[2023-06-17 14:10:36,189] [INFO] DFAST_QC pipeline started.
[2023-06-17 14:10:36,191] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 14:10:36,192] [INFO] DQC Reference Directory: /var/lib/cwl/stgc971d5be-9dfd-4019-95ca-4fc4c4ca2a44/dqc_reference
[2023-06-17 14:10:37,390] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 14:10:37,391] [INFO] Task started: Prodigal
[2023-06-17 14:10:37,392] [INFO] Running command: gunzip -c /var/lib/cwl/stgb7339bc0-b19e-444b-9959-af86c2d66cce/GCA_028690875.1_ASM2869087v1_genomic.fna.gz | prodigal -d GCA_028690875.1_ASM2869087v1_genomic.fna/cds.fna -a GCA_028690875.1_ASM2869087v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 14:10:43,901] [INFO] Task succeeded: Prodigal
[2023-06-17 14:10:43,901] [INFO] Task started: HMMsearch
[2023-06-17 14:10:43,902] [INFO] Running command: hmmsearch --tblout GCA_028690875.1_ASM2869087v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc971d5be-9dfd-4019-95ca-4fc4c4ca2a44/dqc_reference/reference_markers.hmm GCA_028690875.1_ASM2869087v1_genomic.fna/protein.faa > /dev/null
[2023-06-17 14:10:44,141] [INFO] Task succeeded: HMMsearch
[2023-06-17 14:10:44,143] [INFO] Found 6/6 markers.
[2023-06-17 14:10:44,171] [INFO] Query marker FASTA was written to GCA_028690875.1_ASM2869087v1_genomic.fna/markers.fasta
[2023-06-17 14:10:44,171] [INFO] Task started: Blastn
[2023-06-17 14:10:44,172] [INFO] Running command: blastn -query GCA_028690875.1_ASM2869087v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc971d5be-9dfd-4019-95ca-4fc4c4ca2a44/dqc_reference/reference_markers.fasta -out GCA_028690875.1_ASM2869087v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 14:10:44,728] [INFO] Task succeeded: Blastn
[2023-06-17 14:10:44,733] [INFO] Selected 23 target genomes.
[2023-06-17 14:10:44,734] [INFO] Target genome list was writen to GCA_028690875.1_ASM2869087v1_genomic.fna/target_genomes.txt
[2023-06-17 14:10:44,742] [INFO] Task started: fastANI
[2023-06-17 14:10:44,742] [INFO] Running command: fastANI --query /var/lib/cwl/stgb7339bc0-b19e-444b-9959-af86c2d66cce/GCA_028690875.1_ASM2869087v1_genomic.fna.gz --refList GCA_028690875.1_ASM2869087v1_genomic.fna/target_genomes.txt --output GCA_028690875.1_ASM2869087v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 14:10:59,127] [INFO] Task succeeded: fastANI
[2023-06-17 14:10:59,128] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc971d5be-9dfd-4019-95ca-4fc4c4ca2a44/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 14:10:59,128] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc971d5be-9dfd-4019-95ca-4fc4c4ca2a44/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 14:10:59,130] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 14:10:59,131] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-17 14:10:59,131] [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 14:10:59,133] [INFO] DFAST Taxonomy check result was written to GCA_028690875.1_ASM2869087v1_genomic.fna/tc_result.tsv
[2023-06-17 14:10:59,134] [INFO] ===== Taxonomy check completed =====
[2023-06-17 14:10:59,134] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 14:10:59,135] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc971d5be-9dfd-4019-95ca-4fc4c4ca2a44/dqc_reference/checkm_data
[2023-06-17 14:10:59,139] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 14:10:59,170] [INFO] Task started: CheckM
[2023-06-17 14:10:59,170] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_028690875.1_ASM2869087v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_028690875.1_ASM2869087v1_genomic.fna/checkm_input GCA_028690875.1_ASM2869087v1_genomic.fna/checkm_result
[2023-06-17 14:11:25,261] [INFO] Task succeeded: CheckM
[2023-06-17 14:11:25,263] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-17 14:11:25,285] [INFO] ===== Completeness check finished =====
[2023-06-17 14:11:25,286] [INFO] ===== Start GTDB Search =====
[2023-06-17 14:11:25,286] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_028690875.1_ASM2869087v1_genomic.fna/markers.fasta)
[2023-06-17 14:11:25,287] [INFO] Task started: Blastn
[2023-06-17 14:11:25,287] [INFO] Running command: blastn -query GCA_028690875.1_ASM2869087v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc971d5be-9dfd-4019-95ca-4fc4c4ca2a44/dqc_reference/reference_markers_gtdb.fasta -out GCA_028690875.1_ASM2869087v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 14:11:26,000] [INFO] Task succeeded: Blastn
[2023-06-17 14:11:26,005] [INFO] Selected 15 target genomes.
