[2023-06-28 16:00:56,872] [INFO] DFAST_QC pipeline started.
[2023-06-28 16:00:56,874] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 16:00:56,874] [INFO] DQC Reference Directory: /var/lib/cwl/stgccd8065b-8d4b-4739-b2e5-97f37dea8a00/dqc_reference
[2023-06-28 16:00:58,126] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 16:00:58,127] [INFO] Task started: Prodigal
[2023-06-28 16:00:58,127] [INFO] Running command: gunzip -c /var/lib/cwl/stge6e7bd7c-3271-457a-8406-a50f2ff0d625/GCA_019310765.1_ASM1931076v1_genomic.fna.gz | prodigal -d GCA_019310765.1_ASM1931076v1_genomic.fna/cds.fna -a GCA_019310765.1_ASM1931076v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 16:01:07,398] [INFO] Task succeeded: Prodigal
[2023-06-28 16:01:07,399] [INFO] Task started: HMMsearch
[2023-06-28 16:01:07,399] [INFO] Running command: hmmsearch --tblout GCA_019310765.1_ASM1931076v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgccd8065b-8d4b-4739-b2e5-97f37dea8a00/dqc_reference/reference_markers.hmm GCA_019310765.1_ASM1931076v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 16:01:07,628] [INFO] Task succeeded: HMMsearch
[2023-06-28 16:01:07,630] [INFO] Found 6/6 markers.
[2023-06-28 16:01:07,665] [INFO] Query marker FASTA was written to GCA_019310765.1_ASM1931076v1_genomic.fna/markers.fasta
[2023-06-28 16:01:07,665] [INFO] Task started: Blastn
[2023-06-28 16:01:07,666] [INFO] Running command: blastn -query GCA_019310765.1_ASM1931076v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgccd8065b-8d4b-4739-b2e5-97f37dea8a00/dqc_reference/reference_markers.fasta -out GCA_019310765.1_ASM1931076v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 16:01:08,262] [INFO] Task succeeded: Blastn
[2023-06-28 16:01:08,266] [INFO] Selected 19 target genomes.
[2023-06-28 16:01:08,266] [INFO] Target genome list was writen to GCA_019310765.1_ASM1931076v1_genomic.fna/target_genomes.txt
[2023-06-28 16:01:08,267] [INFO] Task started: fastANI
[2023-06-28 16:01:08,267] [INFO] Running command: fastANI --query /var/lib/cwl/stge6e7bd7c-3271-457a-8406-a50f2ff0d625/GCA_019310765.1_ASM1931076v1_genomic.fna.gz --refList GCA_019310765.1_ASM1931076v1_genomic.fna/target_genomes.txt --output GCA_019310765.1_ASM1931076v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 16:01:19,102] [INFO] Task succeeded: fastANI
[2023-06-28 16:01:19,102] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgccd8065b-8d4b-4739-b2e5-97f37dea8a00/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 16:01:19,103] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgccd8065b-8d4b-4739-b2e5-97f37dea8a00/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 16:01:19,106] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 16:01:19,106] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 16:01:19,106] [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
Desulfatiglans anilini	strain=DSM 4660	GCA_000422285.1	90728	90728	type	True	75.4833	61	1196	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 16:01:19,108] [INFO] DFAST Taxonomy check result was written to GCA_019310765.1_ASM1931076v1_genomic.fna/tc_result.tsv
[2023-06-28 16:01:19,108] [INFO] ===== Taxonomy check completed =====
[2023-06-28 16:01:19,108] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 16:01:19,109] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgccd8065b-8d4b-4739-b2e5-97f37dea8a00/dqc_reference/checkm_data
[2023-06-28 16:01:19,109] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 16:01:19,147] [INFO] Task started: CheckM
[2023-06-28 16:01:19,147] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_019310765.1_ASM1931076v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_019310765.1_ASM1931076v1_genomic.fna/checkm_input GCA_019310765.1_ASM1931076v1_genomic.fna/checkm_result
[2023-06-28 16:01:50,758] [INFO] Task succeeded: CheckM
[2023-06-28 16:01:50,759] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 16:01:50,778] [INFO] ===== Completeness check finished =====
[2023-06-28 16:01:50,778] [INFO] ===== Start GTDB Search =====
[2023-06-28 16:01:50,779] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_019310765.1_ASM1931076v1_genomic.fna/markers.fasta)
[2023-06-28 16:01:50,779] [INFO] Task started: Blastn
[2023-06-28 16:01:50,779] [INFO] Running command: blastn -query GCA_019310765.1_ASM1931076v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgccd8065b-8d4b-4739-b2e5-97f37dea8a00/dqc_reference/reference_markers_gtdb.fasta -out GCA_019310765.1_ASM1931076v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 16:01:51,781] [INFO] Task succeeded: Blastn
[2023-06-28 16:01:51,785] [INFO] Selected 23 target genomes.
