[2023-06-18 10:35:28,944] [INFO] DFAST_QC pipeline started.
[2023-06-18 10:35:28,950] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 10:35:28,950] [INFO] DQC Reference Directory: /var/lib/cwl/stg3b00a38b-9354-4c8f-9d79-7851c537a529/dqc_reference
[2023-06-18 10:35:30,190] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 10:35:30,191] [INFO] Task started: Prodigal
[2023-06-18 10:35:30,191] [INFO] Running command: gunzip -c /var/lib/cwl/stg5e90e16b-8f77-4f8b-b531-af70465065c4/GCA_018657185.1_ASM1865718v1_genomic.fna.gz | prodigal -d GCA_018657185.1_ASM1865718v1_genomic.fna/cds.fna -a GCA_018657185.1_ASM1865718v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 10:35:34,365] [INFO] Task succeeded: Prodigal
[2023-06-18 10:35:34,366] [INFO] Task started: HMMsearch
[2023-06-18 10:35:34,366] [INFO] Running command: hmmsearch --tblout GCA_018657185.1_ASM1865718v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3b00a38b-9354-4c8f-9d79-7851c537a529/dqc_reference/reference_markers.hmm GCA_018657185.1_ASM1865718v1_genomic.fna/protein.faa > /dev/null
[2023-06-18 10:35:34,589] [INFO] Task succeeded: HMMsearch
[2023-06-18 10:35:34,590] [INFO] Found 6/6 markers.
[2023-06-18 10:35:34,614] [INFO] Query marker FASTA was written to GCA_018657185.1_ASM1865718v1_genomic.fna/markers.fasta
[2023-06-18 10:35:34,615] [INFO] Task started: Blastn
[2023-06-18 10:35:34,615] [INFO] Running command: blastn -query GCA_018657185.1_ASM1865718v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3b00a38b-9354-4c8f-9d79-7851c537a529/dqc_reference/reference_markers.fasta -out GCA_018657185.1_ASM1865718v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 10:35:35,203] [INFO] Task succeeded: Blastn
[2023-06-18 10:35:35,208] [INFO] Selected 13 target genomes.
[2023-06-18 10:35:35,209] [INFO] Target genome list was writen to GCA_018657185.1_ASM1865718v1_genomic.fna/target_genomes.txt
[2023-06-18 10:35:35,212] [INFO] Task started: fastANI
[2023-06-18 10:35:35,212] [INFO] Running command: fastANI --query /var/lib/cwl/stg5e90e16b-8f77-4f8b-b531-af70465065c4/GCA_018657185.1_ASM1865718v1_genomic.fna.gz --refList GCA_018657185.1_ASM1865718v1_genomic.fna/target_genomes.txt --output GCA_018657185.1_ASM1865718v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 10:35:41,380] [INFO] Task succeeded: fastANI
[2023-06-18 10:35:41,381] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3b00a38b-9354-4c8f-9d79-7851c537a529/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 10:35:41,381] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3b00a38b-9354-4c8f-9d79-7851c537a529/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 10:35:41,383] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-18 10:35:41,384] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-18 10:35:41,384] [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 10:35:41,386] [INFO] DFAST Taxonomy check result was written to GCA_018657185.1_ASM1865718v1_genomic.fna/tc_result.tsv
[2023-06-18 10:35:41,389] [INFO] ===== Taxonomy check completed =====
[2023-06-18 10:35:41,389] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 10:35:41,390] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3b00a38b-9354-4c8f-9d79-7851c537a529/dqc_reference/checkm_data
[2023-06-18 10:35:41,393] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 10:35:41,429] [INFO] Task started: CheckM
[2023-06-18 10:35:41,430] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018657185.1_ASM1865718v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018657185.1_ASM1865718v1_genomic.fna/checkm_input GCA_018657185.1_ASM1865718v1_genomic.fna/checkm_result
[2023-06-18 10:36:02,050] [INFO] Task succeeded: CheckM
[2023-06-18 10:36:02,052] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-18 10:36:02,072] [INFO] ===== Completeness check finished =====
[2023-06-18 10:36:02,073] [INFO] ===== Start GTDB Search =====
[2023-06-18 10:36:02,073] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018657185.1_ASM1865718v1_genomic.fna/markers.fasta)
[2023-06-18 10:36:02,074] [INFO] Task started: Blastn
[2023-06-18 10:36:02,074] [INFO] Running command: blastn -query GCA_018657185.1_ASM1865718v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3b00a38b-9354-4c8f-9d79-7851c537a529/dqc_reference/reference_markers_gtdb.fasta -out GCA_018657185.1_ASM1865718v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 10:36:02,926] [INFO] Task succeeded: Blastn
[2023-06-18 10:36:02,932] [INFO] Selected 18 target genomes.
[2023-06-18 10:36:02,932] [INFO] Target genome list was writen to GCA_018657185.1_ASM1865718v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 10:36:03,037] [INFO] Task started: fastANI
[2023-06-18 10:36:03,038] [INFO] Running command: fastANI --query /var/lib/cwl/stg5e90e16b-8f77-4f8b-b531-af70465065c4/GCA_018657185.1_ASM1865718v1_genomic.fna.gz --refList GCA_018657185.1_ASM1865718v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018657185.1_ASM1865718v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 10:36:08,866] [INFO] Task succeeded: fastANI
[2023-06-18 10:36:08,870] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-18 10:36:08,870] [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_018651745.1	s__JAAZYX01 sp018651745	99.9978	576	584	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__TCS55;g__JAAZYX01	95.0	99.98	99.94	0.97	0.95	16	conclusive
GCA_014239435.1	s__JAAZYX01 sp014239435	78.5658	258	584	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__TCS55;g__JAAZYX01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-18 10:36:08,873] [INFO] GTDB search result was written to GCA_018657185.1_ASM1865718v1_genomic.fna/result_gtdb.tsv
[2023-06-18 10:36:08,874] [INFO] ===== GTDB Search completed =====
[2023-06-18 10:36:08,877] [INFO] DFAST_QC result json was written to GCA_018657185.1_ASM1865718v1_genomic.fna/dqc_result.json
[2023-06-18 10:36:08,878] [INFO] DFAST_QC completed!
[2023-06-18 10:36:08,878] [INFO] Total running time: 0h0m40s