[2023-06-29 14:05:30,407] [INFO] DFAST_QC pipeline started.
[2023-06-29 14:05:30,410] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 14:05:30,410] [INFO] DQC Reference Directory: /var/lib/cwl/stgc0988370-096b-488f-bef7-b2ca3c5e2bb7/dqc_reference
[2023-06-29 14:05:31,699] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 14:05:31,700] [INFO] Task started: Prodigal
[2023-06-29 14:05:31,700] [INFO] Running command: gunzip -c /var/lib/cwl/stg83e11ce6-ca1e-439f-b4d3-6314c2d26182/GCA_011522875.1_ASM1152287v1_genomic.fna.gz | prodigal -d GCA_011522875.1_ASM1152287v1_genomic.fna/cds.fna -a GCA_011522875.1_ASM1152287v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 14:05:36,828] [INFO] Task succeeded: Prodigal
[2023-06-29 14:05:36,828] [INFO] Task started: HMMsearch
[2023-06-29 14:05:36,828] [INFO] Running command: hmmsearch --tblout GCA_011522875.1_ASM1152287v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc0988370-096b-488f-bef7-b2ca3c5e2bb7/dqc_reference/reference_markers.hmm GCA_011522875.1_ASM1152287v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 14:05:37,026] [INFO] Task succeeded: HMMsearch
[2023-06-29 14:05:37,027] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg83e11ce6-ca1e-439f-b4d3-6314c2d26182/GCA_011522875.1_ASM1152287v1_genomic.fna.gz]
[2023-06-29 14:05:37,051] [INFO] Query marker FASTA was written to GCA_011522875.1_ASM1152287v1_genomic.fna/markers.fasta
[2023-06-29 14:05:37,051] [INFO] Task started: Blastn
[2023-06-29 14:05:37,051] [INFO] Running command: blastn -query GCA_011522875.1_ASM1152287v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc0988370-096b-488f-bef7-b2ca3c5e2bb7/dqc_reference/reference_markers.fasta -out GCA_011522875.1_ASM1152287v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 14:05:37,586] [INFO] Task succeeded: Blastn
[2023-06-29 14:05:37,591] [INFO] Selected 14 target genomes.
[2023-06-29 14:05:37,592] [INFO] Target genome list was writen to GCA_011522875.1_ASM1152287v1_genomic.fna/target_genomes.txt
[2023-06-29 14:05:37,595] [INFO] Task started: fastANI
[2023-06-29 14:05:37,595] [INFO] Running command: fastANI --query /var/lib/cwl/stg83e11ce6-ca1e-439f-b4d3-6314c2d26182/GCA_011522875.1_ASM1152287v1_genomic.fna.gz --refList GCA_011522875.1_ASM1152287v1_genomic.fna/target_genomes.txt --output GCA_011522875.1_ASM1152287v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 14:05:49,512] [INFO] Task succeeded: fastANI
[2023-06-29 14:05:49,513] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc0988370-096b-488f-bef7-b2ca3c5e2bb7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 14:05:49,514] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc0988370-096b-488f-bef7-b2ca3c5e2bb7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 14:05:49,517] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 14:05:49,517] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 14:05:49,517] [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
Ilumatobacter fluminis	strain=DSM 18936	GCA_004364865.1	467091	467091	type	True	76.5206	56	462	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 14:05:49,520] [INFO] DFAST Taxonomy check result was written to GCA_011522875.1_ASM1152287v1_genomic.fna/tc_result.tsv
[2023-06-29 14:05:49,520] [INFO] ===== Taxonomy check completed =====
[2023-06-29 14:05:49,521] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 14:05:49,521] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc0988370-096b-488f-bef7-b2ca3c5e2bb7/dqc_reference/checkm_data
[2023-06-29 14:05:49,522] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 14:05:49,547] [INFO] Task started: CheckM
[2023-06-29 14:05:49,548] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_011522875.1_ASM1152287v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_011522875.1_ASM1152287v1_genomic.fna/checkm_input GCA_011522875.1_ASM1152287v1_genomic.fna/checkm_result
[2023-06-29 14:06:12,159] [INFO] Task succeeded: CheckM
[2023-06-29 14:06:12,161] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 86.74%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 14:06:12,184] [INFO] ===== Completeness check finished =====
[2023-06-29 14:06:12,185] [INFO] ===== Start GTDB Search =====
[2023-06-29 14:06:12,185] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_011522875.1_ASM1152287v1_genomic.fna/markers.fasta)
[2023-06-29 14:06:12,186] [INFO] Task started: Blastn
[2023-06-29 14:06:12,186] [INFO] Running command: blastn -query GCA_011522875.1_ASM1152287v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc0988370-096b-488f-bef7-b2ca3c5e2bb7/dqc_reference/reference_markers_gtdb.fasta -out GCA_011522875.1_ASM1152287v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 14:06:12,743] [INFO] Task succeeded: Blastn
[2023-06-29 14:06:12,748] [INFO] Selected 11 target genomes.
[2023-06-29 14:06:12,748] [INFO] Target genome list was writen to GCA_011522875.1_ASM1152287v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 14:06:12,756] [INFO] Task started: fastANI
[2023-06-29 14:06:12,756] [INFO] Running command: fastANI --query /var/lib/cwl/stg83e11ce6-ca1e-439f-b4d3-6314c2d26182/GCA_011522875.1_ASM1152287v1_genomic.fna.gz --refList GCA_011522875.1_ASM1152287v1_genomic.fna/target_genomes_gtdb.txt --output GCA_011522875.1_ASM1152287v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 14:06:17,105] [INFO] Task succeeded: fastANI
[2023-06-29 14:06:17,112] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 14:06:17,113] [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_012269985.1	s__Casp-actino5 sp012269985	98.073	424	462	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Casp-actino5	95.0	98.07	98.07	0.92	0.92	2	conclusive
GCA_002727235.1	s__Casp-actino5 sp002727235	93.9935	387	462	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Casp-actino5	95.0	97.22	95.99	0.84	0.77	5	-
GCA_002501485.1	s__Casp-actino5 sp002501485	90.3955	408	462	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Casp-actino5	95.0	99.77	99.74	0.92	0.90	3	-
GCA_001510385.1	s__Casp-actino5 sp001510385	79.0612	184	462	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Casp-actino5	95.0	99.68	99.68	0.96	0.96	2	-
GCA_017859785.1	s__Casp-actino5 sp017859785	77.1068	60	462	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Casp-actino5	95.0	99.23	98.27	0.91	0.86	15	-
GCA_017859395.1	s__Casp-actino5 sp017859395	76.648	67	462	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Casp-actino5	95.0	99.27	98.20	0.94	0.88	4	-
GCF_004364865.1	s__Ilumatobacter fluminis	76.5206	56	462	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Ilumatobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 14:06:17,115] [INFO] GTDB search result was written to GCA_011522875.1_ASM1152287v1_genomic.fna/result_gtdb.tsv
[2023-06-29 14:06:17,115] [INFO] ===== GTDB Search completed =====
[2023-06-29 14:06:17,118] [INFO] DFAST_QC result json was written to GCA_011522875.1_ASM1152287v1_genomic.fna/dqc_result.json
[2023-06-29 14:06:17,118] [INFO] DFAST_QC completed!
[2023-06-29 14:06:17,119] [INFO] Total running time: 0h0m47s