[2023-06-30 12:22:36,844] [INFO] DFAST_QC pipeline started.
[2023-06-30 12:22:36,851] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 12:22:36,851] [INFO] DQC Reference Directory: /var/lib/cwl/stg6a5a4d34-219a-404f-99ee-f9d5cf90e127/dqc_reference
[2023-06-30 12:22:38,526] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 12:22:38,527] [INFO] Task started: Prodigal
[2023-06-30 12:22:38,527] [INFO] Running command: gunzip -c /var/lib/cwl/stgc8a3a7c0-d734-4bba-b8db-783b15619ce6/GCA_943844285.1_20200430_METABAT_21_1-contigs.fa_genomic.fna.gz | prodigal -d GCA_943844285.1_20200430_METABAT_21_1-contigs.fa_genomic.fna/cds.fna -a GCA_943844285.1_20200430_METABAT_21_1-contigs.fa_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 12:22:48,050] [INFO] Task succeeded: Prodigal
[2023-06-30 12:22:48,050] [INFO] Task started: HMMsearch
[2023-06-30 12:22:48,050] [INFO] Running command: hmmsearch --tblout GCA_943844285.1_20200430_METABAT_21_1-contigs.fa_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6a5a4d34-219a-404f-99ee-f9d5cf90e127/dqc_reference/reference_markers.hmm GCA_943844285.1_20200430_METABAT_21_1-contigs.fa_genomic.fna/protein.faa > /dev/null
[2023-06-30 12:22:48,255] [INFO] Task succeeded: HMMsearch
[2023-06-30 12:22:48,256] [INFO] Found 6/6 markers.
[2023-06-30 12:22:48,279] [INFO] Query marker FASTA was written to GCA_943844285.1_20200430_METABAT_21_1-contigs.fa_genomic.fna/markers.fasta
[2023-06-30 12:22:48,279] [INFO] Task started: Blastn
[2023-06-30 12:22:48,279] [INFO] Running command: blastn -query GCA_943844285.1_20200430_METABAT_21_1-contigs.fa_genomic.fna/markers.fasta -db /var/lib/cwl/stg6a5a4d34-219a-404f-99ee-f9d5cf90e127/dqc_reference/reference_markers.fasta -out GCA_943844285.1_20200430_METABAT_21_1-contigs.fa_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 12:22:48,849] [INFO] Task succeeded: Blastn
[2023-06-30 12:22:48,852] [INFO] Selected 29 target genomes.
[2023-06-30 12:22:48,852] [INFO] Target genome list was writen to GCA_943844285.1_20200430_METABAT_21_1-contigs.fa_genomic.fna/target_genomes.txt
[2023-06-30 12:22:48,854] [INFO] Task started: fastANI
[2023-06-30 12:22:48,855] [INFO] Running command: fastANI --query /var/lib/cwl/stgc8a3a7c0-d734-4bba-b8db-783b15619ce6/GCA_943844285.1_20200430_METABAT_21_1-contigs.fa_genomic.fna.gz --refList GCA_943844285.1_20200430_METABAT_21_1-contigs.fa_genomic.fna/target_genomes.txt --output GCA_943844285.1_20200430_METABAT_21_1-contigs.fa_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 12:23:05,719] [INFO] Task succeeded: fastANI
[2023-06-30 12:23:05,720] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6a5a4d34-219a-404f-99ee-f9d5cf90e127/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 12:23:05,720] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6a5a4d34-219a-404f-99ee-f9d5cf90e127/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 12:23:05,721] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 12:23:05,721] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-30 12:23:05,721] [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
--------------------------------------------------------------------------------
[2023-06-30 12:23:05,723] [INFO] DFAST Taxonomy check result was written to GCA_943844285.1_20200430_METABAT_21_1-contigs.fa_genomic.fna/tc_result.tsv
[2023-06-30 12:23:05,724] [INFO] ===== Taxonomy check completed =====
[2023-06-30 12:23:05,724] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 12:23:05,724] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6a5a4d34-219a-404f-99ee-f9d5cf90e127/dqc_reference/checkm_data
[2023-06-30 12:23:05,727] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 12:23:05,757] [INFO] Task started: CheckM
