[2023-06-29 08:44:14,912] [INFO] DFAST_QC pipeline started.
[2023-06-29 08:44:14,914] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 08:44:14,915] [INFO] DQC Reference Directory: /var/lib/cwl/stg3786cb99-8e58-4eb0-8f1c-00eb98133bb8/dqc_reference
[2023-06-29 08:44:18,030] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 08:44:18,031] [INFO] Task started: Prodigal
[2023-06-29 08:44:18,031] [INFO] Running command: gunzip -c /var/lib/cwl/stg601a8a75-3510-4ae4-b2e0-759bd8574804/GCA_020062465.1_ASM2006246v1_genomic.fna.gz | prodigal -d GCA_020062465.1_ASM2006246v1_genomic.fna/cds.fna -a GCA_020062465.1_ASM2006246v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 08:44:22,209] [INFO] Task succeeded: Prodigal
[2023-06-29 08:44:22,209] [INFO] Task started: HMMsearch
[2023-06-29 08:44:22,209] [INFO] Running command: hmmsearch --tblout GCA_020062465.1_ASM2006246v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3786cb99-8e58-4eb0-8f1c-00eb98133bb8/dqc_reference/reference_markers.hmm GCA_020062465.1_ASM2006246v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 08:44:22,485] [INFO] Task succeeded: HMMsearch
[2023-06-29 08:44:22,487] [INFO] Found 6/6 markers.
[2023-06-29 08:44:22,516] [INFO] Query marker FASTA was written to GCA_020062465.1_ASM2006246v1_genomic.fna/markers.fasta
[2023-06-29 08:44:22,516] [INFO] Task started: Blastn
[2023-06-29 08:44:22,516] [INFO] Running command: blastn -query GCA_020062465.1_ASM2006246v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3786cb99-8e58-4eb0-8f1c-00eb98133bb8/dqc_reference/reference_markers.fasta -out GCA_020062465.1_ASM2006246v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 08:44:23,414] [INFO] Task succeeded: Blastn
[2023-06-29 08:44:23,419] [INFO] Selected 23 target genomes.
[2023-06-29 08:44:23,420] [INFO] Target genome list was writen to GCA_020062465.1_ASM2006246v1_genomic.fna/target_genomes.txt
[2023-06-29 08:44:23,423] [INFO] Task started: fastANI
[2023-06-29 08:44:23,423] [INFO] Running command: fastANI --query /var/lib/cwl/stg601a8a75-3510-4ae4-b2e0-759bd8574804/GCA_020062465.1_ASM2006246v1_genomic.fna.gz --refList GCA_020062465.1_ASM2006246v1_genomic.fna/target_genomes.txt --output GCA_020062465.1_ASM2006246v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 08:44:39,331] [INFO] Task succeeded: fastANI
[2023-06-29 08:44:39,331] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3786cb99-8e58-4eb0-8f1c-00eb98133bb8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 08:44:39,332] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3786cb99-8e58-4eb0-8f1c-00eb98133bb8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 08:44:39,333] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 08:44:39,333] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-29 08:44:39,334] [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
--------------------------------------------------------------------------------
[2023-06-29 08:44:39,336] [INFO] DFAST Taxonomy check result was written to GCA_020062465.1_ASM2006246v1_genomic.fna/tc_result.tsv
[2023-06-29 08:44:39,336] [INFO] ===== Taxonomy check completed =====
[2023-06-29 08:44:39,337] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 08:44:39,337] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3786cb99-8e58-4eb0-8f1c-00eb98133bb8/dqc_reference/checkm_data
[2023-06-29 08:44:39,340] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 08:44:39,363] [INFO] Task started: CheckM
[2023-06-29 08:44:39,364] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_020062465.1_ASM2006246v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_020062465.1_ASM2006246v1_genomic.fna/checkm_input GCA_020062465.1_ASM2006246v1_genomic.fna/checkm_result
[2023-06-29 08:45:00,338] [INFO] Task succeeded: CheckM
[2023-06-29 08:45:00,339] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.82%
Contamintation: 2.43%
Strain heterogeneity: 40.00%
--------------------------------------------------------------------------------
[2023-06-29 08:45:00,363] [INFO] ===== Completeness check finished =====
[2023-06-29 08:45:00,364] [INFO] ===== Start GTDB Search =====
[2023-06-29 08:45:00,364] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_020062465.1_ASM2006246v1_genomic.fna/markers.fasta)
[2023-06-29 08:45:00,364] [INFO] Task started: Blastn
[2023-06-29 08:45:00,365] [INFO] Running command: blastn -query GCA_020062465.1_ASM2006246v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3786cb99-8e58-4eb0-8f1c-00eb98133bb8/dqc_reference/reference_markers_gtdb.fasta -out GCA_020062465.1_ASM2006246v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 08:45:01,232] [INFO] Task succeeded: Blastn
[2023-06-29 08:45:01,252] [INFO] Selected 10 target genomes.
