[2024-01-24 11:51:07,572] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:51:07,574] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:51:07,574] [INFO] DQC Reference Directory: /var/lib/cwl/stgd06f3f24-4dfc-48ae-99d3-8c592cf41442/dqc_reference
[2024-01-24 11:51:08,766] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:51:08,767] [INFO] Task started: Prodigal
[2024-01-24 11:51:08,767] [INFO] Running command: gunzip -c /var/lib/cwl/stg3705795c-61fc-4e0e-a081-442cfc3d6355/GCF_000803025.1_Alipo1.0_genomic.fna.gz | prodigal -d GCF_000803025.1_Alipo1.0_genomic.fna/cds.fna -a GCF_000803025.1_Alipo1.0_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:51:15,378] [INFO] Task succeeded: Prodigal
[2024-01-24 11:51:15,379] [INFO] Task started: HMMsearch
[2024-01-24 11:51:15,379] [INFO] Running command: hmmsearch --tblout GCF_000803025.1_Alipo1.0_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd06f3f24-4dfc-48ae-99d3-8c592cf41442/dqc_reference/reference_markers.hmm GCF_000803025.1_Alipo1.0_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:51:15,628] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:51:15,641] [INFO] Found 6/6 markers.
[2024-01-24 11:51:15,664] [INFO] Query marker FASTA was written to GCF_000803025.1_Alipo1.0_genomic.fna/markers.fasta
[2024-01-24 11:51:15,665] [INFO] Task started: Blastn
[2024-01-24 11:51:15,665] [INFO] Running command: blastn -query GCF_000803025.1_Alipo1.0_genomic.fna/markers.fasta -db /var/lib/cwl/stgd06f3f24-4dfc-48ae-99d3-8c592cf41442/dqc_reference/reference_markers.fasta -out GCF_000803025.1_Alipo1.0_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:51:16,222] [INFO] Task succeeded: Blastn
[2024-01-24 11:51:16,225] [INFO] Selected 17 target genomes.
[2024-01-24 11:51:16,226] [INFO] Target genome list was writen to GCF_000803025.1_Alipo1.0_genomic.fna/target_genomes.txt
[2024-01-24 11:51:16,243] [INFO] Task started: fastANI
[2024-01-24 11:51:16,243] [INFO] Running command: fastANI --query /var/lib/cwl/stg3705795c-61fc-4e0e-a081-442cfc3d6355/GCF_000803025.1_Alipo1.0_genomic.fna.gz --refList GCF_000803025.1_Alipo1.0_genomic.fna/target_genomes.txt --output GCF_000803025.1_Alipo1.0_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:51:27,956] [INFO] Task succeeded: fastANI
[2024-01-24 11:51:27,956] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd06f3f24-4dfc-48ae-99d3-8c592cf41442/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:51:27,957] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd06f3f24-4dfc-48ae-99d3-8c592cf41442/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:51:27,961] [INFO] Found 1 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:51:27,961] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:51:27,961] [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
Anaerovibrio lipolyticus	strain=DSM 3074	GCA_900141865.1	82374	82374	type	True	98.5403	733	822	95	conclusive
--------------------------------------------------------------------------------
[2024-01-24 11:51:27,963] [INFO] DFAST Taxonomy check result was written to GCF_000803025.1_Alipo1.0_genomic.fna/tc_result.tsv
[2024-01-24 11:51:27,963] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:51:27,963] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:51:27,964] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd06f3f24-4dfc-48ae-99d3-8c592cf41442/dqc_reference/checkm_data
[2024-01-24 11:51:27,965] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:51:27,994] [INFO] Task started: CheckM
[2024-01-24 11:51:27,995] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000803025.1_Alipo1.0_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000803025.1_Alipo1.0_genomic.fna/checkm_input GCF_000803025.1_Alipo1.0_genomic.fna/checkm_result
[2024-01-24 11:51:54,357] [INFO] Task succeeded: CheckM
[2024-01-24 11:51:54,358] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 6.71%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:51:54,380] [INFO] ===== Completeness check finished =====
[2024-01-24 11:51:54,381] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:51:54,381] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000803025.1_Alipo1.0_genomic.fna/markers.fasta)
[2024-01-24 11:51:54,381] [INFO] Task started: Blastn
[2024-01-24 11:51:54,381] [INFO] Running command: blastn -query GCF_000803025.1_Alipo1.0_genomic.fna/markers.fasta -db /var/lib/cwl/stgd06f3f24-4dfc-48ae-99d3-8c592cf41442/dqc_reference/reference_markers_gtdb.fasta -out GCF_000803025.1_Alipo1.0_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:51:55,209] [INFO] Task succeeded: Blastn
[2024-01-24 11:51:55,213] [INFO] Selected 6 target genomes.
[2024-01-24 11:51:55,213] [INFO] Target genome list was writen to GCF_000803025.1_Alipo1.0_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:51:55,218] [INFO] Task started: fastANI
[2024-01-24 11:51:55,218] [INFO] Running command: fastANI --query /var/lib/cwl/stg3705795c-61fc-4e0e-a081-442cfc3d6355/GCF_000803025.1_Alipo1.0_genomic.fna.gz --refList GCF_000803025.1_Alipo1.0_genomic.fna/target_genomes_gtdb.txt --output GCF_000803025.1_Alipo1.0_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:51:59,042] [INFO] Task succeeded: fastANI
[2024-01-24 11:51:59,049] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:51:59,049] [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_900141865.1	s__Anaerovibrio lipolyticus	98.5605	732	822	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Anaerovibrio	95.0	97.47	96.05	0.87	0.83	4	conclusive
GCF_000621545.1	s__Anaerovibrio lipolyticus_A	94.6744	635	822	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Anaerovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002372665.1	s__Anaerovibrio lipolyticus_C	94.2028	508	822	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Anaerovibrio	95.0	97.79	96.86	0.90	0.86	3	-
GCF_000622005.1	s__Anaerovibrio sp000622005	86.1279	581	822	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Anaerovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002100115.1	s__Anaerovibrio sp002100115	83.8454	524	822	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Anaerovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902785445.1	s__Anaerovibrio sp902785445	79.6984	234	822	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Anaerovibrio	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:51:59,051] [INFO] GTDB search result was written to GCF_000803025.1_Alipo1.0_genomic.fna/result_gtdb.tsv
[2024-01-24 11:51:59,051] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:51:59,054] [INFO] DFAST_QC result json was written to GCF_000803025.1_Alipo1.0_genomic.fna/dqc_result.json
[2024-01-24 11:51:59,054] [INFO] DFAST_QC completed!
[2024-01-24 11:51:59,054] [INFO] Total running time: 0h0m51s