[2023-06-19 04:59:05,422] [INFO] DFAST_QC pipeline started.
[2023-06-19 04:59:05,426] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 04:59:05,426] [INFO] DQC Reference Directory: /var/lib/cwl/stg691d0705-ed25-443d-9946-69bb315c5c42/dqc_reference
[2023-06-19 04:59:08,654] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 04:59:08,656] [INFO] Task started: Prodigal
[2023-06-19 04:59:08,657] [INFO] Running command: gunzip -c /var/lib/cwl/stg6c66e3c2-594c-443a-a317-e6e721f1488a/GCA_018694335.1_ASM1869433v1_genomic.fna.gz | prodigal -d GCA_018694335.1_ASM1869433v1_genomic.fna/cds.fna -a GCA_018694335.1_ASM1869433v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 04:59:14,287] [INFO] Task succeeded: Prodigal
[2023-06-19 04:59:14,288] [INFO] Task started: HMMsearch
[2023-06-19 04:59:14,288] [INFO] Running command: hmmsearch --tblout GCA_018694335.1_ASM1869433v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg691d0705-ed25-443d-9946-69bb315c5c42/dqc_reference/reference_markers.hmm GCA_018694335.1_ASM1869433v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 04:59:14,598] [INFO] Task succeeded: HMMsearch
[2023-06-19 04:59:14,601] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg6c66e3c2-594c-443a-a317-e6e721f1488a/GCA_018694335.1_ASM1869433v1_genomic.fna.gz]
[2023-06-19 04:59:14,632] [INFO] Query marker FASTA was written to GCA_018694335.1_ASM1869433v1_genomic.fna/markers.fasta
[2023-06-19 04:59:14,633] [INFO] Task started: Blastn
[2023-06-19 04:59:14,633] [INFO] Running command: blastn -query GCA_018694335.1_ASM1869433v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg691d0705-ed25-443d-9946-69bb315c5c42/dqc_reference/reference_markers.fasta -out GCA_018694335.1_ASM1869433v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 04:59:15,205] [INFO] Task succeeded: Blastn
[2023-06-19 04:59:15,210] [INFO] Selected 12 target genomes.
[2023-06-19 04:59:15,210] [INFO] Target genome list was writen to GCA_018694335.1_ASM1869433v1_genomic.fna/target_genomes.txt
[2023-06-19 04:59:15,211] [INFO] Task started: fastANI
[2023-06-19 04:59:15,211] [INFO] Running command: fastANI --query /var/lib/cwl/stg6c66e3c2-594c-443a-a317-e6e721f1488a/GCA_018694335.1_ASM1869433v1_genomic.fna.gz --refList GCA_018694335.1_ASM1869433v1_genomic.fna/target_genomes.txt --output GCA_018694335.1_ASM1869433v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 04:59:21,337] [INFO] Task succeeded: fastANI
[2023-06-19 04:59:21,337] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg691d0705-ed25-443d-9946-69bb315c5c42/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 04:59:21,338] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg691d0705-ed25-443d-9946-69bb315c5c42/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 04:59:21,339] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 04:59:21,340] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-19 04:59:21,340] [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
--------------------------------------------------------------------------------
[2023-06-19 04:59:21,343] [INFO] DFAST Taxonomy check result was written to GCA_018694335.1_ASM1869433v1_genomic.fna/tc_result.tsv
[2023-06-19 04:59:21,344] [INFO] ===== Taxonomy check completed =====
[2023-06-19 04:59:21,344] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 04:59:21,344] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg691d0705-ed25-443d-9946-69bb315c5c42/dqc_reference/checkm_data
[2023-06-19 04:59:21,347] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 04:59:21,391] [INFO] Task started: CheckM
[2023-06-19 04:59:21,392] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018694335.1_ASM1869433v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018694335.1_ASM1869433v1_genomic.fna/checkm_input GCA_018694335.1_ASM1869433v1_genomic.fna/checkm_result
[2023-06-19 04:59:45,619] [INFO] Task succeeded: CheckM
[2023-06-19 04:59:45,621] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 04:59:45,668] [INFO] ===== Completeness check finished =====
[2023-06-19 04:59:45,669] [INFO] ===== Start GTDB Search =====
[2023-06-19 04:59:45,669] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018694335.1_ASM1869433v1_genomic.fna/markers.fasta)
[2023-06-19 04:59:45,670] [INFO] Task started: Blastn
[2023-06-19 04:59:45,670] [INFO] Running command: blastn -query GCA_018694335.1_ASM1869433v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg691d0705-ed25-443d-9946-69bb315c5c42/dqc_reference/reference_markers_gtdb.fasta -out GCA_018694335.1_ASM1869433v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 04:59:46,446] [INFO] Task succeeded: Blastn
[2023-06-19 04:59:46,453] [INFO] Selected 13 target genomes.
[2023-06-19 04:59:46,453] [INFO] Target genome list was writen to GCA_018694335.1_ASM1869433v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 04:59:46,455] [INFO] Task started: fastANI
[2023-06-19 04:59:46,455] [INFO] Running command: fastANI --query /var/lib/cwl/stg6c66e3c2-594c-443a-a317-e6e721f1488a/GCA_018694335.1_ASM1869433v1_genomic.fna.gz --refList GCA_018694335.1_ASM1869433v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018694335.1_ASM1869433v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 04:59:51,810] [INFO] Task succeeded: fastANI
[2023-06-19 04:59:51,817] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 04:59:51,817] [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_018658715.1	s__JABHGY01 sp018658715	99.8067	686	857	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__UBA1611;g__JABHGY01	95.0	99.87	99.62	0.90	0.78	14	conclusive
GCA_016784605.1	s__JABHGY01 sp016784605	82.0893	445	857	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__UBA1611;g__JABHGY01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018671775.1	s__JABHGY01 sp018671775	77.5745	144	857	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__UBA1611;g__JABHGY01	95.0	99.90	99.87	0.94	0.90	16	-
GCA_018674095.1	s__GCA-2722105 sp018674095	77.2762	54	857	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__UBA1611;g__GCA-2722105	95.0	99.41	99.30	0.88	0.82	13	-
--------------------------------------------------------------------------------
[2023-06-19 04:59:51,819] [INFO] GTDB search result was written to GCA_018694335.1_ASM1869433v1_genomic.fna/result_gtdb.tsv
[2023-06-19 04:59:51,823] [INFO] ===== GTDB Search completed =====
[2023-06-19 04:59:51,830] [INFO] DFAST_QC result json was written to GCA_018694335.1_ASM1869433v1_genomic.fna/dqc_result.json
[2023-06-19 04:59:51,830] [INFO] DFAST_QC completed!
[2023-06-19 04:59:51,831] [INFO] Total running time: 0h0m46s