[2023-06-28 04:37:05,899] [INFO] DFAST_QC pipeline started.
[2023-06-28 04:37:05,902] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 04:37:05,902] [INFO] DQC Reference Directory: /var/lib/cwl/stg623b023c-71d5-4fa2-888c-4aa7bf465c3d/dqc_reference
[2023-06-28 04:37:07,228] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 04:37:07,230] [INFO] Task started: Prodigal
[2023-06-28 04:37:07,230] [INFO] Running command: gunzip -c /var/lib/cwl/stg0447c05b-a068-4688-90df-1a0179fe7ef2/GCA_019894795.1_ASM1989479v1_genomic.fna.gz | prodigal -d GCA_019894795.1_ASM1989479v1_genomic.fna/cds.fna -a GCA_019894795.1_ASM1989479v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 04:37:12,073] [INFO] Task succeeded: Prodigal
[2023-06-28 04:37:12,073] [INFO] Task started: HMMsearch
[2023-06-28 04:37:12,074] [INFO] Running command: hmmsearch --tblout GCA_019894795.1_ASM1989479v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg623b023c-71d5-4fa2-888c-4aa7bf465c3d/dqc_reference/reference_markers.hmm GCA_019894795.1_ASM1989479v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 04:37:12,356] [INFO] Task succeeded: HMMsearch
[2023-06-28 04:37:12,358] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg0447c05b-a068-4688-90df-1a0179fe7ef2/GCA_019894795.1_ASM1989479v1_genomic.fna.gz]
[2023-06-28 04:37:12,389] [INFO] Query marker FASTA was written to GCA_019894795.1_ASM1989479v1_genomic.fna/markers.fasta
[2023-06-28 04:37:12,389] [INFO] Task started: Blastn
[2023-06-28 04:37:12,389] [INFO] Running command: blastn -query GCA_019894795.1_ASM1989479v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg623b023c-71d5-4fa2-888c-4aa7bf465c3d/dqc_reference/reference_markers.fasta -out GCA_019894795.1_ASM1989479v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 04:37:12,895] [INFO] Task succeeded: Blastn
[2023-06-28 04:37:12,899] [INFO] Selected 7 target genomes.
[2023-06-28 04:37:12,899] [INFO] Target genome list was writen to GCA_019894795.1_ASM1989479v1_genomic.fna/target_genomes.txt
[2023-06-28 04:37:12,900] [INFO] Task started: fastANI
[2023-06-28 04:37:12,901] [INFO] Running command: fastANI --query /var/lib/cwl/stg0447c05b-a068-4688-90df-1a0179fe7ef2/GCA_019894795.1_ASM1989479v1_genomic.fna.gz --refList GCA_019894795.1_ASM1989479v1_genomic.fna/target_genomes.txt --output GCA_019894795.1_ASM1989479v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 04:37:16,087] [INFO] Task succeeded: fastANI
[2023-06-28 04:37:16,087] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg623b023c-71d5-4fa2-888c-4aa7bf465c3d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 04:37:16,088] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg623b023c-71d5-4fa2-888c-4aa7bf465c3d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 04:37:16,089] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 04:37:16,090] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 04:37:16,090] [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
--------------------------------------------------------------------------------
[2023-06-28 04:37:16,092] [INFO] DFAST Taxonomy check result was written to GCA_019894795.1_ASM1989479v1_genomic.fna/tc_result.tsv
[2023-06-28 04:37:16,092] [INFO] ===== Taxonomy check completed =====
[2023-06-28 04:37:16,092] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 04:37:16,093] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg623b023c-71d5-4fa2-888c-4aa7bf465c3d/dqc_reference/checkm_data
[2023-06-28 04:37:16,095] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 04:37:16,131] [INFO] Task started: CheckM
[2023-06-28 04:37:16,131] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_019894795.1_ASM1989479v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_019894795.1_ASM1989479v1_genomic.fna/checkm_input GCA_019894795.1_ASM1989479v1_genomic.fna/checkm_result
[2023-06-28 04:37:38,950] [INFO] Task succeeded: CheckM
[2023-06-28 04:37:38,951] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 04:37:38,972] [INFO] ===== Completeness check finished =====
[2023-06-28 04:37:38,972] [INFO] ===== Start GTDB Search =====
[2023-06-28 04:37:38,972] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_019894795.1_ASM1989479v1_genomic.fna/markers.fasta)
[2023-06-28 04:37:38,973] [INFO] Task started: Blastn
[2023-06-28 04:37:38,973] [INFO] Running command: blastn -query GCA_019894795.1_ASM1989479v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg623b023c-71d5-4fa2-888c-4aa7bf465c3d/dqc_reference/reference_markers_gtdb.fasta -out GCA_019894795.1_ASM1989479v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 04:37:39,405] [INFO] Task succeeded: Blastn
[2023-06-28 04:37:39,409] [INFO] Selected 12 target genomes.
[2023-06-28 04:37:39,409] [INFO] Target genome list was writen to GCA_019894795.1_ASM1989479v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 04:37:39,430] [INFO] Task started: fastANI
[2023-06-28 04:37:39,431] [INFO] Running command: fastANI --query /var/lib/cwl/stg0447c05b-a068-4688-90df-1a0179fe7ef2/GCA_019894795.1_ASM1989479v1_genomic.fna.gz --refList GCA_019894795.1_ASM1989479v1_genomic.fna/target_genomes_gtdb.txt --output GCA_019894795.1_ASM1989479v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 04:37:43,506] [INFO] Task succeeded: fastANI
[2023-06-28 04:37:43,510] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 04:37:43,511] [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_019057375.1	s__UBA460 sp002505645	77.0594	109	825	d__Archaea;p__Asgardarchaeota;c__Heimdallarchaeia;o__UBA460;f__UBA460;g__UBA460	95.0	99.91	99.89	0.94	0.94	3	-
GCA_019057815.1	s__18H4-34 sp019057815	76.5956	52	825	d__Archaea;p__Asgardarchaeota;c__Heimdallarchaeia;o__UBA460;f__UBA460;g__18H4-34	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016839985.1	s__UBA460 sp016839985	75.6259	54	825	d__Archaea;p__Asgardarchaeota;c__Heimdallarchaeia;o__UBA460;f__UBA460;g__UBA460	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 04:37:43,513] [INFO] GTDB search result was written to GCA_019894795.1_ASM1989479v1_genomic.fna/result_gtdb.tsv
[2023-06-28 04:37:43,513] [INFO] ===== GTDB Search completed =====
[2023-06-28 04:37:43,516] [INFO] DFAST_QC result json was written to GCA_019894795.1_ASM1989479v1_genomic.fna/dqc_result.json
[2023-06-28 04:37:43,516] [INFO] DFAST_QC completed!
[2023-06-28 04:37:43,517] [INFO] Total running time: 0h0m38s