[2023-06-28 23:57:23,513] [INFO] DFAST_QC pipeline started.
[2023-06-28 23:57:23,516] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 23:57:23,517] [INFO] DQC Reference Directory: /var/lib/cwl/stge4a06ac6-5767-485b-9686-b9517f54a8c0/dqc_reference
[2023-06-28 23:57:24,892] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 23:57:24,898] [INFO] Task started: Prodigal
[2023-06-28 23:57:24,898] [INFO] Running command: gunzip -c /var/lib/cwl/stg35532185-654b-4b7c-a372-63ab9340295b/GCA_017548775.1_ASM1754877v1_genomic.fna.gz | prodigal -d GCA_017548775.1_ASM1754877v1_genomic.fna/cds.fna -a GCA_017548775.1_ASM1754877v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 23:57:27,934] [INFO] Task succeeded: Prodigal
[2023-06-28 23:57:27,934] [INFO] Task started: HMMsearch
[2023-06-28 23:57:27,935] [INFO] Running command: hmmsearch --tblout GCA_017548775.1_ASM1754877v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge4a06ac6-5767-485b-9686-b9517f54a8c0/dqc_reference/reference_markers.hmm GCA_017548775.1_ASM1754877v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 23:57:28,168] [INFO] Task succeeded: HMMsearch
[2023-06-28 23:57:28,169] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg35532185-654b-4b7c-a372-63ab9340295b/GCA_017548775.1_ASM1754877v1_genomic.fna.gz]
[2023-06-28 23:57:28,191] [INFO] Query marker FASTA was written to GCA_017548775.1_ASM1754877v1_genomic.fna/markers.fasta
[2023-06-28 23:57:28,191] [INFO] Task started: Blastn
[2023-06-28 23:57:28,191] [INFO] Running command: blastn -query GCA_017548775.1_ASM1754877v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge4a06ac6-5767-485b-9686-b9517f54a8c0/dqc_reference/reference_markers.fasta -out GCA_017548775.1_ASM1754877v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 23:57:28,835] [INFO] Task succeeded: Blastn
[2023-06-28 23:57:28,839] [INFO] Selected 25 target genomes.
[2023-06-28 23:57:28,839] [INFO] Target genome list was writen to GCA_017548775.1_ASM1754877v1_genomic.fna/target_genomes.txt
[2023-06-28 23:57:28,844] [INFO] Task started: fastANI
[2023-06-28 23:57:28,844] [INFO] Running command: fastANI --query /var/lib/cwl/stg35532185-654b-4b7c-a372-63ab9340295b/GCA_017548775.1_ASM1754877v1_genomic.fna.gz --refList GCA_017548775.1_ASM1754877v1_genomic.fna/target_genomes.txt --output GCA_017548775.1_ASM1754877v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 23:57:43,354] [INFO] Task succeeded: fastANI
[2023-06-28 23:57:43,355] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge4a06ac6-5767-485b-9686-b9517f54a8c0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 23:57:43,355] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge4a06ac6-5767-485b-9686-b9517f54a8c0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 23:57:43,357] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 23:57:43,357] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 23:57:43,357] [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 23:57:43,359] [INFO] DFAST Taxonomy check result was written to GCA_017548775.1_ASM1754877v1_genomic.fna/tc_result.tsv
[2023-06-28 23:57:43,360] [INFO] ===== Taxonomy check completed =====
[2023-06-28 23:57:43,360] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 23:57:43,360] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge4a06ac6-5767-485b-9686-b9517f54a8c0/dqc_reference/checkm_data
[2023-06-28 23:57:43,363] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 23:57:43,396] [INFO] Task started: CheckM
[2023-06-28 23:57:43,396] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_017548775.1_ASM1754877v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_017548775.1_ASM1754877v1_genomic.fna/checkm_input GCA_017548775.1_ASM1754877v1_genomic.fna/checkm_result
[2023-06-28 23:58:01,204] [INFO] Task succeeded: CheckM
[2023-06-28 23:58:01,206] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 59.04%
Contamintation: 11.57%
Strain heterogeneity: 91.67%
--------------------------------------------------------------------------------
[2023-06-28 23:58:01,230] [INFO] ===== Completeness check finished =====
[2023-06-28 23:58:01,230] [INFO] ===== Start GTDB Search =====
[2023-06-28 23:58:01,231] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_017548775.1_ASM1754877v1_genomic.fna/markers.fasta)
[2023-06-28 23:58:01,231] [INFO] Task started: Blastn
[2023-06-28 23:58:01,231] [INFO] Running command: blastn -query GCA_017548775.1_ASM1754877v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge4a06ac6-5767-485b-9686-b9517f54a8c0/dqc_reference/reference_markers_gtdb.fasta -out GCA_017548775.1_ASM1754877v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 23:58:02,191] [INFO] Task succeeded: Blastn
[2023-06-28 23:58:02,195] [INFO] Selected 7 target genomes.
[2023-06-28 23:58:02,195] [INFO] Target genome list was writen to GCA_017548775.1_ASM1754877v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 23:58:02,205] [INFO] Task started: fastANI
[2023-06-28 23:58:02,206] [INFO] Running command: fastANI --query /var/lib/cwl/stg35532185-654b-4b7c-a372-63ab9340295b/GCA_017548775.1_ASM1754877v1_genomic.fna.gz --refList GCA_017548775.1_ASM1754877v1_genomic.fna/target_genomes_gtdb.txt --output GCA_017548775.1_ASM1754877v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 23:58:05,234] [INFO] Task succeeded: fastANI
[2023-06-28 23:58:05,246] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 23:58:05,247] [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_017538995.1	s__UBA3766 sp017538995	92.397	318	398	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA3766	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016284175.1	s__UBA3766 sp016284175	92.0742	330	398	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA3766	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017962225.1	s__UBA3766 sp017962225	90.251	287	398	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA3766	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017618075.1	s__UBA3766 sp017618075	89.4708	313	398	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA3766	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900100245.1	s__UBA3766 sp900100245	87.6878	317	398	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA3766	95.0	95.14	95.14	0.89	0.89	2	-
GCA_902765365.1	s__UBA3766 sp902765365	85.9905	274	398	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA3766	95.0	98.95	98.95	0.86	0.86	2	-
GCA_016285575.1	s__UBA3766 sp016285575	79.1663	109	398	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA3766	95.0	95.58	95.34	0.86	0.83	4	-
--------------------------------------------------------------------------------
[2023-06-28 23:58:05,249] [INFO] GTDB search result was written to GCA_017548775.1_ASM1754877v1_genomic.fna/result_gtdb.tsv
[2023-06-28 23:58:05,250] [INFO] ===== GTDB Search completed =====
[2023-06-28 23:58:05,255] [INFO] DFAST_QC result json was written to GCA_017548775.1_ASM1754877v1_genomic.fna/dqc_result.json
[2023-06-28 23:58:05,256] [INFO] DFAST_QC completed!
[2023-06-28 23:58:05,256] [INFO] Total running time: 0h0m42s