[2024-01-25 19:41:35,685] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:41:35,687] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:41:35,687] [INFO] DQC Reference Directory: /var/lib/cwl/stgf1d9b84d-b5f5-4c37-9689-9c526d30f25c/dqc_reference
[2024-01-25 19:41:36,927] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:41:36,928] [INFO] Task started: Prodigal
[2024-01-25 19:41:36,928] [INFO] Running command: gunzip -c /var/lib/cwl/stgc3cdf879-2327-4dee-af34-c01e58b9a517/GCF_000429945.1_ASM42994v1_genomic.fna.gz | prodigal -d GCF_000429945.1_ASM42994v1_genomic.fna/cds.fna -a GCF_000429945.1_ASM42994v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:41:50,454] [INFO] Task succeeded: Prodigal
[2024-01-25 19:41:50,455] [INFO] Task started: HMMsearch
[2024-01-25 19:41:50,455] [INFO] Running command: hmmsearch --tblout GCF_000429945.1_ASM42994v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf1d9b84d-b5f5-4c37-9689-9c526d30f25c/dqc_reference/reference_markers.hmm GCF_000429945.1_ASM42994v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:41:50,855] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:41:50,856] [INFO] Found 6/6 markers.
[2024-01-25 19:41:50,905] [INFO] Query marker FASTA was written to GCF_000429945.1_ASM42994v1_genomic.fna/markers.fasta
[2024-01-25 19:41:50,906] [INFO] Task started: Blastn
[2024-01-25 19:41:50,906] [INFO] Running command: blastn -query GCF_000429945.1_ASM42994v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf1d9b84d-b5f5-4c37-9689-9c526d30f25c/dqc_reference/reference_markers.fasta -out GCF_000429945.1_ASM42994v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:41:51,479] [INFO] Task succeeded: Blastn
[2024-01-25 19:41:51,482] [INFO] Selected 16 target genomes.
[2024-01-25 19:41:51,482] [INFO] Target genome list was writen to GCF_000429945.1_ASM42994v1_genomic.fna/target_genomes.txt
[2024-01-25 19:41:51,490] [INFO] Task started: fastANI
[2024-01-25 19:41:51,490] [INFO] Running command: fastANI --query /var/lib/cwl/stgc3cdf879-2327-4dee-af34-c01e58b9a517/GCF_000429945.1_ASM42994v1_genomic.fna.gz --refList GCF_000429945.1_ASM42994v1_genomic.fna/target_genomes.txt --output GCF_000429945.1_ASM42994v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:42:03,109] [INFO] Task succeeded: fastANI
[2024-01-25 19:42:03,109] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf1d9b84d-b5f5-4c37-9689-9c526d30f25c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:42:03,109] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf1d9b84d-b5f5-4c37-9689-9c526d30f25c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:42:03,114] [INFO] Found 3 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:42:03,114] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:42:03,114] [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
Desulfogranum japonicum	strain=DSM 18378	GCA_000429945.1	231447	231447	type	True	100.0	1871	1878	95	conclusive
Desulfobulbus rhabdoformis	strain=DSM 8777	GCA_016919065.1	34032	34032	type	True	77.1041	96	1878	95	below_threshold
Desulfobulbus propionicus	strain=DSM 2032	GCA_000186885.1	894	894	type	True	76.8373	63	1878	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:42:03,115] [INFO] DFAST Taxonomy check result was written to GCF_000429945.1_ASM42994v1_genomic.fna/tc_result.tsv
[2024-01-25 19:42:03,116] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:42:03,116] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:42:03,116] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf1d9b84d-b5f5-4c37-9689-9c526d30f25c/dqc_reference/checkm_data
[2024-01-25 19:42:03,117] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:42:03,172] [INFO] Task started: CheckM
[2024-01-25 19:42:03,172] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000429945.1_ASM42994v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000429945.1_ASM42994v1_genomic.fna/checkm_input GCF_000429945.1_ASM42994v1_genomic.fna/checkm_result
[2024-01-25 19:42:44,691] [INFO] Task succeeded: CheckM
[2024-01-25 19:42:44,692] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:42:44,709] [INFO] ===== Completeness check finished =====
[2024-01-25 19:42:44,709] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:42:44,709] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000429945.1_ASM42994v1_genomic.fna/markers.fasta)
[2024-01-25 19:42:44,709] [INFO] Task started: Blastn
[2024-01-25 19:42:44,710] [INFO] Running command: blastn -query GCF_000429945.1_ASM42994v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf1d9b84d-b5f5-4c37-9689-9c526d30f25c/dqc_reference/reference_markers_gtdb.fasta -out GCF_000429945.1_ASM42994v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:42:45,463] [INFO] Task succeeded: Blastn
[2024-01-25 19:42:45,466] [INFO] Selected 24 target genomes.
[2024-01-25 19:42:45,466] [INFO] Target genome list was writen to GCF_000429945.1_ASM42994v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:42:45,484] [INFO] Task started: fastANI
[2024-01-25 19:42:45,485] [INFO] Running command: fastANI --query /var/lib/cwl/stgc3cdf879-2327-4dee-af34-c01e58b9a517/GCF_000429945.1_ASM42994v1_genomic.fna.gz --refList GCF_000429945.1_ASM42994v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000429945.1_ASM42994v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:43:00,268] [INFO] Task succeeded: fastANI
[2024-01-25 19:43:00,273] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:43:00,273] [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_000429945.1	s__Desulfobulbus_A japonicus	100.0	1871	1878	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfobulbaceae;g__Desulfobulbus_A	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002748755.1	s__Desulfobulbus_A propionicus_B	77.6209	135	1878	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfobulbaceae;g__Desulfobulbus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016919065.1	s__Desulfobulbus rhabdoformis	77.1041	96	1878	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfobulbaceae;g__Desulfobulbus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000186885.1	s__Desulfobulbus propionicus	76.8373	63	1878	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfobulbaceae;g__Desulfobulbus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015493715.1	s__DRLX01 sp015493715	75.9597	54	1878	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfobulbaceae;g__DRLX01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:43:00,274] [INFO] GTDB search result was written to GCF_000429945.1_ASM42994v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:43:00,275] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:43:00,277] [INFO] DFAST_QC result json was written to GCF_000429945.1_ASM42994v1_genomic.fna/dqc_result.json
[2024-01-25 19:43:00,277] [INFO] DFAST_QC completed!
[2024-01-25 19:43:00,277] [INFO] Total running time: 0h1m25s