[2023-06-13 08:51:52,830] [INFO] DFAST_QC pipeline started.
[2023-06-13 08:51:52,833] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 08:51:52,833] [INFO] DQC Reference Directory: /var/lib/cwl/stg71a0a206-7bfd-4841-a851-b501386868c2/dqc_reference
[2023-06-13 08:51:54,199] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 08:51:54,200] [INFO] Task started: Prodigal
[2023-06-13 08:51:54,200] [INFO] Running command: gunzip -c /var/lib/cwl/stg91c0a478-0849-41b8-b664-f07d98627910/GCA_022793065.1_ASM2279306v1_genomic.fna.gz | prodigal -d GCA_022793065.1_ASM2279306v1_genomic.fna/cds.fna -a GCA_022793065.1_ASM2279306v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 08:52:04,306] [INFO] Task succeeded: Prodigal
[2023-06-13 08:52:04,307] [INFO] Task started: HMMsearch
[2023-06-13 08:52:04,307] [INFO] Running command: hmmsearch --tblout GCA_022793065.1_ASM2279306v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg71a0a206-7bfd-4841-a851-b501386868c2/dqc_reference/reference_markers.hmm GCA_022793065.1_ASM2279306v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 08:52:04,599] [INFO] Task succeeded: HMMsearch
[2023-06-13 08:52:04,600] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg91c0a478-0849-41b8-b664-f07d98627910/GCA_022793065.1_ASM2279306v1_genomic.fna.gz]
[2023-06-13 08:52:04,633] [INFO] Query marker FASTA was written to GCA_022793065.1_ASM2279306v1_genomic.fna/markers.fasta
[2023-06-13 08:52:04,633] [INFO] Task started: Blastn
[2023-06-13 08:52:04,634] [INFO] Running command: blastn -query GCA_022793065.1_ASM2279306v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg71a0a206-7bfd-4841-a851-b501386868c2/dqc_reference/reference_markers.fasta -out GCA_022793065.1_ASM2279306v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 08:52:05,198] [INFO] Task succeeded: Blastn
[2023-06-13 08:52:05,203] [INFO] Selected 23 target genomes.
[2023-06-13 08:52:05,204] [INFO] Target genome list was writen to GCA_022793065.1_ASM2279306v1_genomic.fna/target_genomes.txt
[2023-06-13 08:52:05,209] [INFO] Task started: fastANI
[2023-06-13 08:52:05,209] [INFO] Running command: fastANI --query /var/lib/cwl/stg91c0a478-0849-41b8-b664-f07d98627910/GCA_022793065.1_ASM2279306v1_genomic.fna.gz --refList GCA_022793065.1_ASM2279306v1_genomic.fna/target_genomes.txt --output GCA_022793065.1_ASM2279306v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 08:52:17,297] [INFO] Task succeeded: fastANI
[2023-06-13 08:52:17,298] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg71a0a206-7bfd-4841-a851-b501386868c2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 08:52:17,298] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg71a0a206-7bfd-4841-a851-b501386868c2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 08:52:17,304] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 08:52:17,305] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 08:52:17,305] [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
Eisenbergiella tayi	strain=DSM 26961	GCA_001881565.1	1432052	1432052	type	True	76.3205	53	1259	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 08:52:17,307] [INFO] DFAST Taxonomy check result was written to GCA_022793065.1_ASM2279306v1_genomic.fna/tc_result.tsv
[2023-06-13 08:52:17,308] [INFO] ===== Taxonomy check completed =====
[2023-06-13 08:52:17,308] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 08:52:17,309] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg71a0a206-7bfd-4841-a851-b501386868c2/dqc_reference/checkm_data
[2023-06-13 08:52:17,310] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 08:52:17,359] [INFO] Task started: CheckM
[2023-06-13 08:52:17,359] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022793065.1_ASM2279306v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022793065.1_ASM2279306v1_genomic.fna/checkm_input GCA_022793065.1_ASM2279306v1_genomic.fna/checkm_result
[2023-06-13 08:52:52,213] [INFO] Task succeeded: CheckM
[2023-06-13 08:52:52,214] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-06-13 08:52:52,239] [INFO] ===== Completeness check finished =====
[2023-06-13 08:52:52,239] [INFO] ===== Start GTDB Search =====
[2023-06-13 08:52:52,239] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022793065.1_ASM2279306v1_genomic.fna/markers.fasta)
[2023-06-13 08:52:52,240] [INFO] Task started: Blastn
[2023-06-13 08:52:52,240] [INFO] Running command: blastn -query GCA_022793065.1_ASM2279306v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg71a0a206-7bfd-4841-a851-b501386868c2/dqc_reference/reference_markers_gtdb.fasta -out GCA_022793065.1_ASM2279306v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 08:52:52,967] [INFO] Task succeeded: Blastn
[2023-06-13 08:52:52,971] [INFO] Selected 21 target genomes.
[2023-06-13 08:52:52,971] [INFO] Target genome list was writen to GCA_022793065.1_ASM2279306v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 08:52:52,977] [INFO] Task started: fastANI
[2023-06-13 08:52:52,977] [INFO] Running command: fastANI --query /var/lib/cwl/stg91c0a478-0849-41b8-b664-f07d98627910/GCA_022793065.1_ASM2279306v1_genomic.fna.gz --refList GCA_022793065.1_ASM2279306v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022793065.1_ASM2279306v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 08:53:04,850] [INFO] Task succeeded: fastANI
[2023-06-13 08:53:04,865] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-13 08:53:04,865] [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_910584435.1	s__Acetatifactor sp910584435	79.1588	512	1259	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910586435.1	s__Acetatifactor sp910586435	78.642	435	1259	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910578185.1	s__Acetatifactor sp910578185	77.3424	301	1259	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900755865.1	s__Acetatifactor sp900755865	77.0973	80	1259	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor	95.0	98.03	98.03	0.82	0.82	2	-
GCA_910584865.1	s__Acetatifactor sp910584865	77.0742	174	1259	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910576125.1	s__Acetatifactor sp910576125	76.9786	131	1259	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor	95.0	100.00	100.00	1.00	1.00	2	-
GCA_910584235.1	s__Acetatifactor sp910584235	76.9701	137	1259	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910578815.1	s__Acetatifactor sp910578815	76.6469	114	1259	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016303085.1	s__Acetatifactor sp016303085	76.6374	80	1259	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003612485.1	s__Acetatifactor sp003612485	76.6336	148	1259	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor	95.0	98.96	98.96	0.94	0.94	2	-
GCA_910586485.1	s__Acetatifactor sp910586485	76.3568	131	1259	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012520645.1	s__JAAYNV01 sp012520645	75.995	60	1259	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__JAAYNV01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017936785.1	s__UBA2882 sp017936785	75.7681	51	1259	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA2882	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 08:53:04,867] [INFO] GTDB search result was written to GCA_022793065.1_ASM2279306v1_genomic.fna/result_gtdb.tsv
[2023-06-13 08:53:04,868] [INFO] ===== GTDB Search completed =====
[2023-06-13 08:53:04,871] [INFO] DFAST_QC result json was written to GCA_022793065.1_ASM2279306v1_genomic.fna/dqc_result.json
[2023-06-13 08:53:04,871] [INFO] DFAST_QC completed!
[2023-06-13 08:53:04,871] [INFO] Total running time: 0h1m12s