[2023-06-13 06:11:32,719] [INFO] DFAST_QC pipeline started.
[2023-06-13 06:11:32,721] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 06:11:32,721] [INFO] DQC Reference Directory: /var/lib/cwl/stgc2106049-9e45-4bc0-beee-f04d1939de44/dqc_reference
[2023-06-13 06:11:33,989] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 06:11:33,990] [INFO] Task started: Prodigal
[2023-06-13 06:11:33,991] [INFO] Running command: gunzip -c /var/lib/cwl/stg1db3b30c-a0fd-4761-9d40-d6c4aa97426b/GCA_022708225.1_ASM2270822v1_genomic.fna.gz | prodigal -d GCA_022708225.1_ASM2270822v1_genomic.fna/cds.fna -a GCA_022708225.1_ASM2270822v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 06:11:45,392] [INFO] Task succeeded: Prodigal
[2023-06-13 06:11:45,393] [INFO] Task started: HMMsearch
[2023-06-13 06:11:45,393] [INFO] Running command: hmmsearch --tblout GCA_022708225.1_ASM2270822v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc2106049-9e45-4bc0-beee-f04d1939de44/dqc_reference/reference_markers.hmm GCA_022708225.1_ASM2270822v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 06:11:45,665] [INFO] Task succeeded: HMMsearch
[2023-06-13 06:11:45,666] [INFO] Found 6/6 markers.
[2023-06-13 06:11:45,691] [INFO] Query marker FASTA was written to GCA_022708225.1_ASM2270822v1_genomic.fna/markers.fasta
[2023-06-13 06:11:45,692] [INFO] Task started: Blastn
[2023-06-13 06:11:45,692] [INFO] Running command: blastn -query GCA_022708225.1_ASM2270822v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc2106049-9e45-4bc0-beee-f04d1939de44/dqc_reference/reference_markers.fasta -out GCA_022708225.1_ASM2270822v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 06:11:46,290] [INFO] Task succeeded: Blastn
[2023-06-13 06:11:46,294] [INFO] Selected 27 target genomes.
[2023-06-13 06:11:46,295] [INFO] Target genome list was writen to GCA_022708225.1_ASM2270822v1_genomic.fna/target_genomes.txt
[2023-06-13 06:11:46,318] [INFO] Task started: fastANI
[2023-06-13 06:11:46,318] [INFO] Running command: fastANI --query /var/lib/cwl/stg1db3b30c-a0fd-4761-9d40-d6c4aa97426b/GCA_022708225.1_ASM2270822v1_genomic.fna.gz --refList GCA_022708225.1_ASM2270822v1_genomic.fna/target_genomes.txt --output GCA_022708225.1_ASM2270822v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 06:12:09,129] [INFO] Task succeeded: fastANI
[2023-06-13 06:12:09,129] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc2106049-9e45-4bc0-beee-f04d1939de44/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 06:12:09,130] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc2106049-9e45-4bc0-beee-f04d1939de44/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 06:12:09,132] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 06:12:09,132] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-13 06:12:09,133] [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 06:12:09,139] [INFO] DFAST Taxonomy check result was written to GCA_022708225.1_ASM2270822v1_genomic.fna/tc_result.tsv
[2023-06-13 06:12:09,140] [INFO] ===== Taxonomy check completed =====
[2023-06-13 06:12:09,140] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 06:12:09,141] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc2106049-9e45-4bc0-beee-f04d1939de44/dqc_reference/checkm_data
[2023-06-13 06:12:09,144] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 06:12:09,188] [INFO] Task started: CheckM
[2023-06-13 06:12:09,188] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022708225.1_ASM2270822v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022708225.1_ASM2270822v1_genomic.fna/checkm_input GCA_022708225.1_ASM2270822v1_genomic.fna/checkm_result
[2023-06-13 06:12:45,941] [INFO] Task succeeded: CheckM
[2023-06-13 06:12:45,942] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 06:12:45,963] [INFO] ===== Completeness check finished =====
[2023-06-13 06:12:45,963] [INFO] ===== Start GTDB Search =====
[2023-06-13 06:12:45,964] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022708225.1_ASM2270822v1_genomic.fna/markers.fasta)
[2023-06-13 06:12:45,964] [INFO] Task started: Blastn
[2023-06-13 06:12:45,964] [INFO] Running command: blastn -query GCA_022708225.1_ASM2270822v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc2106049-9e45-4bc0-beee-f04d1939de44/dqc_reference/reference_markers_gtdb.fasta -out GCA_022708225.1_ASM2270822v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 06:12:46,730] [INFO] Task succeeded: Blastn
[2023-06-13 06:12:46,735] [INFO] Selected 9 target genomes.
[2023-06-13 06:12:46,735] [INFO] Target genome list was writen to GCA_022708225.1_ASM2270822v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 06:12:46,740] [INFO] Task started: fastANI
[2023-06-13 06:12:46,740] [INFO] Running command: fastANI --query /var/lib/cwl/stg1db3b30c-a0fd-4761-9d40-d6c4aa97426b/GCA_022708225.1_ASM2270822v1_genomic.fna.gz --refList GCA_022708225.1_ASM2270822v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022708225.1_ASM2270822v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 06:12:51,643] [INFO] Task succeeded: fastANI
[2023-06-13 06:12:51,656] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 06:12:51,656] [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_002071385.1	s__DMER64 sp002071385	99.852	585	641	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__DMER64	95.0	99.62	99.43	0.93	0.90	7	conclusive
GCA_002305545.1	s__DMER64 sp002305545	85.7806	551	641	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__DMER64	95.0	99.79	99.75	0.96	0.96	3	-
GCA_002070565.1	s__DMER64 sp002070565	83.4901	463	641	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__DMER64	95.0	99.14	99.14	0.85	0.85	2	-
GCA_002409325.1	s__DMER64 sp002409325	83.1897	521	641	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__DMER64	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001603455.1	s__DMER64 sp001603455	78.9102	236	641	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__DMER64	95.0	99.83	99.68	0.89	0.76	4	-
GCA_001512865.1	s__DMER64 sp001512865	78.1952	226	641	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__DMER64	95.0	99.73	99.73	0.89	0.89	2	-
--------------------------------------------------------------------------------
[2023-06-13 06:12:51,659] [INFO] GTDB search result was written to GCA_022708225.1_ASM2270822v1_genomic.fna/result_gtdb.tsv
[2023-06-13 06:12:51,659] [INFO] ===== GTDB Search completed =====
[2023-06-13 06:12:51,663] [INFO] DFAST_QC result json was written to GCA_022708225.1_ASM2270822v1_genomic.fna/dqc_result.json
[2023-06-13 06:12:51,663] [INFO] DFAST_QC completed!
[2023-06-13 06:12:51,664] [INFO] Total running time: 0h1m19s