[2023-06-28 10:15:52,550] [INFO] DFAST_QC pipeline started.
[2023-06-28 10:15:52,630] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 10:15:52,630] [INFO] DQC Reference Directory: /var/lib/cwl/stg70793f4f-eacf-403a-8bca-2c1b26222b23/dqc_reference
[2023-06-28 10:15:53,886] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 10:15:53,887] [INFO] Task started: Prodigal
[2023-06-28 10:15:53,888] [INFO] Running command: gunzip -c /var/lib/cwl/stg07f00a9c-f048-44df-bbd1-944f4b9a604f/GCA_019310845.1_ASM1931084v1_genomic.fna.gz | prodigal -d GCA_019310845.1_ASM1931084v1_genomic.fna/cds.fna -a GCA_019310845.1_ASM1931084v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 10:15:58,508] [INFO] Task succeeded: Prodigal
[2023-06-28 10:15:58,509] [INFO] Task started: HMMsearch
[2023-06-28 10:15:58,509] [INFO] Running command: hmmsearch --tblout GCA_019310845.1_ASM1931084v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg70793f4f-eacf-403a-8bca-2c1b26222b23/dqc_reference/reference_markers.hmm GCA_019310845.1_ASM1931084v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 10:15:58,732] [INFO] Task succeeded: HMMsearch
[2023-06-28 10:15:58,733] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg07f00a9c-f048-44df-bbd1-944f4b9a604f/GCA_019310845.1_ASM1931084v1_genomic.fna.gz]
[2023-06-28 10:15:58,784] [INFO] Query marker FASTA was written to GCA_019310845.1_ASM1931084v1_genomic.fna/markers.fasta
[2023-06-28 10:15:58,785] [INFO] Task started: Blastn
[2023-06-28 10:15:58,785] [INFO] Running command: blastn -query GCA_019310845.1_ASM1931084v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg70793f4f-eacf-403a-8bca-2c1b26222b23/dqc_reference/reference_markers.fasta -out GCA_019310845.1_ASM1931084v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 10:15:59,543] [INFO] Task succeeded: Blastn
[2023-06-28 10:15:59,550] [INFO] Selected 30 target genomes.
[2023-06-28 10:15:59,550] [INFO] Target genome list was writen to GCA_019310845.1_ASM1931084v1_genomic.fna/target_genomes.txt
[2023-06-28 10:15:59,552] [INFO] Task started: fastANI
[2023-06-28 10:15:59,552] [INFO] Running command: fastANI --query /var/lib/cwl/stg07f00a9c-f048-44df-bbd1-944f4b9a604f/GCA_019310845.1_ASM1931084v1_genomic.fna.gz --refList GCA_019310845.1_ASM1931084v1_genomic.fna/target_genomes.txt --output GCA_019310845.1_ASM1931084v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 10:16:19,601] [INFO] Task succeeded: fastANI
[2023-06-28 10:16:19,601] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg70793f4f-eacf-403a-8bca-2c1b26222b23/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 10:16:19,602] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg70793f4f-eacf-403a-8bca-2c1b26222b23/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 10:16:19,614] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 10:16:19,614] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 10:16:19,615] [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
Desulfosarcina widdelii	strain=PP31	GCA_009688965.1	947919	947919	type	True	77.4303	87	435	95	below_threshold
Desulfosarcina ovata subsp. sediminis	strain=28bB2T	GCA_009688985.1	885957	83564	type	True	77.3504	71	435	95	below_threshold
Desulfosarcina ovata subsp. ovata	strain=oXyS1	GCA_009689005.1	2752305	83564	type	True	77.2972	69	435	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 10:16:19,617] [INFO] DFAST Taxonomy check result was written to GCA_019310845.1_ASM1931084v1_genomic.fna/tc_result.tsv
[2023-06-28 10:16:19,618] [INFO] ===== Taxonomy check completed =====
[2023-06-28 10:16:19,618] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 10:16:19,618] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg70793f4f-eacf-403a-8bca-2c1b26222b23/dqc_reference/checkm_data
[2023-06-28 10:16:19,620] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 10:16:19,645] [INFO] Task started: CheckM
[2023-06-28 10:16:19,646] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_019310845.1_ASM1931084v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_019310845.1_ASM1931084v1_genomic.fna/checkm_input GCA_019310845.1_ASM1931084v1_genomic.fna/checkm_result
[2023-06-28 10:16:40,408] [INFO] Task succeeded: CheckM
[2023-06-28 10:16:40,409] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 61.46%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 10:16:40,434] [INFO] ===== Completeness check finished =====
[2023-06-28 10:16:40,434] [INFO] ===== Start GTDB Search =====
[2023-06-28 10:16:40,435] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_019310845.1_ASM1931084v1_genomic.fna/markers.fasta)
[2023-06-28 10:16:40,435] [INFO] Task started: Blastn
[2023-06-28 10:16:40,435] [INFO] Running command: blastn -query GCA_019310845.1_ASM1931084v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg70793f4f-eacf-403a-8bca-2c1b26222b23/dqc_reference/reference_markers_gtdb.fasta -out GCA_019310845.1_ASM1931084v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 10:16:41,599] [INFO] Task succeeded: Blastn
[2023-06-28 10:16:41,610] [INFO] Selected 16 target genomes.
[2023-06-28 10:16:41,610] [INFO] Target genome list was writen to GCA_019310845.1_ASM1931084v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 10:16:41,621] [INFO] Task started: fastANI
[2023-06-28 10:16:41,621] [INFO] Running command: fastANI --query /var/lib/cwl/stg07f00a9c-f048-44df-bbd1-944f4b9a604f/GCA_019310845.1_ASM1931084v1_genomic.fna.gz --refList GCA_019310845.1_ASM1931084v1_genomic.fna/target_genomes_gtdb.txt --output GCA_019310845.1_ASM1931084v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 10:16:51,965] [INFO] Task succeeded: fastANI
[2023-06-28 10:16:51,979] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 10:16:51,980] [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_011042305.1	s__UBA2174 sp011042305	99.1653	390	435	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__UBA2174;g__UBA2174	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002327445.1	s__UBA2174 sp002327445	84.3217	366	435	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__UBA2174;g__UBA2174	95.0	99.95	99.95	0.95	0.95	2	-
GCA_002432195.1	s__UBA5852 sp002432195	77.7206	118	435	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__UBA5852;g__UBA5852	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011390035.1	s__JAABTE01 sp011390035	77.7029	58	435	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfococcaceae;g__JAABTE01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016218685.1	s__Desulfatitalea sp016218685	77.5214	67	435	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfosarcinaceae;g__Desulfatitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011389855.1	s__JAABTD01 sp011389855	77.4376	92	435	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfococcaceae;g__JAABTD01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009688965.1	s__Desulfosarcina widdelii	77.4303	87	435	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfosarcinaceae;g__Desulfosarcina	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 10:16:51,982] [INFO] GTDB search result was written to GCA_019310845.1_ASM1931084v1_genomic.fna/result_gtdb.tsv
[2023-06-28 10:16:51,983] [INFO] ===== GTDB Search completed =====
[2023-06-28 10:16:51,987] [INFO] DFAST_QC result json was written to GCA_019310845.1_ASM1931084v1_genomic.fna/dqc_result.json
[2023-06-28 10:16:51,987] [INFO] DFAST_QC completed!
[2023-06-28 10:16:51,988] [INFO] Total running time: 0h0m59s