[2024-01-24 13:19:11,931] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:19:11,932] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:19:11,933] [INFO] DQC Reference Directory: /var/lib/cwl/stg1a3354f4-ff57-4a24-8e5c-946cffaa43f6/dqc_reference
[2024-01-24 13:19:13,220] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:19:13,221] [INFO] Task started: Prodigal
[2024-01-24 13:19:13,221] [INFO] Running command: gunzip -c /var/lib/cwl/stg13b420dd-8ca2-4538-8bec-ece78edb23a7/GCF_008830225.1_ASM883022v1_genomic.fna.gz | prodigal -d GCF_008830225.1_ASM883022v1_genomic.fna/cds.fna -a GCF_008830225.1_ASM883022v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:19:25,836] [INFO] Task succeeded: Prodigal
[2024-01-24 13:19:25,836] [INFO] Task started: HMMsearch
[2024-01-24 13:19:25,836] [INFO] Running command: hmmsearch --tblout GCF_008830225.1_ASM883022v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1a3354f4-ff57-4a24-8e5c-946cffaa43f6/dqc_reference/reference_markers.hmm GCF_008830225.1_ASM883022v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:19:26,190] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:19:26,191] [INFO] Found 6/6 markers.
[2024-01-24 13:19:26,245] [INFO] Query marker FASTA was written to GCF_008830225.1_ASM883022v1_genomic.fna/markers.fasta
[2024-01-24 13:19:26,246] [INFO] Task started: Blastn
[2024-01-24 13:19:26,246] [INFO] Running command: blastn -query GCF_008830225.1_ASM883022v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1a3354f4-ff57-4a24-8e5c-946cffaa43f6/dqc_reference/reference_markers.fasta -out GCF_008830225.1_ASM883022v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:27,000] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:27,006] [INFO] Selected 14 target genomes.
[2024-01-24 13:19:27,006] [INFO] Target genome list was writen to GCF_008830225.1_ASM883022v1_genomic.fna/target_genomes.txt
[2024-01-24 13:19:27,016] [INFO] Task started: fastANI
[2024-01-24 13:19:27,016] [INFO] Running command: fastANI --query /var/lib/cwl/stg13b420dd-8ca2-4538-8bec-ece78edb23a7/GCF_008830225.1_ASM883022v1_genomic.fna.gz --refList GCF_008830225.1_ASM883022v1_genomic.fna/target_genomes.txt --output GCF_008830225.1_ASM883022v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:19:37,125] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:37,125] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1a3354f4-ff57-4a24-8e5c-946cffaa43f6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:19:37,126] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1a3354f4-ff57-4a24-8e5c-946cffaa43f6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:19:37,138] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:19:37,138] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:19:37,139] [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
Pseudodesulfovibrio tunisiensis	strain=RB22	GCA_022809775.1	463192	463192	type	True	78.6454	393	1114	95	below_threshold
Pseudodesulfovibrio indicus	strain=J2	GCA_001563225.1	1716143	1716143	type	True	78.5533	363	1114	95	below_threshold
Pseudodesulfovibrio hydrargyri	strain=BerOc1	GCA_001874525.1	2125990	2125990	type	True	78.5208	348	1114	95	below_threshold
Pseudodesulfovibrio indicus	strain=DSM 101483	GCA_004365595.1	1716143	1716143	type	True	78.5179	357	1114	95	below_threshold
Pseudodesulfovibrio cashew	strain=SRB007	GCA_009762795.1	2678688	2678688	type	True	78.4406	306	1114	95	below_threshold
Pseudodesulfovibrio mercurii	strain=ND132	GCA_000189295.2	641491	641491	type	True	78.3386	345	1114	95	below_threshold
Pseudodesulfovibrio aespoeensis	strain=Aspo-2	GCA_000176915.2	182210	182210	type	True	78.2126	326	1114	95	below_threshold
Paucidesulfovibrio longus	strain=DSM 6739	GCA_000420485.1	889	889	type	True	78.1652	270	1114	95	below_threshold
Pseudodesulfovibrio alkaliphilus	strain=F-1	GCA_009729555.1	2661613	2661613	type	True	78.0022	282	1114	95	below_threshold
Pseudodesulfovibrio sediminis	strain=SF6	GCA_020886695.1	2810563	2810563	type	True	77.3362	206	1114	95	below_threshold
Pseudodesulfovibrio profundus	strain=500-1	GCA_900217235.1	57320	57320	type	True	77.2831	170	1114	95	below_threshold
Fundidesulfovibrio putealis	strain=DSM 16056	GCA_000429325.1	270496	270496	type	True	77.0201	148	1114	95	below_threshold
Desulfovibrio vulgaris	strain=Hildenborough	GCA_000195755.1	881	881	type	True	76.6499	104	1114	95	below_threshold
Desulfovibrio carbinoliphilus subsp. oakridgensis	strain=FW-101-2B	GCA_000177215.2	694327	345370	type	True	76.4244	138	1114	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:19:37,141] [INFO] DFAST Taxonomy check result was written to GCF_008830225.1_ASM883022v1_genomic.fna/tc_result.tsv
