[2023-06-27 06:06:17,966] [INFO] DFAST_QC pipeline started.
[2023-06-27 06:06:17,970] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 06:06:17,970] [INFO] DQC Reference Directory: /var/lib/cwl/stgd9d004a6-3cfc-4f1b-985d-9f2858dc5cfd/dqc_reference
[2023-06-27 06:06:19,198] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 06:06:19,199] [INFO] Task started: Prodigal
[2023-06-27 06:06:19,199] [INFO] Running command: gunzip -c /var/lib/cwl/stg6d6f6fed-8786-4196-88c6-0637cebb4bc0/GCA_002697115.1_ASM269711v1_genomic.fna.gz | prodigal -d GCA_002697115.1_ASM269711v1_genomic.fna/cds.fna -a GCA_002697115.1_ASM269711v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 06:06:23,802] [INFO] Task succeeded: Prodigal
[2023-06-27 06:06:23,803] [INFO] Task started: HMMsearch
[2023-06-27 06:06:23,803] [INFO] Running command: hmmsearch --tblout GCA_002697115.1_ASM269711v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd9d004a6-3cfc-4f1b-985d-9f2858dc5cfd/dqc_reference/reference_markers.hmm GCA_002697115.1_ASM269711v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 06:06:24,036] [INFO] Task succeeded: HMMsearch
[2023-06-27 06:06:24,038] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg6d6f6fed-8786-4196-88c6-0637cebb4bc0/GCA_002697115.1_ASM269711v1_genomic.fna.gz]
[2023-06-27 06:06:24,067] [INFO] Query marker FASTA was written to GCA_002697115.1_ASM269711v1_genomic.fna/markers.fasta
[2023-06-27 06:06:24,068] [INFO] Task started: Blastn
[2023-06-27 06:06:24,068] [INFO] Running command: blastn -query GCA_002697115.1_ASM269711v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd9d004a6-3cfc-4f1b-985d-9f2858dc5cfd/dqc_reference/reference_markers.fasta -out GCA_002697115.1_ASM269711v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 06:06:24,550] [INFO] Task succeeded: Blastn
[2023-06-27 06:06:24,554] [INFO] Selected 5 target genomes.
[2023-06-27 06:06:24,555] [INFO] Target genome list was writen to GCA_002697115.1_ASM269711v1_genomic.fna/target_genomes.txt
[2023-06-27 06:06:24,558] [INFO] Task started: fastANI
[2023-06-27 06:06:24,558] [INFO] Running command: fastANI --query /var/lib/cwl/stg6d6f6fed-8786-4196-88c6-0637cebb4bc0/GCA_002697115.1_ASM269711v1_genomic.fna.gz --refList GCA_002697115.1_ASM269711v1_genomic.fna/target_genomes.txt --output GCA_002697115.1_ASM269711v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 06:06:27,802] [INFO] Task succeeded: fastANI
[2023-06-27 06:06:27,803] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd9d004a6-3cfc-4f1b-985d-9f2858dc5cfd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 06:06:27,803] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd9d004a6-3cfc-4f1b-985d-9f2858dc5cfd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 06:06:27,805] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 06:06:27,805] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-27 06:06:27,806] [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
--------------------------------------------------------------------------------
[2023-06-27 06:06:27,808] [INFO] DFAST Taxonomy check result was written to GCA_002697115.1_ASM269711v1_genomic.fna/tc_result.tsv
[2023-06-27 06:06:27,809] [INFO] ===== Taxonomy check completed =====
[2023-06-27 06:06:27,809] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 06:06:27,809] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd9d004a6-3cfc-4f1b-985d-9f2858dc5cfd/dqc_reference/checkm_data
[2023-06-27 06:06:27,813] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 06:06:27,868] [INFO] Task started: CheckM
[2023-06-27 06:06:27,868] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_002697115.1_ASM269711v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_002697115.1_ASM269711v1_genomic.fna/checkm_input GCA_002697115.1_ASM269711v1_genomic.fna/checkm_result
[2023-06-27 06:06:49,597] [INFO] Task succeeded: CheckM
[2023-06-27 06:06:49,599] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 58.33%
Contamintation: 9.09%
Strain heterogeneity: 8.33%
--------------------------------------------------------------------------------
[2023-06-27 06:06:49,632] [INFO] ===== Completeness check finished =====
[2023-06-27 06:06:49,632] [INFO] ===== Start GTDB Search =====
[2023-06-27 06:06:49,633] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_002697115.1_ASM269711v1_genomic.fna/markers.fasta)
[2023-06-27 06:06:49,633] [INFO] Task started: Blastn
[2023-06-27 06:06:49,633] [INFO] Running command: blastn -query GCA_002697115.1_ASM269711v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd9d004a6-3cfc-4f1b-985d-9f2858dc5cfd/dqc_reference/reference_markers_gtdb.fasta -out GCA_002697115.1_ASM269711v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 06:06:50,095] [INFO] Task succeeded: Blastn
[2023-06-27 06:06:50,099] [INFO] Selected 8 target genomes.
[2023-06-27 06:06:50,099] [INFO] Target genome list was writen to GCA_002697115.1_ASM269711v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 06:06:50,108] [INFO] Task started: fastANI
[2023-06-27 06:06:50,108] [INFO] Running command: fastANI --query /var/lib/cwl/stg6d6f6fed-8786-4196-88c6-0637cebb4bc0/GCA_002697115.1_ASM269711v1_genomic.fna.gz --refList GCA_002697115.1_ASM269711v1_genomic.fna/target_genomes_gtdb.txt --output GCA_002697115.1_ASM269711v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 06:06:55,811] [INFO] Task succeeded: fastANI
[2023-06-27 06:06:55,818] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-27 06:06:55,818] [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_002705165.1	s__UBA721 sp002705165	97.8998	376	587	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__UBA721	95.0	97.82	97.82	0.67	0.67	2	conclusive
GCA_002698965.1	s__UBA721 sp002698965	88.4558	449	587	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__UBA721	95.0	99.68	99.68	0.87	0.87	2	-
GCA_002709045.1	s__UBA721 sp002709045	79.007	247	587	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__UBA721	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002701385.1	s__UBA721 sp002701385	78.0087	112	587	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__UBA721	95.0	97.70	97.13	0.90	0.85	6	-
GCA_002717145.1	s__UBA721 sp002717145	78.0029	137	587	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__UBA721	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002348315.1	s__UBA721 sp002348315	77.4054	92	587	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__UBA721	95.0	99.57	99.57	0.92	0.92	2	-
--------------------------------------------------------------------------------
[2023-06-27 06:06:55,820] [INFO] GTDB search result was written to GCA_002697115.1_ASM269711v1_genomic.fna/result_gtdb.tsv
[2023-06-27 06:06:55,821] [INFO] ===== GTDB Search completed =====
[2023-06-27 06:06:55,826] [INFO] DFAST_QC result json was written to GCA_002697115.1_ASM269711v1_genomic.fna/dqc_result.json
[2023-06-27 06:06:55,826] [INFO] DFAST_QC completed!
[2023-06-27 06:06:55,826] [INFO] Total running time: 0h0m38s