[2023-06-28 16:01:51,785] [INFO] Target genome list was writen to GCA_019310765.1_ASM1931076v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 16:01:51,787] [INFO] Task started: fastANI
[2023-06-28 16:01:51,787] [INFO] Running command: fastANI --query /var/lib/cwl/stge6e7bd7c-3271-457a-8406-a50f2ff0d625/GCA_019310765.1_ASM1931076v1_genomic.fna.gz --refList GCA_019310765.1_ASM1931076v1_genomic.fna/target_genomes_gtdb.txt --output GCA_019310765.1_ASM1931076v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 16:02:07,256] [INFO] Task succeeded: fastANI
[2023-06-28 16:02:07,269] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 16:02:07,269] [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_011051075.1	s__Desulfacyla sp011051075	98.9807	725	1196	d__Bacteria;p__Desulfobacterota;c__DSM-4660;o__Desulfatiglandales;f__Desulfatiglandaceae;g__Desulfacyla	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_014382715.1	s__Desulfacyla euxinica	77.7668	279	1196	d__Bacteria;p__Desulfobacterota;c__DSM-4660;o__Desulfatiglandales;f__Desulfatiglandaceae;g__Desulfacyla	95.0	99.00	98.56	0.73	0.65	3	-
GCA_014382905.1	s__Desulfacyla sp014382905	77.3947	201	1196	d__Bacteria;p__Desulfobacterota;c__DSM-4660;o__Desulfatiglandales;f__Desulfatiglandaceae;g__Desulfacyla	95.0	98.82	98.20	0.84	0.79	5	-
GCA_016783065.1	s__JABMQV01 sp016783065	77.2113	90	1196	d__Bacteria;p__Desulfobacterota;c__DSM-4660;o__Desulfatiglandales;f__Desulfatiglandaceae;g__JABMQV01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016844935.1	s__NaphS2 sp016844935	76.7033	111	1196	d__Bacteria;p__Desulfobacterota;c__DSM-4660;o__Desulfatiglandales;f__Desulfatiglandaceae;g__NaphS2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013203065.1	s__JABMQV01 sp013203065	76.4938	52	1196	d__Bacteria;p__Desulfobacterota;c__DSM-4660;o__Desulfatiglandales;f__Desulfatiglandaceae;g__JABMQV01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013349725.1	s__DUZB01 sp013349725	76.4497	68	1196	d__Bacteria;p__Desulfobacterota;c__DSM-4660;o__Desulfatiglandales;f__Desulfatiglandaceae;g__DUZB01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000179315.1	s__NaphS2 sp000179315	76.4261	78	1196	d__Bacteria;p__Desulfobacterota;c__DSM-4660;o__Desulfatiglandales;f__Desulfatiglandaceae;g__NaphS2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900498135.1	s__Desulfatiglans sp900498135	75.8791	60	1196	d__Bacteria;p__Desulfobacterota;c__DSM-4660;o__Desulfatiglandales;f__Desulfatiglandaceae;g__Desulfatiglans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000422285.1	s__Desulfatiglans anilini	75.5017	60	1196	d__Bacteria;p__Desulfobacterota;c__DSM-4660;o__Desulfatiglandales;f__Desulfatiglandaceae;g__Desulfatiglans	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 16:02:07,271] [INFO] GTDB search result was written to GCA_019310765.1_ASM1931076v1_genomic.fna/result_gtdb.tsv
[2023-06-28 16:02:07,272] [INFO] ===== GTDB Search completed =====
[2023-06-28 16:02:07,274] [INFO] DFAST_QC result json was written to GCA_019310765.1_ASM1931076v1_genomic.fna/dqc_result.json
[2023-06-28 16:02:07,275] [INFO] DFAST_QC completed!
[2023-06-28 16:02:07,275] [INFO] Total running time: 0h1m10s