[2023-06-28 12:28:38,565] [INFO] DFAST_QC pipeline started.
[2023-06-28 12:28:38,569] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 12:28:38,569] [INFO] DQC Reference Directory: /var/lib/cwl/stg28f26d53-8337-4535-8230-56f143102be9/dqc_reference
[2023-06-28 12:28:39,792] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 12:28:39,793] [INFO] Task started: Prodigal
[2023-06-28 12:28:39,793] [INFO] Running command: gunzip -c /var/lib/cwl/stg16c5d1c1-0b40-402a-a77d-ddea140ea702/GCA_020853075.1_ASM2085307v1_genomic.fna.gz | prodigal -d GCA_020853075.1_ASM2085307v1_genomic.fna/cds.fna -a GCA_020853075.1_ASM2085307v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 12:28:49,974] [INFO] Task succeeded: Prodigal
[2023-06-28 12:28:49,975] [INFO] Task started: HMMsearch
[2023-06-28 12:28:49,975] [INFO] Running command: hmmsearch --tblout GCA_020853075.1_ASM2085307v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg28f26d53-8337-4535-8230-56f143102be9/dqc_reference/reference_markers.hmm GCA_020853075.1_ASM2085307v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 12:28:50,253] [INFO] Task succeeded: HMMsearch
[2023-06-28 12:28:50,254] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg16c5d1c1-0b40-402a-a77d-ddea140ea702/GCA_020853075.1_ASM2085307v1_genomic.fna.gz]
[2023-06-28 12:28:50,294] [INFO] Query marker FASTA was written to GCA_020853075.1_ASM2085307v1_genomic.fna/markers.fasta
[2023-06-28 12:28:50,294] [INFO] Task started: Blastn
[2023-06-28 12:28:50,294] [INFO] Running command: blastn -query GCA_020853075.1_ASM2085307v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg28f26d53-8337-4535-8230-56f143102be9/dqc_reference/reference_markers.fasta -out GCA_020853075.1_ASM2085307v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 12:28:50,964] [INFO] Task succeeded: Blastn
[2023-06-28 12:28:50,969] [INFO] Selected 25 target genomes.
[2023-06-28 12:28:50,970] [INFO] Target genome list was writen to GCA_020853075.1_ASM2085307v1_genomic.fna/target_genomes.txt
[2023-06-28 12:28:50,972] [INFO] Task started: fastANI
[2023-06-28 12:28:50,973] [INFO] Running command: fastANI --query /var/lib/cwl/stg16c5d1c1-0b40-402a-a77d-ddea140ea702/GCA_020853075.1_ASM2085307v1_genomic.fna.gz --refList GCA_020853075.1_ASM2085307v1_genomic.fna/target_genomes.txt --output GCA_020853075.1_ASM2085307v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 12:29:07,562] [INFO] Task succeeded: fastANI
[2023-06-28 12:29:07,562] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg28f26d53-8337-4535-8230-56f143102be9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 12:29:07,563] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg28f26d53-8337-4535-8230-56f143102be9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 12:29:07,570] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 12:29:07,570] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 12:29:07,570] [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
Litorilinea aerophila	strain=ATCC BAA-2444	GCA_006569185.2	1204385	1204385	type	True	75.6237	55	1137	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 12:29:07,573] [INFO] DFAST Taxonomy check result was written to GCA_020853075.1_ASM2085307v1_genomic.fna/tc_result.tsv
[2023-06-28 12:29:07,574] [INFO] ===== Taxonomy check completed =====
[2023-06-28 12:29:07,574] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 12:29:07,574] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg28f26d53-8337-4535-8230-56f143102be9/dqc_reference/checkm_data
[2023-06-28 12:29:07,576] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 12:29:07,619] [INFO] Task started: CheckM
[2023-06-28 12:29:07,619] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_020853075.1_ASM2085307v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_020853075.1_ASM2085307v1_genomic.fna/checkm_input GCA_020853075.1_ASM2085307v1_genomic.fna/checkm_result
[2023-06-28 12:29:41,342] [INFO] Task succeeded: CheckM
[2023-06-28 12:29:41,344] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 78.03%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 12:29:41,373] [INFO] ===== Completeness check finished =====
[2023-06-28 12:29:41,373] [INFO] ===== Start GTDB Search =====
[2023-06-28 12:29:41,373] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_020853075.1_ASM2085307v1_genomic.fna/markers.fasta)
[2023-06-28 12:29:41,374] [INFO] Task started: Blastn
[2023-06-28 12:29:41,374] [INFO] Running command: blastn -query GCA_020853075.1_ASM2085307v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg28f26d53-8337-4535-8230-56f143102be9/dqc_reference/reference_markers_gtdb.fasta -out GCA_020853075.1_ASM2085307v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 12:29:42,425] [INFO] Task succeeded: Blastn
[2023-06-28 12:29:42,430] [INFO] Selected 29 target genomes.
[2023-06-28 12:29:42,430] [INFO] Target genome list was writen to GCA_020853075.1_ASM2085307v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 12:29:42,436] [INFO] Task started: fastANI
[2023-06-28 12:29:42,437] [INFO] Running command: fastANI --query /var/lib/cwl/stg16c5d1c1-0b40-402a-a77d-ddea140ea702/GCA_020853075.1_ASM2085307v1_genomic.fna.gz --refList GCA_020853075.1_ASM2085307v1_genomic.fna/target_genomes_gtdb.txt --output GCA_020853075.1_ASM2085307v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 12:29:56,993] [INFO] Task succeeded: fastANI
[2023-06-28 12:29:57,000] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 12:29:57,000] [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_016876015.1	s__VGOD01 sp016876015	75.8528	59	1137	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__CG2-30-64-16;f__CG2-30-64-16;g__VGOD01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011334325.1	s__DTPP01 sp011334325	75.6643	62	1137	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__DTPP01;f__DTPP01;g__DTPP01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014874485.1	s__DTLA01 sp014874485	75.5314	55	1137	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__DTLA01;f__DTLA01;g__DTLA01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014383605.1	s__NIOZ-UU15 sp014383605	75.5237	60	1137	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__UBA3071;f__UBA3071;g__NIOZ-UU15	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011367385.1	s__SpSt-583 sp011367385	75.4474	58	1137	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__UBA6663;g__SpSt-583	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016707605.1	s__Promineofilum sp016707605	75.1544	61	1137	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Promineofilales;f__Promineofilaceae;g__Promineofilum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900066015.1	s__Promineofilum breve	74.8781	52	1137	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Promineofilales;f__Promineofilaceae;g__Promineofilum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 12:29:57,003] [INFO] GTDB search result was written to GCA_020853075.1_ASM2085307v1_genomic.fna/result_gtdb.tsv
[2023-06-28 12:29:57,003] [INFO] ===== GTDB Search completed =====
[2023-06-28 12:29:57,006] [INFO] DFAST_QC result json was written to GCA_020853075.1_ASM2085307v1_genomic.fna/dqc_result.json
[2023-06-28 12:29:57,006] [INFO] DFAST_QC completed!
[2023-06-28 12:29:57,006] [INFO] Total running time: 0h1m18s