[2023-06-27 02:40:41,528] [INFO] DFAST_QC pipeline started.
[2023-06-27 02:40:41,531] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 02:40:41,531] [INFO] DQC Reference Directory: /var/lib/cwl/stgb910f213-72a3-4e97-b75a-8c7e3068f763/dqc_reference
[2023-06-27 02:40:42,778] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 02:40:42,779] [INFO] Task started: Prodigal
[2023-06-27 02:40:42,780] [INFO] Running command: gunzip -c /var/lib/cwl/stg89a7d535-cb29-4a7a-b294-56f054cbbcb9/GCA_026400875.1_ASM2640087v1_genomic.fna.gz | prodigal -d GCA_026400875.1_ASM2640087v1_genomic.fna/cds.fna -a GCA_026400875.1_ASM2640087v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 02:41:01,461] [INFO] Task succeeded: Prodigal
[2023-06-27 02:41:01,461] [INFO] Task started: HMMsearch
[2023-06-27 02:41:01,461] [INFO] Running command: hmmsearch --tblout GCA_026400875.1_ASM2640087v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb910f213-72a3-4e97-b75a-8c7e3068f763/dqc_reference/reference_markers.hmm GCA_026400875.1_ASM2640087v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 02:41:01,818] [INFO] Task succeeded: HMMsearch
[2023-06-27 02:41:01,820] [INFO] Found 6/6 markers.
[2023-06-27 02:41:01,880] [INFO] Query marker FASTA was written to GCA_026400875.1_ASM2640087v1_genomic.fna/markers.fasta
[2023-06-27 02:41:01,881] [INFO] Task started: Blastn
[2023-06-27 02:41:01,881] [INFO] Running command: blastn -query GCA_026400875.1_ASM2640087v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb910f213-72a3-4e97-b75a-8c7e3068f763/dqc_reference/reference_markers.fasta -out GCA_026400875.1_ASM2640087v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 02:41:02,504] [INFO] Task succeeded: Blastn
[2023-06-27 02:41:02,518] [INFO] Selected 23 target genomes.
[2023-06-27 02:41:02,519] [INFO] Target genome list was writen to GCA_026400875.1_ASM2640087v1_genomic.fna/target_genomes.txt
[2023-06-27 02:41:02,524] [INFO] Task started: fastANI
[2023-06-27 02:41:02,525] [INFO] Running command: fastANI --query /var/lib/cwl/stg89a7d535-cb29-4a7a-b294-56f054cbbcb9/GCA_026400875.1_ASM2640087v1_genomic.fna.gz --refList GCA_026400875.1_ASM2640087v1_genomic.fna/target_genomes.txt --output GCA_026400875.1_ASM2640087v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 02:41:21,686] [INFO] Task succeeded: fastANI
[2023-06-27 02:41:21,686] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb910f213-72a3-4e97-b75a-8c7e3068f763/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 02:41:21,687] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb910f213-72a3-4e97-b75a-8c7e3068f763/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 02:41:21,693] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 02:41:21,693] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-27 02:41:21,694] [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
Fuerstiella marisgermanici	strain=NH11	GCA_001983935.1	1891926	1891926	type	True	75.4364	67	1902	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-27 02:41:21,726] [INFO] DFAST Taxonomy check result was written to GCA_026400875.1_ASM2640087v1_genomic.fna/tc_result.tsv
[2023-06-27 02:41:21,727] [INFO] ===== Taxonomy check completed =====
[2023-06-27 02:41:21,727] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 02:41:21,727] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb910f213-72a3-4e97-b75a-8c7e3068f763/dqc_reference/checkm_data
[2023-06-27 02:41:21,730] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 02:41:21,795] [INFO] Task started: CheckM
[2023-06-27 02:41:21,796] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_026400875.1_ASM2640087v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_026400875.1_ASM2640087v1_genomic.fna/checkm_input GCA_026400875.1_ASM2640087v1_genomic.fna/checkm_result
[2023-06-27 02:42:19,240] [INFO] Task succeeded: CheckM
[2023-06-27 02:42:19,242] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 02:42:19,265] [INFO] ===== Completeness check finished =====
[2023-06-27 02:42:19,265] [INFO] ===== Start GTDB Search =====
[2023-06-27 02:42:19,266] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_026400875.1_ASM2640087v1_genomic.fna/markers.fasta)
[2023-06-27 02:42:19,266] [INFO] Task started: Blastn
[2023-06-27 02:42:19,266] [INFO] Running command: blastn -query GCA_026400875.1_ASM2640087v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb910f213-72a3-4e97-b75a-8c7e3068f763/dqc_reference/reference_markers_gtdb.fasta -out GCA_026400875.1_ASM2640087v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 02:42:20,048] [INFO] Task succeeded: Blastn
[2023-06-27 02:42:20,053] [INFO] Selected 23 target genomes.
[2023-06-27 02:42:20,053] [INFO] Target genome list was writen to GCA_026400875.1_ASM2640087v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 02:42:20,066] [INFO] Task started: fastANI
[2023-06-27 02:42:20,066] [INFO] Running command: fastANI --query /var/lib/cwl/stg89a7d535-cb29-4a7a-b294-56f054cbbcb9/GCA_026400875.1_ASM2640087v1_genomic.fna.gz --refList GCA_026400875.1_ASM2640087v1_genomic.fna/target_genomes_gtdb.txt --output GCA_026400875.1_ASM2640087v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 02:42:44,897] [INFO] Task succeeded: fastANI
[2023-06-27 02:42:44,913] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-27 02:42:44,913] [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_003670925.1	s__SXXK01 sp003670925	99.08	1591	1902	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__SXXK01	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_003669615.1	s__SXXK01 sp003669615	76.808	104	1902	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__SXXK01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903871805.1	s__SXXK01 sp903871805	76.5642	79	1902	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__SXXK01	95.0	99.56	99.46	0.84	0.84	3	-
GCA_016795145.1	s__SXXK01 sp016795145	76.0091	135	1902	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__SXXK01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903896675.1	s__SXXK01 sp903896675	75.6789	78	1902	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__SXXK01	95.0	99.51	99.43	0.86	0.84	7	-
GCA_005791255.1	s__SXXK01 sp005791255	75.649	59	1902	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__SXXK01	95.0	98.10	98.10	0.89	0.89	2	-
GCA_903924405.1	s__SXXK01 sp903924405	75.562	75	1902	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__SXXK01	95.0	99.71	99.71	0.88	0.88	2	-
GCF_001983935.1	s__Fuerstia marisgermanicae	75.4528	66	1902	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Fuerstia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-27 02:42:44,916] [INFO] GTDB search result was written to GCA_026400875.1_ASM2640087v1_genomic.fna/result_gtdb.tsv
[2023-06-27 02:42:44,916] [INFO] ===== GTDB Search completed =====
[2023-06-27 02:42:44,924] [INFO] DFAST_QC result json was written to GCA_026400875.1_ASM2640087v1_genomic.fna/dqc_result.json
[2023-06-27 02:42:44,924] [INFO] DFAST_QC completed!
[2023-06-27 02:42:44,924] [INFO] Total running time: 0h2m3s