[2023-06-13 17:12:16,874] [INFO] DFAST_QC pipeline started.
[2023-06-13 17:12:16,876] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 17:12:16,876] [INFO] DQC Reference Directory: /var/lib/cwl/stg60c49a53-9575-44e5-bc35-9170588481e9/dqc_reference
[2023-06-13 17:12:18,077] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 17:12:18,078] [INFO] Task started: Prodigal
[2023-06-13 17:12:18,078] [INFO] Running command: gunzip -c /var/lib/cwl/stg75e6d1d4-b1c7-44e4-87ff-bd0ae447af09/GCA_022769385.1_ASM2276938v1_genomic.fna.gz | prodigal -d GCA_022769385.1_ASM2276938v1_genomic.fna/cds.fna -a GCA_022769385.1_ASM2276938v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 17:12:21,272] [INFO] Task succeeded: Prodigal
[2023-06-13 17:12:21,272] [INFO] Task started: HMMsearch
[2023-06-13 17:12:21,272] [INFO] Running command: hmmsearch --tblout GCA_022769385.1_ASM2276938v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg60c49a53-9575-44e5-bc35-9170588481e9/dqc_reference/reference_markers.hmm GCA_022769385.1_ASM2276938v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 17:12:21,432] [INFO] Task succeeded: HMMsearch
[2023-06-13 17:12:21,434] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg75e6d1d4-b1c7-44e4-87ff-bd0ae447af09/GCA_022769385.1_ASM2276938v1_genomic.fna.gz]
[2023-06-13 17:12:21,452] [INFO] Query marker FASTA was written to GCA_022769385.1_ASM2276938v1_genomic.fna/markers.fasta
[2023-06-13 17:12:21,452] [INFO] Task started: Blastn
[2023-06-13 17:12:21,452] [INFO] Running command: blastn -query GCA_022769385.1_ASM2276938v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg60c49a53-9575-44e5-bc35-9170588481e9/dqc_reference/reference_markers.fasta -out GCA_022769385.1_ASM2276938v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 17:12:21,896] [INFO] Task succeeded: Blastn
[2023-06-13 17:12:21,899] [INFO] Selected 14 target genomes.
[2023-06-13 17:12:21,899] [INFO] Target genome list was writen to GCA_022769385.1_ASM2276938v1_genomic.fna/target_genomes.txt
[2023-06-13 17:12:21,902] [INFO] Task started: fastANI
[2023-06-13 17:12:21,903] [INFO] Running command: fastANI --query /var/lib/cwl/stg75e6d1d4-b1c7-44e4-87ff-bd0ae447af09/GCA_022769385.1_ASM2276938v1_genomic.fna.gz --refList GCA_022769385.1_ASM2276938v1_genomic.fna/target_genomes.txt --output GCA_022769385.1_ASM2276938v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 17:12:28,332] [INFO] Task succeeded: fastANI
[2023-06-13 17:12:28,332] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg60c49a53-9575-44e5-bc35-9170588481e9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 17:12:28,332] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg60c49a53-9575-44e5-bc35-9170588481e9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 17:12:28,334] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 17:12:28,334] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-13 17:12:28,334] [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
--------------------------------------------------------------------------------
[2023-06-13 17:12:28,335] [INFO] DFAST Taxonomy check result was written to GCA_022769385.1_ASM2276938v1_genomic.fna/tc_result.tsv
[2023-06-13 17:12:28,336] [INFO] ===== Taxonomy check completed =====
[2023-06-13 17:12:28,336] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 17:12:28,336] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg60c49a53-9575-44e5-bc35-9170588481e9/dqc_reference/checkm_data
[2023-06-13 17:12:28,339] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 17:12:28,359] [INFO] Task started: CheckM
[2023-06-13 17:12:28,359] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022769385.1_ASM2276938v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022769385.1_ASM2276938v1_genomic.fna/checkm_input GCA_022769385.1_ASM2276938v1_genomic.fna/checkm_result
[2023-06-13 17:12:44,641] [INFO] Task succeeded: CheckM
[2023-06-13 17:12:44,642] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-13 17:12:44,659] [INFO] ===== Completeness check finished =====
[2023-06-13 17:12:44,659] [INFO] ===== Start GTDB Search =====
[2023-06-13 17:12:44,660] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022769385.1_ASM2276938v1_genomic.fna/markers.fasta)
[2023-06-13 17:12:44,660] [INFO] Task started: Blastn
[2023-06-13 17:12:44,660] [INFO] Running command: blastn -query GCA_022769385.1_ASM2276938v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg60c49a53-9575-44e5-bc35-9170588481e9/dqc_reference/reference_markers_gtdb.fasta -out GCA_022769385.1_ASM2276938v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 17:12:45,112] [INFO] Task succeeded: Blastn
[2023-06-13 17:12:45,115] [INFO] Selected 16 target genomes.
[2023-06-13 17:12:45,116] [INFO] Target genome list was writen to GCA_022769385.1_ASM2276938v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 17:12:45,128] [INFO] Task started: fastANI
[2023-06-13 17:12:45,128] [INFO] Running command: fastANI --query /var/lib/cwl/stg75e6d1d4-b1c7-44e4-87ff-bd0ae447af09/GCA_022769385.1_ASM2276938v1_genomic.fna.gz --refList GCA_022769385.1_ASM2276938v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022769385.1_ASM2276938v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 17:12:50,193] [INFO] Task succeeded: fastANI
[2023-06-13 17:12:50,196] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 17:12:50,196] [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_016293805.1	s__UMGS973 sp016293805	98.7466	455	516	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Anaerovoracaceae;g__UMGS973	95.0	98.91	98.91	0.92	0.92	2	conclusive
GCA_900547295.1	s__UMGS973 sp900547295	77.7287	61	516	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Anaerovoracaceae;g__UMGS973	95.0	98.40	98.37	0.82	0.81	3	-
--------------------------------------------------------------------------------
[2023-06-13 17:12:50,198] [INFO] GTDB search result was written to GCA_022769385.1_ASM2276938v1_genomic.fna/result_gtdb.tsv
[2023-06-13 17:12:50,199] [INFO] ===== GTDB Search completed =====
[2023-06-13 17:12:50,201] [INFO] DFAST_QC result json was written to GCA_022769385.1_ASM2276938v1_genomic.fna/dqc_result.json
[2023-06-13 17:12:50,201] [INFO] DFAST_QC completed!
[2023-06-13 17:12:50,201] [INFO] Total running time: 0h0m33s