[2023-06-18 21:35:33,203] [INFO] DFAST_QC pipeline started.
[2023-06-18 21:35:33,207] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 21:35:33,207] [INFO] DQC Reference Directory: /var/lib/cwl/stg266d9961-72ca-4708-bdd7-3c26bd8368bd/dqc_reference
[2023-06-18 21:35:34,783] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 21:35:34,784] [INFO] Task started: Prodigal
[2023-06-18 21:35:34,784] [INFO] Running command: gunzip -c /var/lib/cwl/stgd842ee4d-b164-40d4-a92e-5d51122ddee9/GCA_018694875.1_ASM1869487v1_genomic.fna.gz | prodigal -d GCA_018694875.1_ASM1869487v1_genomic.fna/cds.fna -a GCA_018694875.1_ASM1869487v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 21:35:39,277] [INFO] Task succeeded: Prodigal
[2023-06-18 21:35:39,278] [INFO] Task started: HMMsearch
[2023-06-18 21:35:39,278] [INFO] Running command: hmmsearch --tblout GCA_018694875.1_ASM1869487v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg266d9961-72ca-4708-bdd7-3c26bd8368bd/dqc_reference/reference_markers.hmm GCA_018694875.1_ASM1869487v1_genomic.fna/protein.faa > /dev/null
[2023-06-18 21:35:39,534] [INFO] Task succeeded: HMMsearch
[2023-06-18 21:35:39,536] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgd842ee4d-b164-40d4-a92e-5d51122ddee9/GCA_018694875.1_ASM1869487v1_genomic.fna.gz]
[2023-06-18 21:35:39,571] [INFO] Query marker FASTA was written to GCA_018694875.1_ASM1869487v1_genomic.fna/markers.fasta
[2023-06-18 21:35:39,572] [INFO] Task started: Blastn
[2023-06-18 21:35:39,572] [INFO] Running command: blastn -query GCA_018694875.1_ASM1869487v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg266d9961-72ca-4708-bdd7-3c26bd8368bd/dqc_reference/reference_markers.fasta -out GCA_018694875.1_ASM1869487v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 21:35:40,189] [INFO] Task succeeded: Blastn
[2023-06-18 21:35:40,198] [INFO] Selected 13 target genomes.
[2023-06-18 21:35:40,198] [INFO] Target genome list was writen to GCA_018694875.1_ASM1869487v1_genomic.fna/target_genomes.txt
[2023-06-18 21:35:40,201] [INFO] Task started: fastANI
[2023-06-18 21:35:40,201] [INFO] Running command: fastANI --query /var/lib/cwl/stgd842ee4d-b164-40d4-a92e-5d51122ddee9/GCA_018694875.1_ASM1869487v1_genomic.fna.gz --refList GCA_018694875.1_ASM1869487v1_genomic.fna/target_genomes.txt --output GCA_018694875.1_ASM1869487v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 21:35:47,277] [INFO] Task succeeded: fastANI
[2023-06-18 21:35:47,277] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg266d9961-72ca-4708-bdd7-3c26bd8368bd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 21:35:47,277] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg266d9961-72ca-4708-bdd7-3c26bd8368bd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 21:35:47,279] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-18 21:35:47,279] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-18 21:35:47,279] [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
--------------------------------------------------------------------------------
[2023-06-18 21:35:47,283] [INFO] DFAST Taxonomy check result was written to GCA_018694875.1_ASM1869487v1_genomic.fna/tc_result.tsv
[2023-06-18 21:35:47,284] [INFO] ===== Taxonomy check completed =====
[2023-06-18 21:35:47,284] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 21:35:47,284] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg266d9961-72ca-4708-bdd7-3c26bd8368bd/dqc_reference/checkm_data
[2023-06-18 21:35:47,287] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 21:35:47,312] [INFO] Task started: CheckM
[2023-06-18 21:35:47,313] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018694875.1_ASM1869487v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018694875.1_ASM1869487v1_genomic.fna/checkm_input GCA_018694875.1_ASM1869487v1_genomic.fna/checkm_result
[2023-06-18 21:36:08,204] [INFO] Task succeeded: CheckM
[2023-06-18 21:36:08,205] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 77.78%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-18 21:36:08,237] [INFO] ===== Completeness check finished =====
[2023-06-18 21:36:08,237] [INFO] ===== Start GTDB Search =====
[2023-06-18 21:36:08,238] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018694875.1_ASM1869487v1_genomic.fna/markers.fasta)
[2023-06-18 21:36:08,238] [INFO] Task started: Blastn
[2023-06-18 21:36:08,238] [INFO] Running command: blastn -query GCA_018694875.1_ASM1869487v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg266d9961-72ca-4708-bdd7-3c26bd8368bd/dqc_reference/reference_markers_gtdb.fasta -out GCA_018694875.1_ASM1869487v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 21:36:09,000] [INFO] Task succeeded: Blastn
[2023-06-18 21:36:09,008] [INFO] Selected 20 target genomes.
[2023-06-18 21:36:09,008] [INFO] Target genome list was writen to GCA_018694875.1_ASM1869487v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 21:36:09,017] [INFO] Task started: fastANI
[2023-06-18 21:36:09,017] [INFO] Running command: fastANI --query /var/lib/cwl/stgd842ee4d-b164-40d4-a92e-5d51122ddee9/GCA_018694875.1_ASM1869487v1_genomic.fna.gz --refList GCA_018694875.1_ASM1869487v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018694875.1_ASM1869487v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 21:36:16,538] [INFO] Task succeeded: fastANI
[2023-06-18 21:36:16,547] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-18 21:36:16,548] [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_018692355.1	s__GCA-2722105 sp018692355	99.1634	443	571	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__UBA1611;g__GCA-2722105	95.0	99.23	99.02	0.79	0.73	14	conclusive
GCA_015658495.1	s__GCA-2722105 sp015658495	81.0824	206	571	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__UBA1611;g__GCA-2722105	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018674095.1	s__GCA-2722105 sp018674095	79.3043	176	571	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__UBA1611;g__GCA-2722105	95.0	99.41	99.30	0.88	0.82	13	-
GCA_018649625.1	s__GCA-2722105 sp018649625	77.3973	133	571	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__UBA1611;g__GCA-2722105	95.0	99.96	99.90	0.93	0.85	15	-
--------------------------------------------------------------------------------
[2023-06-18 21:36:16,550] [INFO] GTDB search result was written to GCA_018694875.1_ASM1869487v1_genomic.fna/result_gtdb.tsv
[2023-06-18 21:36:16,550] [INFO] ===== GTDB Search completed =====
[2023-06-18 21:36:16,552] [INFO] DFAST_QC result json was written to GCA_018694875.1_ASM1869487v1_genomic.fna/dqc_result.json
[2023-06-18 21:36:16,552] [INFO] DFAST_QC completed!
[2023-06-18 21:36:16,552] [INFO] Total running time: 0h0m43s