[2023-06-28 16:36:25,945] [INFO] DFAST_QC pipeline started.
[2023-06-28 16:36:25,948] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 16:36:25,948] [INFO] DQC Reference Directory: /var/lib/cwl/stge431f0eb-6b73-413a-9bad-45a137f4a811/dqc_reference
[2023-06-28 16:36:27,094] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 16:36:27,095] [INFO] Task started: Prodigal
[2023-06-28 16:36:27,095] [INFO] Running command: gunzip -c /var/lib/cwl/stga80822cb-c2c0-43ab-8d7a-ee6f15119dd5/GCA_012727545.1_ASM1272754v1_genomic.fna.gz | prodigal -d GCA_012727545.1_ASM1272754v1_genomic.fna/cds.fna -a GCA_012727545.1_ASM1272754v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 16:36:30,331] [INFO] Task succeeded: Prodigal
[2023-06-28 16:36:30,331] [INFO] Task started: HMMsearch
[2023-06-28 16:36:30,331] [INFO] Running command: hmmsearch --tblout GCA_012727545.1_ASM1272754v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge431f0eb-6b73-413a-9bad-45a137f4a811/dqc_reference/reference_markers.hmm GCA_012727545.1_ASM1272754v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 16:36:30,506] [INFO] Task succeeded: HMMsearch
[2023-06-28 16:36:30,507] [WARNING] Found 5/6 markers. [/var/lib/cwl/stga80822cb-c2c0-43ab-8d7a-ee6f15119dd5/GCA_012727545.1_ASM1272754v1_genomic.fna.gz]
[2023-06-28 16:36:30,526] [INFO] Query marker FASTA was written to GCA_012727545.1_ASM1272754v1_genomic.fna/markers.fasta
[2023-06-28 16:36:30,527] [INFO] Task started: Blastn
[2023-06-28 16:36:30,527] [INFO] Running command: blastn -query GCA_012727545.1_ASM1272754v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge431f0eb-6b73-413a-9bad-45a137f4a811/dqc_reference/reference_markers.fasta -out GCA_012727545.1_ASM1272754v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 16:36:31,074] [INFO] Task succeeded: Blastn
[2023-06-28 16:36:31,078] [INFO] Selected 9 target genomes.
[2023-06-28 16:36:31,078] [INFO] Target genome list was writen to GCA_012727545.1_ASM1272754v1_genomic.fna/target_genomes.txt
[2023-06-28 16:36:31,079] [INFO] Task started: fastANI
[2023-06-28 16:36:31,079] [INFO] Running command: fastANI --query /var/lib/cwl/stga80822cb-c2c0-43ab-8d7a-ee6f15119dd5/GCA_012727545.1_ASM1272754v1_genomic.fna.gz --refList GCA_012727545.1_ASM1272754v1_genomic.fna/target_genomes.txt --output GCA_012727545.1_ASM1272754v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 16:36:34,173] [INFO] Task succeeded: fastANI
[2023-06-28 16:36:34,173] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge431f0eb-6b73-413a-9bad-45a137f4a811/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 16:36:34,174] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge431f0eb-6b73-413a-9bad-45a137f4a811/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 16:36:34,175] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 16:36:34,175] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 16:36:34,175] [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 16:36:34,177] [INFO] DFAST Taxonomy check result was written to GCA_012727545.1_ASM1272754v1_genomic.fna/tc_result.tsv
[2023-06-28 16:36:34,179] [INFO] ===== Taxonomy check completed =====
[2023-06-28 16:36:34,179] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 16:36:34,179] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge431f0eb-6b73-413a-9bad-45a137f4a811/dqc_reference/checkm_data
[2023-06-28 16:36:34,183] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 16:36:34,204] [INFO] Task started: CheckM
[2023-06-28 16:36:34,204] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_012727545.1_ASM1272754v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_012727545.1_ASM1272754v1_genomic.fna/checkm_input GCA_012727545.1_ASM1272754v1_genomic.fna/checkm_result
[2023-06-28 16:36:50,770] [INFO] Task succeeded: CheckM
[2023-06-28 16:36:50,772] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 76.52%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-28 16:36:50,791] [INFO] ===== Completeness check finished =====
[2023-06-28 16:36:50,791] [INFO] ===== Start GTDB Search =====
[2023-06-28 16:36:50,791] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_012727545.1_ASM1272754v1_genomic.fna/markers.fasta)
[2023-06-28 16:36:50,792] [INFO] Task started: Blastn
[2023-06-28 16:36:50,792] [INFO] Running command: blastn -query GCA_012727545.1_ASM1272754v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge431f0eb-6b73-413a-9bad-45a137f4a811/dqc_reference/reference_markers_gtdb.fasta -out GCA_012727545.1_ASM1272754v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 16:36:51,551] [INFO] Task succeeded: Blastn
[2023-06-28 16:36:51,556] [INFO] Selected 8 target genomes.
[2023-06-28 16:36:51,556] [INFO] Target genome list was writen to GCA_012727545.1_ASM1272754v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 16:36:51,560] [INFO] Task started: fastANI
[2023-06-28 16:36:51,560] [INFO] Running command: fastANI --query /var/lib/cwl/stga80822cb-c2c0-43ab-8d7a-ee6f15119dd5/GCA_012727545.1_ASM1272754v1_genomic.fna.gz --refList GCA_012727545.1_ASM1272754v1_genomic.fna/target_genomes_gtdb.txt --output GCA_012727545.1_ASM1272754v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 16:36:54,580] [INFO] Task succeeded: fastANI
[2023-06-28 16:36:54,587] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 16:36:54,587] [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_012727545.1	s__Syner-03 sp012727545	100.0	324	328	d__Bacteria;p__Synergistota;c__Synergistia;o__Synergistales;f__Synergistaceae;g__Syner-03	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002428495.1	s__Syner-03 sp002428495	87.7914	289	328	d__Bacteria;p__Synergistota;c__Synergistia;o__Synergistales;f__Synergistaceae;g__Syner-03	95.0	99.46	99.46	0.97	0.97	2	-
GCA_002839185.1	s__Syner-03 sp002839185	87.4136	305	328	d__Bacteria;p__Synergistota;c__Synergistia;o__Synergistales;f__Synergistaceae;g__Syner-03	95.0	98.77	98.13	0.94	0.86	5	-
GCA_012513245.1	s__Syner-03 sp012513245	82.3199	235	328	d__Bacteria;p__Synergistota;c__Synergistia;o__Synergistales;f__Synergistaceae;g__Syner-03	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002316795.1	s__Syner-03 sp002316795	81.1296	200	328	d__Bacteria;p__Synergistota;c__Synergistia;o__Synergistales;f__Synergistaceae;g__Syner-03	95.0	99.61	99.43	0.90	0.87	7	-
GCA_002306075.1	s__Syner-03 sp002306075	79.405	144	328	d__Bacteria;p__Synergistota;c__Synergistia;o__Synergistales;f__Synergistaceae;g__Syner-03	95.0	99.59	99.50	0.89	0.87	4	-
--------------------------------------------------------------------------------
[2023-06-28 16:36:54,595] [INFO] GTDB search result was written to GCA_012727545.1_ASM1272754v1_genomic.fna/result_gtdb.tsv
[2023-06-28 16:36:54,598] [INFO] ===== GTDB Search completed =====
[2023-06-28 16:36:54,605] [INFO] DFAST_QC result json was written to GCA_012727545.1_ASM1272754v1_genomic.fna/dqc_result.json
[2023-06-28 16:36:54,605] [INFO] DFAST_QC completed!
[2023-06-28 16:36:54,605] [INFO] Total running time: 0h0m29s