[2023-06-30 12:23:05,757] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_943844285.1_20200430_METABAT_21_1-contigs.fa_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_943844285.1_20200430_METABAT_21_1-contigs.fa_genomic.fna/checkm_input GCA_943844285.1_20200430_METABAT_21_1-contigs.fa_genomic.fna/checkm_result
[2023-06-30 12:23:36,621] [INFO] Task succeeded: CheckM
[2023-06-30 12:23:36,622] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 12:23:36,637] [INFO] ===== Completeness check finished =====
[2023-06-30 12:23:36,638] [INFO] ===== Start GTDB Search =====
[2023-06-30 12:23:36,638] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_943844285.1_20200430_METABAT_21_1-contigs.fa_genomic.fna/markers.fasta)
[2023-06-30 12:23:36,638] [INFO] Task started: Blastn
[2023-06-30 12:23:36,638] [INFO] Running command: blastn -query GCA_943844285.1_20200430_METABAT_21_1-contigs.fa_genomic.fna/markers.fasta -db /var/lib/cwl/stg6a5a4d34-219a-404f-99ee-f9d5cf90e127/dqc_reference/reference_markers_gtdb.fasta -out GCA_943844285.1_20200430_METABAT_21_1-contigs.fa_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 12:23:37,361] [INFO] Task succeeded: Blastn
[2023-06-30 12:23:37,364] [INFO] Selected 18 target genomes.
[2023-06-30 12:23:37,364] [INFO] Target genome list was writen to GCA_943844285.1_20200430_METABAT_21_1-contigs.fa_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 12:23:37,369] [INFO] Task started: fastANI
[2023-06-30 12:23:37,370] [INFO] Running command: fastANI --query /var/lib/cwl/stgc8a3a7c0-d734-4bba-b8db-783b15619ce6/GCA_943844285.1_20200430_METABAT_21_1-contigs.fa_genomic.fna.gz --refList GCA_943844285.1_20200430_METABAT_21_1-contigs.fa_genomic.fna/target_genomes_gtdb.txt --output GCA_943844285.1_20200430_METABAT_21_1-contigs.fa_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 12:23:45,201] [INFO] Task succeeded: fastANI
[2023-06-30 12:23:45,207] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 12:23:45,208] [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_905480165.1	s__UBA952 sp905480165	98.9929	543	926	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__UBA952	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_018665005.1	s__UBA952 sp018665005	92.7056	548	926	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__UBA952	95.0	98.77	98.77	0.77	0.77	2	-
GCA_011522905.1	s__UBA952 sp011522905	78.3372	260	926	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__UBA952	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003331365.1	s__UBA952 sp003331365	77.9986	250	926	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__UBA952	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905182495.1	s__UBA952 sp905182495	77.4412	132	926	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__UBA952	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002167775.1	s__UBA952 sp002167775	77.1268	131	926	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__UBA952	95.0	98.23	98.23	0.91	0.91	2	-
GCA_002480215.1	s__UBA952 sp002480215	77.0393	115	926	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__UBA952	95.0	99.70	99.70	0.81	0.81	2	-
GCA_016183815.1	s__M2408 sp016183815	75.8843	54	926	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__M2408	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 12:23:45,209] [INFO] GTDB search result was written to GCA_943844285.1_20200430_METABAT_21_1-contigs.fa_genomic.fna/result_gtdb.tsv
[2023-06-30 12:23:45,210] [INFO] ===== GTDB Search completed =====
[2023-06-30 12:23:45,213] [INFO] DFAST_QC result json was written to GCA_943844285.1_20200430_METABAT_21_1-contigs.fa_genomic.fna/dqc_result.json
[2023-06-30 12:23:45,213] [INFO] DFAST_QC completed!
[2023-06-30 12:23:45,213] [INFO] Total running time: 0h1m8s