[2023-06-17 14:11:26,005] [INFO] Target genome list was writen to GCA_028690875.1_ASM2869087v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 14:11:26,012] [INFO] Task started: fastANI
[2023-06-17 14:11:26,012] [INFO] Running command: fastANI --query /var/lib/cwl/stgb7339bc0-b19e-444b-9959-af86c2d66cce/GCA_028690875.1_ASM2869087v1_genomic.fna.gz --refList GCA_028690875.1_ASM2869087v1_genomic.fna/target_genomes_gtdb.txt --output GCA_028690875.1_ASM2869087v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 14:11:31,456] [INFO] Task succeeded: fastANI
[2023-06-17 14:11:31,469] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-17 14:11:31,469] [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_002410505.1	s__UBA5456 sp002410505	78.9669	148	799	d__Bacteria;p__Cloacimonadota;c__Cloacimonadia;o__Cloacimonadales;f__Cloacimonadaceae;g__UBA5456	95.0	99.37	99.18	0.92	0.87	14	-
GCA_017994635.1	s__UBA5456 sp017994635	78.6413	228	799	d__Bacteria;p__Cloacimonadota;c__Cloacimonadia;o__Cloacimonadales;f__Cloacimonadaceae;g__UBA5456	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018433885.1	s__UBA5456 sp018433885	78.4321	142	799	d__Bacteria;p__Cloacimonadota;c__Cloacimonadia;o__Cloacimonadales;f__Cloacimonadaceae;g__UBA5456	95.0	98.12	97.39	0.90	0.88	3	-
GCA_002412625.1	s__UBA5456 sp002412625	77.6351	149	799	d__Bacteria;p__Cloacimonadota;c__Cloacimonadia;o__Cloacimonadales;f__Cloacimonadaceae;g__UBA5456	95.0	99.97	99.97	0.94	0.94	2	-
GCA_002427325.1	s__UBA5456 sp002427325	76.8737	51	799	d__Bacteria;p__Cloacimonadota;c__Cloacimonadia;o__Cloacimonadales;f__Cloacimonadaceae;g__UBA5456	95.0	98.98	98.98	0.90	0.90	2	-
GCA_002428685.1	s__Cloacimonas sp002428685	76.4757	65	799	d__Bacteria;p__Cloacimonadota;c__Cloacimonadia;o__Cloacimonadales;f__Cloacimonadaceae;g__Cloacimonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-17 14:11:31,471] [INFO] GTDB search result was written to GCA_028690875.1_ASM2869087v1_genomic.fna/result_gtdb.tsv
[2023-06-17 14:11:31,472] [INFO] ===== GTDB Search completed =====
[2023-06-17 14:11:31,475] [INFO] DFAST_QC result json was written to GCA_028690875.1_ASM2869087v1_genomic.fna/dqc_result.json
[2023-06-17 14:11:31,475] [INFO] DFAST_QC completed!
[2023-06-17 14:11:31,475] [INFO] Total running time: 0h0m55s