[2023-06-17 03:42:10,593] [INFO] DFAST_QC pipeline started.
[2023-06-17 03:42:10,605] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 03:42:10,605] [INFO] DQC Reference Directory: /var/lib/cwl/stg632ce625-d15d-43b7-be1b-b13ef3757a47/dqc_reference
[2023-06-17 03:42:12,017] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 03:42:12,018] [INFO] Task started: Prodigal
[2023-06-17 03:42:12,018] [INFO] Running command: gunzip -c /var/lib/cwl/stg29a5a58c-a2f1-4330-ac60-acd1efa6ac69/GCA_013336325.1_ASM1333632v1_genomic.fna.gz | prodigal -d GCA_013336325.1_ASM1333632v1_genomic.fna/cds.fna -a GCA_013336325.1_ASM1333632v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 03:42:15,695] [INFO] Task succeeded: Prodigal
[2023-06-17 03:42:15,695] [INFO] Task started: HMMsearch
[2023-06-17 03:42:15,695] [INFO] Running command: hmmsearch --tblout GCA_013336325.1_ASM1333632v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg632ce625-d15d-43b7-be1b-b13ef3757a47/dqc_reference/reference_markers.hmm GCA_013336325.1_ASM1333632v1_genomic.fna/protein.faa > /dev/null
[2023-06-17 03:42:15,894] [INFO] Task succeeded: HMMsearch
[2023-06-17 03:42:15,895] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg29a5a58c-a2f1-4330-ac60-acd1efa6ac69/GCA_013336325.1_ASM1333632v1_genomic.fna.gz]
[2023-06-17 03:42:15,928] [INFO] Query marker FASTA was written to GCA_013336325.1_ASM1333632v1_genomic.fna/markers.fasta
[2023-06-17 03:42:15,929] [INFO] Task started: Blastn
[2023-06-17 03:42:15,929] [INFO] Running command: blastn -query GCA_013336325.1_ASM1333632v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg632ce625-d15d-43b7-be1b-b13ef3757a47/dqc_reference/reference_markers.fasta -out GCA_013336325.1_ASM1333632v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 03:42:16,573] [INFO] Task succeeded: Blastn
[2023-06-17 03:42:16,578] [INFO] Selected 14 target genomes.
[2023-06-17 03:42:16,578] [INFO] Target genome list was writen to GCA_013336325.1_ASM1333632v1_genomic.fna/target_genomes.txt
[2023-06-17 03:42:16,581] [INFO] Task started: fastANI
[2023-06-17 03:42:16,581] [INFO] Running command: fastANI --query /var/lib/cwl/stg29a5a58c-a2f1-4330-ac60-acd1efa6ac69/GCA_013336325.1_ASM1333632v1_genomic.fna.gz --refList GCA_013336325.1_ASM1333632v1_genomic.fna/target_genomes.txt --output GCA_013336325.1_ASM1333632v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 03:42:26,700] [INFO] Task succeeded: fastANI
[2023-06-17 03:42:26,701] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg632ce625-d15d-43b7-be1b-b13ef3757a47/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 03:42:26,701] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg632ce625-d15d-43b7-be1b-b13ef3757a47/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 03:42:26,705] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 03:42:26,705] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-17 03:42:26,705] [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
--------------------------------------------------------------------------------
[2023-06-17 03:42:26,711] [INFO] DFAST Taxonomy check result was written to GCA_013336325.1_ASM1333632v1_genomic.fna/tc_result.tsv
[2023-06-17 03:42:26,712] [INFO] ===== Taxonomy check completed =====
[2023-06-17 03:42:26,712] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 03:42:26,713] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg632ce625-d15d-43b7-be1b-b13ef3757a47/dqc_reference/checkm_data
[2023-06-17 03:42:26,716] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 03:42:26,756] [INFO] Task started: CheckM
[2023-06-17 03:42:26,756] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_013336325.1_ASM1333632v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_013336325.1_ASM1333632v1_genomic.fna/checkm_input GCA_013336325.1_ASM1333632v1_genomic.fna/checkm_result
[2023-06-17 03:42:45,478] [INFO] Task succeeded: CheckM
[2023-06-17 03:42:45,479] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 50.55%
Contamintation: 4.69%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-06-17 03:42:45,508] [INFO] ===== Completeness check finished =====
[2023-06-17 03:42:45,508] [INFO] ===== Start GTDB Search =====
[2023-06-17 03:42:45,509] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_013336325.1_ASM1333632v1_genomic.fna/markers.fasta)
[2023-06-17 03:42:45,509] [INFO] Task started: Blastn
[2023-06-17 03:42:45,510] [INFO] Running command: blastn -query GCA_013336325.1_ASM1333632v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg632ce625-d15d-43b7-be1b-b13ef3757a47/dqc_reference/reference_markers_gtdb.fasta -out GCA_013336325.1_ASM1333632v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 03:42:46,351] [INFO] Task succeeded: Blastn
[2023-06-17 03:42:46,354] [INFO] Selected 12 target genomes.
[2023-06-17 03:42:46,355] [INFO] Target genome list was writen to GCA_013336325.1_ASM1333632v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 03:42:46,360] [INFO] Task started: fastANI
[2023-06-17 03:42:46,361] [INFO] Running command: fastANI --query /var/lib/cwl/stg29a5a58c-a2f1-4330-ac60-acd1efa6ac69/GCA_013336325.1_ASM1333632v1_genomic.fna.gz --refList GCA_013336325.1_ASM1333632v1_genomic.fna/target_genomes_gtdb.txt --output GCA_013336325.1_ASM1333632v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 03:42:53,639] [INFO] Task succeeded: fastANI
[2023-06-17 03:42:53,647] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-17 03:42:53,647] [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_013360875.1	s__UBA12294 sp013360875	80.0994	93	167	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__EnvOPS12;g__UBA12294	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013388685.1	s__UBA12294 sp013388685	79.5091	90	167	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__EnvOPS12;g__UBA12294	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016223135.1	s__UBA12294 sp016223135	79.3702	84	167	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__EnvOPS12;g__UBA12294	95.0	99.98	99.98	0.97	0.97	2	-
GCA_002418205.1	s__UBA12294 sp002418205	78.772	89	167	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__EnvOPS12;g__UBA12294	95.0	99.83	99.80	0.91	0.90	3	-
GCA_011331405.1	s__UBA12294 sp011331405	77.8611	55	167	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__EnvOPS12;g__UBA12294	95.0	99.98	99.98	0.99	0.99	2	-
GCA_016721115.1	s__UBA12294 sp016721115	77.7594	61	167	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__EnvOPS12;g__UBA12294	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-17 03:42:53,650] [INFO] GTDB search result was written to GCA_013336325.1_ASM1333632v1_genomic.fna/result_gtdb.tsv
[2023-06-17 03:42:53,651] [INFO] ===== GTDB Search completed =====
[2023-06-17 03:42:53,653] [INFO] DFAST_QC result json was written to GCA_013336325.1_ASM1333632v1_genomic.fna/dqc_result.json
[2023-06-17 03:42:53,654] [INFO] DFAST_QC completed!
[2023-06-17 03:42:53,654] [INFO] Total running time: 0h0m43s