[2023-06-29 08:45:01,253] [INFO] Target genome list was writen to GCA_020062465.1_ASM2006246v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 08:45:01,257] [INFO] Task started: fastANI
[2023-06-29 08:45:01,258] [INFO] Running command: fastANI --query /var/lib/cwl/stg601a8a75-3510-4ae4-b2e0-759bd8574804/GCA_020062465.1_ASM2006246v1_genomic.fna.gz --refList GCA_020062465.1_ASM2006246v1_genomic.fna/target_genomes_gtdb.txt --output GCA_020062465.1_ASM2006246v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 08:45:07,468] [INFO] Task succeeded: fastANI
[2023-06-29 08:45:07,482] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 08:45:07,482] [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_018333535.1	s__RBG-16-49-23 sp018333535	83.3732	271	382	d__Bacteria;p__Desulfobacterota;c__BSN033;o__BSN033;f__UBA1163;g__RBG-16-49-23	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016875255.1	s__RBG-16-49-23 sp016875255	82.6878	235	382	d__Bacteria;p__Desulfobacterota;c__BSN033;o__BSN033;f__UBA1163;g__RBG-16-49-23	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018333715.1	s__RBG-16-49-23 sp018333715	81.9706	205	382	d__Bacteria;p__Desulfobacterota;c__BSN033;o__BSN033;f__UBA1163;g__RBG-16-49-23	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016874935.1	s__RBG-16-49-23 sp016874935	81.1534	225	382	d__Bacteria;p__Desulfobacterota;c__BSN033;o__BSN033;f__UBA1163;g__RBG-16-49-23	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001798855.1	s__RBG-16-49-23 sp001798855	80.6751	241	382	d__Bacteria;p__Desulfobacterota;c__BSN033;o__BSN033;f__UBA1163;g__RBG-16-49-23	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016875155.1	s__RBG-16-49-23 sp016875155	78.1143	146	382	d__Bacteria;p__Desulfobacterota;c__BSN033;o__BSN033;f__UBA1163;g__RBG-16-49-23	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013388635.1	s__JACAEX01 sp013388635	76.6	84	382	d__Bacteria;p__Desulfobacterota;c__BSN033;o__BSN033;f__UBA1163;g__JACAEX01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 08:45:07,484] [INFO] GTDB search result was written to GCA_020062465.1_ASM2006246v1_genomic.fna/result_gtdb.tsv
[2023-06-29 08:45:07,485] [INFO] ===== GTDB Search completed =====
[2023-06-29 08:45:07,489] [INFO] DFAST_QC result json was written to GCA_020062465.1_ASM2006246v1_genomic.fna/dqc_result.json
[2023-06-29 08:45:07,489] [INFO] DFAST_QC completed!
[2023-06-29 08:45:07,489] [INFO] Total running time: 0h0m53s