[2023-06-19 14:29:21,772] [INFO] DFAST_QC pipeline started.
[2023-06-19 14:29:21,775] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 14:29:21,775] [INFO] DQC Reference Directory: /var/lib/cwl/stgeadbaf32-57f0-43dd-ae2a-7517adff74d2/dqc_reference
[2023-06-19 14:29:25,447] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 14:29:25,448] [INFO] Task started: Prodigal
[2023-06-19 14:29:25,449] [INFO] Running command: gunzip -c /var/lib/cwl/stg99e759b1-bb4b-4532-9020-55821fcaecd2/GCA_018435745.1_R3_genomic.fna.gz | prodigal -d GCA_018435745.1_R3_genomic.fna/cds.fna -a GCA_018435745.1_R3_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 14:29:31,564] [INFO] Task succeeded: Prodigal
[2023-06-19 14:29:31,564] [INFO] Task started: HMMsearch
[2023-06-19 14:29:31,564] [INFO] Running command: hmmsearch --tblout GCA_018435745.1_R3_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgeadbaf32-57f0-43dd-ae2a-7517adff74d2/dqc_reference/reference_markers.hmm GCA_018435745.1_R3_genomic.fna/protein.faa > /dev/null
[2023-06-19 14:29:31,808] [INFO] Task succeeded: HMMsearch
[2023-06-19 14:29:31,810] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg99e759b1-bb4b-4532-9020-55821fcaecd2/GCA_018435745.1_R3_genomic.fna.gz]
[2023-06-19 14:29:31,847] [INFO] Query marker FASTA was written to GCA_018435745.1_R3_genomic.fna/markers.fasta
[2023-06-19 14:29:31,848] [INFO] Task started: Blastn
[2023-06-19 14:29:31,848] [INFO] Running command: blastn -query GCA_018435745.1_R3_genomic.fna/markers.fasta -db /var/lib/cwl/stgeadbaf32-57f0-43dd-ae2a-7517adff74d2/dqc_reference/reference_markers.fasta -out GCA_018435745.1_R3_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 14:29:32,329] [INFO] Task succeeded: Blastn
[2023-06-19 14:29:32,335] [INFO] Selected 7 target genomes.
[2023-06-19 14:29:32,336] [INFO] Target genome list was writen to GCA_018435745.1_R3_genomic.fna/target_genomes.txt
[2023-06-19 14:29:32,338] [INFO] Task started: fastANI
[2023-06-19 14:29:32,339] [INFO] Running command: fastANI --query /var/lib/cwl/stg99e759b1-bb4b-4532-9020-55821fcaecd2/GCA_018435745.1_R3_genomic.fna.gz --refList GCA_018435745.1_R3_genomic.fna/target_genomes.txt --output GCA_018435745.1_R3_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 14:29:35,785] [INFO] Task succeeded: fastANI
[2023-06-19 14:29:35,786] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgeadbaf32-57f0-43dd-ae2a-7517adff74d2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 14:29:35,787] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgeadbaf32-57f0-43dd-ae2a-7517adff74d2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 14:29:35,792] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 14:29:35,792] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-19 14:29:35,792] [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
Methanoculleus sediminis	strain=S3Fa	GCA_001017125.1	1550566	1550566	type	True	76.5364	56	580	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-19 14:29:35,794] [INFO] DFAST Taxonomy check result was written to GCA_018435745.1_R3_genomic.fna/tc_result.tsv
[2023-06-19 14:29:35,795] [INFO] ===== Taxonomy check completed =====
[2023-06-19 14:29:35,795] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 14:29:35,795] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgeadbaf32-57f0-43dd-ae2a-7517adff74d2/dqc_reference/checkm_data
[2023-06-19 14:29:35,797] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 14:29:35,826] [INFO] Task started: CheckM
[2023-06-19 14:29:35,827] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018435745.1_R3_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018435745.1_R3_genomic.fna/checkm_input GCA_018435745.1_R3_genomic.fna/checkm_result
[2023-06-19 14:30:00,495] [INFO] Task succeeded: CheckM
[2023-06-19 14:30:00,497] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 14:30:00,524] [INFO] ===== Completeness check finished =====
[2023-06-19 14:30:00,524] [INFO] ===== Start GTDB Search =====
[2023-06-19 14:30:00,525] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018435745.1_R3_genomic.fna/markers.fasta)
[2023-06-19 14:30:00,525] [INFO] Task started: Blastn
[2023-06-19 14:30:00,525] [INFO] Running command: blastn -query GCA_018435745.1_R3_genomic.fna/markers.fasta -db /var/lib/cwl/stgeadbaf32-57f0-43dd-ae2a-7517adff74d2/dqc_reference/reference_markers_gtdb.fasta -out GCA_018435745.1_R3_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 14:30:01,022] [INFO] Task succeeded: Blastn
[2023-06-19 14:30:01,027] [INFO] Selected 8 target genomes.
[2023-06-19 14:30:01,027] [INFO] Target genome list was writen to GCA_018435745.1_R3_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 14:30:01,033] [INFO] Task started: fastANI
[2023-06-19 14:30:01,033] [INFO] Running command: fastANI --query /var/lib/cwl/stg99e759b1-bb4b-4532-9020-55821fcaecd2/GCA_018435745.1_R3_genomic.fna.gz --refList GCA_018435745.1_R3_genomic.fna/target_genomes_gtdb.txt --output GCA_018435745.1_R3_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 14:30:04,191] [INFO] Task succeeded: fastANI
[2023-06-19 14:30:04,198] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 14:30:04,199] [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_018432765.1	s__SD8 sp018432765	98.9004	399	580	d__Archaea;p__Halobacteriota;c__Methanomicrobia;o__Methanomicrobiales;f__Methanoregulaceae;g__SD8	95.0	99.01	99.01	0.81	0.81	2	conclusive
GCA_002509485.1	s__SD8 sp002509485	94.0736	359	580	d__Archaea;p__Halobacteriota;c__Methanomicrobia;o__Methanomicrobiales;f__Methanoregulaceae;g__SD8	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001412335.1	s__SD8 sp001412335	92.4228	348	580	d__Archaea;p__Halobacteriota;c__Methanomicrobia;o__Methanomicrobiales;f__Methanoregulaceae;g__SD8	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002503825.1	s__UBA467 sp002503825	77.2899	74	580	d__Archaea;p__Halobacteriota;c__Methanomicrobia;o__Methanomicrobiales;f__Methanoregulaceae;g__UBA467	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018263335.1	s__Methanolinea_A sp002067155	76.9789	81	580	d__Archaea;p__Halobacteriota;c__Methanomicrobia;o__Methanomicrobiales;f__Methanoregulaceae;g__Methanolinea_A	95.0	99.35	99.35	0.89	0.89	2	-
--------------------------------------------------------------------------------
[2023-06-19 14:30:04,201] [INFO] GTDB search result was written to GCA_018435745.1_R3_genomic.fna/result_gtdb.tsv
[2023-06-19 14:30:04,201] [INFO] ===== GTDB Search completed =====
[2023-06-19 14:30:04,206] [INFO] DFAST_QC result json was written to GCA_018435745.1_R3_genomic.fna/dqc_result.json
[2023-06-19 14:30:04,206] [INFO] DFAST_QC completed!
[2023-06-19 14:30:04,206] [INFO] Total running time: 0h0m42s