[2024-01-24 13:58:10,648] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:58:10,653] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:58:10,653] [INFO] DQC Reference Directory: /var/lib/cwl/stg70d513e4-7f22-4244-967a-ef5f57fb52cc/dqc_reference
[2024-01-24 13:58:12,172] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:58:12,178] [INFO] Task started: Prodigal
[2024-01-24 13:58:12,179] [INFO] Running command: gunzip -c /var/lib/cwl/stg6e154640-d3cb-43f1-b974-33411a539f01/GCF_005116655.2_ASM511665v2_genomic.fna.gz | prodigal -d GCF_005116655.2_ASM511665v2_genomic.fna/cds.fna -a GCF_005116655.2_ASM511665v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:58:29,944] [INFO] Task succeeded: Prodigal
[2024-01-24 13:58:29,945] [INFO] Task started: HMMsearch
[2024-01-24 13:58:29,945] [INFO] Running command: hmmsearch --tblout GCF_005116655.2_ASM511665v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg70d513e4-7f22-4244-967a-ef5f57fb52cc/dqc_reference/reference_markers.hmm GCF_005116655.2_ASM511665v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:58:30,289] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:58:30,291] [INFO] Found 6/6 markers.
[2024-01-24 13:58:30,346] [INFO] Query marker FASTA was written to GCF_005116655.2_ASM511665v2_genomic.fna/markers.fasta
[2024-01-24 13:58:30,346] [INFO] Task started: Blastn
[2024-01-24 13:58:30,346] [INFO] Running command: blastn -query GCF_005116655.2_ASM511665v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg70d513e4-7f22-4244-967a-ef5f57fb52cc/dqc_reference/reference_markers.fasta -out GCF_005116655.2_ASM511665v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:30,937] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:30,941] [INFO] Selected 20 target genomes.
[2024-01-24 13:58:30,941] [INFO] Target genome list was writen to GCF_005116655.2_ASM511665v2_genomic.fna/target_genomes.txt
[2024-01-24 13:58:30,952] [INFO] Task started: fastANI
[2024-01-24 13:58:30,953] [INFO] Running command: fastANI --query /var/lib/cwl/stg6e154640-d3cb-43f1-b974-33411a539f01/GCF_005116655.2_ASM511665v2_genomic.fna.gz --refList GCF_005116655.2_ASM511665v2_genomic.fna/target_genomes.txt --output GCF_005116655.2_ASM511665v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:58:46,415] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:46,416] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg70d513e4-7f22-4244-967a-ef5f57fb52cc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:58:46,416] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg70d513e4-7f22-4244-967a-ef5f57fb52cc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:58:46,422] [INFO] Found 5 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:58:46,423] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:58:46,423] [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
Desulfosediminicola flagellatus	strain=IMCC35005	GCA_005116655.2	2569541	2569541	type	True	100.0	2250	2250	95	conclusive
Desulfotalea psychrophila	strain=LSv54	GCA_000025945.1	84980	84980	type	True	79.2346	66	2250	95	below_threshold
Desulfosediminicola ganghwensis	strain=IMCC35004	GCA_005116675.2	2569540	2569540	type	True	78.5202	241	2250	95	below_threshold
Desulfomarina profundi	strain=KT2	GCA_019703855.1	2772557	2772557	type	True	77.9063	87	2250	95	below_threshold
Desulfopila aestuarii	strain=DSM 18488	GCA_900143695.1	231440	231440	type	True	77.639	187	2250	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:58:46,424] [INFO] DFAST Taxonomy check result was written to GCF_005116655.2_ASM511665v2_genomic.fna/tc_result.tsv
[2024-01-24 13:58:46,425] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:58:46,425] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:58:46,425] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg70d513e4-7f22-4244-967a-ef5f57fb52cc/dqc_reference/checkm_data
[2024-01-24 13:58:46,426] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:58:46,497] [INFO] Task started: CheckM
[2024-01-24 13:58:46,497] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_005116655.2_ASM511665v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_005116655.2_ASM511665v2_genomic.fna/checkm_input GCF_005116655.2_ASM511665v2_genomic.fna/checkm_result
[2024-01-24 13:59:39,400] [INFO] Task succeeded: CheckM
[2024-01-24 13:59:39,402] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:59:39,424] [INFO] ===== Completeness check finished =====
[2024-01-24 13:59:39,425] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:59:39,425] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_005116655.2_ASM511665v2_genomic.fna/markers.fasta)
[2024-01-24 13:59:39,426] [INFO] Task started: Blastn
[2024-01-24 13:59:39,426] [INFO] Running command: blastn -query GCF_005116655.2_ASM511665v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg70d513e4-7f22-4244-967a-ef5f57fb52cc/dqc_reference/reference_markers_gtdb.fasta -out GCF_005116655.2_ASM511665v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:59:40,184] [INFO] Task succeeded: Blastn
[2024-01-24 13:59:40,188] [INFO] Selected 26 target genomes.
[2024-01-24 13:59:40,188] [INFO] Target genome list was writen to GCF_005116655.2_ASM511665v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:59:40,256] [INFO] Task started: fastANI
[2024-01-24 13:59:40,257] [INFO] Running command: fastANI --query /var/lib/cwl/stg6e154640-d3cb-43f1-b974-33411a539f01/GCF_005116655.2_ASM511665v2_genomic.fna.gz --refList GCF_005116655.2_ASM511665v2_genomic.fna/target_genomes_gtdb.txt --output GCF_005116655.2_ASM511665v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:00:00,397] [INFO] Task succeeded: fastANI
[2024-01-24 14:00:00,404] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:00:00,405] [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_005116655.2	s__Desulfopila sp005116655	100.0	2249	2250	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfocapsaceae;g__Desulfopila	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000025945.1	s__Desulfotalea psychrophila	79.0791	64	2250	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfocapsaceae;g__Desulfotalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005116675.2	s__Desulfopila sp005116675	78.5087	241	2250	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfocapsaceae;g__Desulfopila	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010646885.1	s__Desulfopila sp010646885	77.9795	169	2250	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfocapsaceae;g__Desulfopila	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900143695.1	s__Desulfopila aestuarii	77.6454	188	2250	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfocapsaceae;g__Desulfopila	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018820855.1	s__Desulfocapsa sp018820855	76.2501	51	2250	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfocapsaceae;g__Desulfocapsa	95.0	99.68	99.21	0.96	0.95	4	-
--------------------------------------------------------------------------------
[2024-01-24 14:00:00,406] [INFO] GTDB search result was written to GCF_005116655.2_ASM511665v2_genomic.fna/result_gtdb.tsv
[2024-01-24 14:00:00,407] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:00:00,410] [INFO] DFAST_QC result json was written to GCF_005116655.2_ASM511665v2_genomic.fna/dqc_result.json
[2024-01-24 14:00:00,410] [INFO] DFAST_QC completed!
[2024-01-24 14:00:00,410] [INFO] Total running time: 0h1m50s