:11:31,259] [INFO] DFAST_QC result json was written to GCF_900141835.1_IMG-taxon_2585428088_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 15:11:31,260] [INFO] DFAST_QC completed!
[2024-01-24 15:11:31,260] [INFO] Total running time: 0h1m11s