[2023-06-29 22:57:55,151] [INFO] DFAST_QC pipeline started.
[2023-06-29 22:57:55,153] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 22:57:55,153] [INFO] DQC Reference Directory: /var/lib/cwl/stgbe69c392-6e78-4ccb-a4bb-995399baf6a7/dqc_reference
[2023-06-29 22:57:56,343] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 22:57:56,344] [INFO] Task started: Prodigal
[2023-06-29 22:57:56,344] [INFO] Running command: gunzip -c /var/lib/cwl/stgfcb8a44a-25ad-455f-9b9b-6cedc8a8f979/GCA_016219175.1_ASM1621917v1_genomic.fna.gz | prodigal -d GCA_016219175.1_ASM1621917v1_genomic.fna/cds.fna -a GCA_016219175.1_ASM1621917v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 22:58:07,906] [INFO] Task succeeded: Prodigal
[2023-06-29 22:58:07,906] [INFO] Task started: HMMsearch
[2023-06-29 22:58:07,906] [INFO] Running command: hmmsearch --tblout GCA_016219175.1_ASM1621917v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbe69c392-6e78-4ccb-a4bb-995399baf6a7/dqc_reference/reference_markers.hmm GCA_016219175.1_ASM1621917v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 22:58:08,192] [INFO] Task succeeded: HMMsearch
[2023-06-29 22:58:08,193] [INFO] Found 6/6 markers.
[2023-06-29 22:58:08,231] [INFO] Query marker FASTA was written to GCA_016219175.1_ASM1621917v1_genomic.fna/markers.fasta
[2023-06-29 22:58:08,231] [INFO] Task started: Blastn
[2023-06-29 22:58:08,231] [INFO] Running command: blastn -query GCA_016219175.1_ASM1621917v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbe69c392-6e78-4ccb-a4bb-995399baf6a7/dqc_reference/reference_markers.fasta -out GCA_016219175.1_ASM1621917v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 22:58:08,794] [INFO] Task succeeded: Blastn
[2023-06-29 22:58:08,799] [INFO] Selected 20 target genomes.
[2023-06-29 22:58:08,800] [INFO] Target genome list was writen to GCA_016219175.1_ASM1621917v1_genomic.fna/target_genomes.txt
[2023-06-29 22:58:08,803] [INFO] Task started: fastANI
[2023-06-29 22:58:08,803] [INFO] Running command: fastANI --query /var/lib/cwl/stgfcb8a44a-25ad-455f-9b9b-6cedc8a8f979/GCA_016219175.1_ASM1621917v1_genomic.fna.gz --refList GCA_016219175.1_ASM1621917v1_genomic.fna/target_genomes.txt --output GCA_016219175.1_ASM1621917v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 22:58:20,987] [INFO] Task succeeded: fastANI
[2023-06-29 22:58:20,988] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbe69c392-6e78-4ccb-a4bb-995399baf6a7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 22:58:20,989] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbe69c392-6e78-4ccb-a4bb-995399baf6a7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 22:58:20,996] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 22:58:20,996] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 22:58:20,996] [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
Desulfurivibrio alkaliphilus	strain=AHT 2	GCA_000092205.1	427923	427923	type	True	76.118	92	1354	95	below_threshold
Desulfogranum mediterraneum	strain=DSM 13871	GCA_000429965.1	160661	160661	type	True	75.6313	77	1354	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 22:58:20,999] [INFO] DFAST Taxonomy check result was written to GCA_016219175.1_ASM1621917v1_genomic.fna/tc_result.tsv
[2023-06-29 22:58:20,999] [INFO] ===== Taxonomy check completed =====
[2023-06-29 22:58:21,000] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 22:58:21,000] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbe69c392-6e78-4ccb-a4bb-995399baf6a7/dqc_reference/checkm_data
[2023-06-29 22:58:21,001] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 22:58:21,045] [INFO] Task started: CheckM
[2023-06-29 22:58:21,045] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_016219175.1_ASM1621917v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_016219175.1_ASM1621917v1_genomic.fna/checkm_input GCA_016219175.1_ASM1621917v1_genomic.fna/checkm_result
[2023-06-29 22:58:58,815] [INFO] Task succeeded: CheckM
[2023-06-29 22:58:58,817] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.95%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 22:58:58,840] [INFO] ===== Completeness check finished =====
[2023-06-29 22:58:58,840] [INFO] ===== Start GTDB Search =====
[2023-06-29 22:58:58,841] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_016219175.1_ASM1621917v1_genomic.fna/markers.fasta)
[2023-06-29 22:58:58,841] [INFO] Task started: Blastn
[2023-06-29 22:58:58,841] [INFO] Running command: blastn -query GCA_016219175.1_ASM1621917v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbe69c392-6e78-4ccb-a4bb-995399baf6a7/dqc_reference/reference_markers_gtdb.fasta -out GCA_016219175.1_ASM1621917v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 22:58:59,650] [INFO] Task succeeded: Blastn
[2023-06-29 22:58:59,655] [INFO] Selected 13 target genomes.
[2023-06-29 22:58:59,655] [INFO] Target genome list was writen to GCA_016219175.1_ASM1621917v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 22:58:59,695] [INFO] Task started: fastANI
[2023-06-29 22:58:59,696] [INFO] Running command: fastANI --query /var/lib/cwl/stgfcb8a44a-25ad-455f-9b9b-6cedc8a8f979/GCA_016219175.1_ASM1621917v1_genomic.fna.gz --refList GCA_016219175.1_ASM1621917v1_genomic.fna/target_genomes_gtdb.txt --output GCA_016219175.1_ASM1621917v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 22:59:09,464] [INFO] Task succeeded: fastANI
[2023-06-29 22:59:09,480] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 22:59:09,480] [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_016219175.1	s__SURF-16 sp016219175	100.0	1352	1354	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfurivibrionaceae;g__SURF-16	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_016208225.1	s__SURF-16 sp016208225	80.368	523	1354	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfurivibrionaceae;g__SURF-16	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003605035.1	s__SURF-16 sp003605035	79.784	616	1354	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfurivibrionaceae;g__SURF-16	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018897105.1	s__SURF-16 sp018897105	79.745	601	1354	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfurivibrionaceae;g__SURF-16	95.0	99.97	99.97	0.95	0.95	2	-
GCA_018816555.1	s__SURF-16 sp018816555	79.4786	597	1354	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfurivibrionaceae;g__SURF-16	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001914235.1	s__DB1 sp001914235	78.4582	405	1354	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfurivibrionaceae;g__DB1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009773475.1	s__UBA2270 sp009773475	76.3906	77	1354	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfocapsaceae;g__UBA2270	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001799225.1	s__XYD12-FULL-50-9 sp001799225	76.1024	70	1354	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfurivibrionaceae;g__XYD12-FULL-50-9	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 22:59:09,482] [INFO] GTDB search result was written to GCA_016219175.1_ASM1621917v1_genomic.fna/result_gtdb.tsv
[2023-06-29 22:59:09,483] [INFO] ===== GTDB Search completed =====
[2023-06-29 22:59:09,486] [INFO] DFAST_QC result json was written to GCA_016219175.1_ASM1621917v1_genomic.fna/dqc_result.json
[2023-06-29 22:59:09,486] [INFO] DFAST_QC completed!
[2023-06-29 22:59:09,486] [INFO] Total running time: 0h1m14s