[2023-06-19 14:07:08,736] [INFO] DFAST_QC pipeline started.
[2023-06-19 14:07:08,739] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 14:07:08,739] [INFO] DQC Reference Directory: /var/lib/cwl/stgc7dfdcfd-0c80-44eb-8121-9a1b90730f55/dqc_reference
[2023-06-19 14:07:10,063] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 14:07:10,064] [INFO] Task started: Prodigal
[2023-06-19 14:07:10,064] [INFO] Running command: gunzip -c /var/lib/cwl/stg169af076-9f50-49c5-971c-3fc4fdefde82/GCA_018064455.1_ASM1806445v1_genomic.fna.gz | prodigal -d GCA_018064455.1_ASM1806445v1_genomic.fna/cds.fna -a GCA_018064455.1_ASM1806445v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 14:07:14,129] [INFO] Task succeeded: Prodigal
[2023-06-19 14:07:14,130] [INFO] Task started: HMMsearch
[2023-06-19 14:07:14,130] [INFO] Running command: hmmsearch --tblout GCA_018064455.1_ASM1806445v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc7dfdcfd-0c80-44eb-8121-9a1b90730f55/dqc_reference/reference_markers.hmm GCA_018064455.1_ASM1806445v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 14:07:14,375] [INFO] Task succeeded: HMMsearch
[2023-06-19 14:07:14,376] [INFO] Found 6/6 markers.
[2023-06-19 14:07:14,404] [INFO] Query marker FASTA was written to GCA_018064455.1_ASM1806445v1_genomic.fna/markers.fasta
[2023-06-19 14:07:14,404] [INFO] Task started: Blastn
[2023-06-19 14:07:14,404] [INFO] Running command: blastn -query GCA_018064455.1_ASM1806445v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc7dfdcfd-0c80-44eb-8121-9a1b90730f55/dqc_reference/reference_markers.fasta -out GCA_018064455.1_ASM1806445v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 14:07:15,045] [INFO] Task succeeded: Blastn
[2023-06-19 14:07:15,052] [INFO] Selected 21 target genomes.
[2023-06-19 14:07:15,053] [INFO] Target genome list was writen to GCA_018064455.1_ASM1806445v1_genomic.fna/target_genomes.txt
[2023-06-19 14:07:15,060] [INFO] Task started: fastANI
[2023-06-19 14:07:15,060] [INFO] Running command: fastANI --query /var/lib/cwl/stg169af076-9f50-49c5-971c-3fc4fdefde82/GCA_018064455.1_ASM1806445v1_genomic.fna.gz --refList GCA_018064455.1_ASM1806445v1_genomic.fna/target_genomes.txt --output GCA_018064455.1_ASM1806445v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 14:07:24,616] [INFO] Task succeeded: fastANI
[2023-06-19 14:07:24,617] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc7dfdcfd-0c80-44eb-8121-9a1b90730f55/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 14:07:24,617] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc7dfdcfd-0c80-44eb-8121-9a1b90730f55/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 14:07:24,621] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 14:07:24,621] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-19 14:07:24,621] [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
--------------------------------------------------------------------------------
[2023-06-19 14:07:24,623] [INFO] DFAST Taxonomy check result was written to GCA_018064455.1_ASM1806445v1_genomic.fna/tc_result.tsv
[2023-06-19 14:07:24,624] [INFO] ===== Taxonomy check completed =====
[2023-06-19 14:07:24,625] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 14:07:24,625] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc7dfdcfd-0c80-44eb-8121-9a1b90730f55/dqc_reference/checkm_data
[2023-06-19 14:07:24,629] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 14:07:24,658] [INFO] Task started: CheckM
[2023-06-19 14:07:24,658] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018064455.1_ASM1806445v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018064455.1_ASM1806445v1_genomic.fna/checkm_input GCA_018064455.1_ASM1806445v1_genomic.fna/checkm_result
[2023-06-19 14:07:44,496] [INFO] Task succeeded: CheckM
[2023-06-19 14:07:44,497] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 94.60%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 14:07:44,526] [INFO] ===== Completeness check finished =====
[2023-06-19 14:07:44,526] [INFO] ===== Start GTDB Search =====
[2023-06-19 14:07:44,527] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018064455.1_ASM1806445v1_genomic.fna/markers.fasta)
[2023-06-19 14:07:44,527] [INFO] Task started: Blastn
[2023-06-19 14:07:44,527] [INFO] Running command: blastn -query GCA_018064455.1_ASM1806445v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc7dfdcfd-0c80-44eb-8121-9a1b90730f55/dqc_reference/reference_markers_gtdb.fasta -out GCA_018064455.1_ASM1806445v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 14:07:45,541] [INFO] Task succeeded: Blastn
[2023-06-19 14:07:45,545] [INFO] Selected 19 target genomes.
[2023-06-19 14:07:45,545] [INFO] Target genome list was writen to GCA_018064455.1_ASM1806445v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 14:07:45,556] [INFO] Task started: fastANI
[2023-06-19 14:07:45,556] [INFO] Running command: fastANI --query /var/lib/cwl/stg169af076-9f50-49c5-971c-3fc4fdefde82/GCA_018064455.1_ASM1806445v1_genomic.fna.gz --refList GCA_018064455.1_ASM1806445v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018064455.1_ASM1806445v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 14:07:51,462] [INFO] Task succeeded: fastANI
[2023-06-19 14:07:51,476] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 14:07:51,476] [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_018064455.1	s__UBA1227 sp018064455	100.0	542	542	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UBA1227	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002314555.1	s__UBA1227 sp002314555	80.1704	124	542	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UBA1227	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018065925.1	s__UBA1227 sp018065925	80.0928	199	542	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UBA1227	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017538005.1	s__UBA1227 sp017538005	78.3682	76	542	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UBA1227	95.0	98.36	98.36	0.75	0.75	2	-
GCA_002314645.1	s__UBA1227 sp002314645	77.8948	86	542	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UBA1227	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017451425.1	s__UBA1227 sp017451425	77.8476	109	542	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UBA1227	95.0	95.47	95.37	0.83	0.82	4	-
GCA_900771085.1	s__RUG420 sp900771085	77.7472	67	542	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__RUG420	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012520505.1	s__UBA1227 sp012520505	76.5483	61	542	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UBA1227	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-19 14:07:51,478] [INFO] GTDB search result was written to GCA_018064455.1_ASM1806445v1_genomic.fna/result_gtdb.tsv
[2023-06-19 14:07:51,479] [INFO] ===== GTDB Search completed =====
[2023-06-19 14:07:51,483] [INFO] DFAST_QC result json was written to GCA_018064455.1_ASM1806445v1_genomic.fna/dqc_result.json
[2023-06-19 14:07:51,483] [INFO] DFAST_QC completed!
[2023-06-19 14:07:51,483] [INFO] Total running time: 0h0m43s