[2023-06-29 08:44:33,308] [INFO] DFAST_QC pipeline started.
[2023-06-29 08:44:33,320] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 08:44:33,320] [INFO] DQC Reference Directory: /var/lib/cwl/stge7faf48c-b142-4692-ad1d-3ca53403e67e/dqc_reference
[2023-06-29 08:44:34,583] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 08:44:34,584] [INFO] Task started: Prodigal
[2023-06-29 08:44:34,585] [INFO] Running command: gunzip -c /var/lib/cwl/stg0ce0abfa-1103-4667-b56d-4dce2390b22a/GCA_020052765.1_ASM2005276v1_genomic.fna.gz | prodigal -d GCA_020052765.1_ASM2005276v1_genomic.fna/cds.fna -a GCA_020052765.1_ASM2005276v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 08:44:39,495] [INFO] Task succeeded: Prodigal
[2023-06-29 08:44:39,495] [INFO] Task started: HMMsearch
[2023-06-29 08:44:39,495] [INFO] Running command: hmmsearch --tblout GCA_020052765.1_ASM2005276v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge7faf48c-b142-4692-ad1d-3ca53403e67e/dqc_reference/reference_markers.hmm GCA_020052765.1_ASM2005276v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 08:44:39,716] [INFO] Task succeeded: HMMsearch
[2023-06-29 08:44:39,717] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg0ce0abfa-1103-4667-b56d-4dce2390b22a/GCA_020052765.1_ASM2005276v1_genomic.fna.gz]
[2023-06-29 08:44:39,750] [INFO] Query marker FASTA was written to GCA_020052765.1_ASM2005276v1_genomic.fna/markers.fasta
[2023-06-29 08:44:39,750] [INFO] Task started: Blastn
[2023-06-29 08:44:39,750] [INFO] Running command: blastn -query GCA_020052765.1_ASM2005276v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge7faf48c-b142-4692-ad1d-3ca53403e67e/dqc_reference/reference_markers.fasta -out GCA_020052765.1_ASM2005276v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 08:44:40,268] [INFO] Task succeeded: Blastn
[2023-06-29 08:44:40,271] [INFO] Selected 12 target genomes.
[2023-06-29 08:44:40,272] [INFO] Target genome list was writen to GCA_020052765.1_ASM2005276v1_genomic.fna/target_genomes.txt
[2023-06-29 08:44:40,276] [INFO] Task started: fastANI
[2023-06-29 08:44:40,276] [INFO] Running command: fastANI --query /var/lib/cwl/stg0ce0abfa-1103-4667-b56d-4dce2390b22a/GCA_020052765.1_ASM2005276v1_genomic.fna.gz --refList GCA_020052765.1_ASM2005276v1_genomic.fna/target_genomes.txt --output GCA_020052765.1_ASM2005276v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 08:44:47,571] [INFO] Task succeeded: fastANI
[2023-06-29 08:44:47,571] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge7faf48c-b142-4692-ad1d-3ca53403e67e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 08:44:47,571] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge7faf48c-b142-4692-ad1d-3ca53403e67e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 08:44:47,579] [INFO] Found 4 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 08:44:47,580] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 08:44:47,580] [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
Desulfobulbus elongatus	strain=DSM 2908	GCA_000621145.1	53332	53332	type	True	77.8002	102	547	95	below_threshold
Desulfobulbus propionicus	strain=DSM 2032	GCA_000186885.1	894	894	type	True	77.6167	88	547	95	below_threshold
Desulfurivibrio alkaliphilus	strain=AHT 2	GCA_000092205.1	427923	427923	type	True	77.2037	64	547	95	below_threshold
Desulfogranum mediterraneum	strain=DSM 13871	GCA_000429965.1	160661	160661	type	True	76.5966	80	547	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 08:44:47,586] [INFO] DFAST Taxonomy check result was written to GCA_020052765.1_ASM2005276v1_genomic.fna/tc_result.tsv
[2023-06-29 08:44:47,587] [INFO] ===== Taxonomy check completed =====
[2023-06-29 08:44:47,587] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 08:44:47,587] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge7faf48c-b142-4692-ad1d-3ca53403e67e/dqc_reference/checkm_data
[2023-06-29 08:44:47,588] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 08:44:47,617] [INFO] Task started: CheckM
[2023-06-29 08:44:47,617] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_020052765.1_ASM2005276v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_020052765.1_ASM2005276v1_genomic.fna/checkm_input GCA_020052765.1_ASM2005276v1_genomic.fna/checkm_result
[2023-06-29 08:45:08,625] [INFO] Task succeeded: CheckM
[2023-06-29 08:45:08,627] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 51.04%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 08:45:08,646] [INFO] ===== Completeness check finished =====
[2023-06-29 08:45:08,647] [INFO] ===== Start GTDB Search =====
[2023-06-29 08:45:08,647] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_020052765.1_ASM2005276v1_genomic.fna/markers.fasta)
[2023-06-29 08:45:08,648] [INFO] Task started: Blastn
[2023-06-29 08:45:08,648] [INFO] Running command: blastn -query GCA_020052765.1_ASM2005276v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge7faf48c-b142-4692-ad1d-3ca53403e67e/dqc_reference/reference_markers_gtdb.fasta -out GCA_020052765.1_ASM2005276v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 08:45:09,242] [INFO] Task succeeded: Blastn
[2023-06-29 08:45:09,246] [INFO] Selected 10 target genomes.
[2023-06-29 08:45:09,247] [INFO] Target genome list was writen to GCA_020052765.1_ASM2005276v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 08:45:09,257] [INFO] Task started: fastANI
[2023-06-29 08:45:09,257] [INFO] Running command: fastANI --query /var/lib/cwl/stg0ce0abfa-1103-4667-b56d-4dce2390b22a/GCA_020052765.1_ASM2005276v1_genomic.fna.gz --refList GCA_020052765.1_ASM2005276v1_genomic.fna/target_genomes_gtdb.txt --output GCA_020052765.1_ASM2005276v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 08:45:14,496] [INFO] Task succeeded: fastANI
[2023-06-29 08:45:14,507] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 08:45:14,508] [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
GCA_003508005.1	s__UBA10518 sp003508005	85.2727	292	547	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfobulbaceae;g__UBA10518	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003604995.1	s__UBA10518 sp003604995	82.6766	216	547	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfobulbaceae;g__UBA10518	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011372855.1	s__UBA10518 sp011372855	78.5392	135	547	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfobulbaceae;g__UBA10518	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015484845.1	s__DRKI01 sp015484845	78.4063	133	547	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfobulbaceae;g__DRKI01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017998195.1	s__Desulfobulbus sp017998195	77.9496	96	547	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfobulbaceae;g__Desulfobulbus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002897615.1	s__BMS3Abin13 sp002897615	77.178	108	547	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfobulbaceae;g__BMS3Abin13	95.0	97.72	95.88	0.93	0.92	3	-
--------------------------------------------------------------------------------
[2023-06-29 08:45:14,510] [INFO] GTDB search result was written to GCA_020052765.1_ASM2005276v1_genomic.fna/result_gtdb.tsv
[2023-06-29 08:45:14,511] [INFO] ===== GTDB Search completed =====
[2023-06-29 08:45:14,514] [INFO] DFAST_QC result json was written to GCA_020052765.1_ASM2005276v1_genomic.fna/dqc_result.json
[2023-06-29 08:45:14,514] [INFO] DFAST_QC completed!
[2023-06-29 08:45:14,514] [INFO] Total running time: 0h0m41s