[2024-01-24 13:19:37,141] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:19:37,141] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:19:37,142] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1a3354f4-ff57-4a24-8e5c-946cffaa43f6/dqc_reference/checkm_data
[2024-01-24 13:19:37,143] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:19:37,179] [INFO] Task started: CheckM
[2024-01-24 13:19:37,179] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008830225.1_ASM883022v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008830225.1_ASM883022v1_genomic.fna/checkm_input GCF_008830225.1_ASM883022v1_genomic.fna/checkm_result
[2024-01-24 13:20:18,192] [INFO] Task succeeded: CheckM
[2024-01-24 13:20:18,194] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:20:18,214] [INFO] ===== Completeness check finished =====
[2024-01-24 13:20:18,214] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:20:18,214] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008830225.1_ASM883022v1_genomic.fna/markers.fasta)
[2024-01-24 13:20:18,215] [INFO] Task started: Blastn
[2024-01-24 13:20:18,215] [INFO] Running command: blastn -query GCF_008830225.1_ASM883022v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1a3354f4-ff57-4a24-8e5c-946cffaa43f6/dqc_reference/reference_markers_gtdb.fasta -out GCF_008830225.1_ASM883022v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:20:19,261] [INFO] Task succeeded: Blastn
[2024-01-24 13:20:19,265] [INFO] Selected 11 target genomes.
[2024-01-24 13:20:19,265] [INFO] Target genome list was writen to GCF_008830225.1_ASM883022v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:20:19,286] [INFO] Task started: fastANI
[2024-01-24 13:20:19,286] [INFO] Running command: fastANI --query /var/lib/cwl/stg13b420dd-8ca2-4538-8bec-ece78edb23a7/GCF_008830225.1_ASM883022v1_genomic.fna.gz --refList GCF_008830225.1_ASM883022v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008830225.1_ASM883022v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:20:26,793] [INFO] Task succeeded: fastANI
[2024-01-24 13:20:26,810] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:20:26,811] [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_008830225.1	s__Pseudodesulfovibrio senegalensis	100.0	1113	1114	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Pseudodesulfovibrio	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_008001235.1	s__Pseudodesulfovibrio sp008001235	80.5331	583	1114	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Pseudodesulfovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001311825.1	s__Pseudodesulfovibrio brasiliensis	78.8995	326	1114	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Pseudodesulfovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001874525.1	s__Pseudodesulfovibrio hydrargyri	78.5158	349	1114	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Pseudodesulfovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015709315.1	s__Pseudodesulfovibrio sp015709315	78.3683	349	1114	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Pseudodesulfovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017351175.1	s__Pseudodesulfovibrio sp017351175	78.3602	324	1114	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Pseudodesulfovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000375485.1	s__Pseudodesulfovibrio oxyclinae	78.3276	279	1114	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Pseudodesulfovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000420485.1	s__Paucidesulfovibrio longus	78.1786	269	1114	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Paucidesulfovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009729555.1	s__Pseudodesulfovibrio sp009729555	78.0112	280	1114	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Pseudodesulfovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004025585.1	s__Pseudodesulfovibrio sp004025585	77.9675	274	1114	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Pseudodesulfovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016342345.1	s__Pseudodesulfovibrio sp016342345	77.1061	158	1114	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Pseudodesulfovibrio	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:20:26,812] [INFO] GTDB search result was written to GCF_008830225.1_ASM883022v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:20:26,813] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:20:26,816] [INFO] DFAST_QC result json was written to GCF_008830225.1_ASM883022v1_genomic.fna/dqc_result.json
[2024-01-24 13:20:26,817] [INFO] DFAST_QC completed!
[2024-01-24 13:20:26,817] [INFO] Total running time: 0h1m15s