[2023-06-29 15:10:15,398] [INFO] DFAST_QC pipeline started.
[2023-06-29 15:10:15,400] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 15:10:15,401] [INFO] DQC Reference Directory: /var/lib/cwl/stg5dc02412-2211-40f3-8b18-891f5e2e19c3/dqc_reference
[2023-06-29 15:10:16,890] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 15:10:16,891] [INFO] Task started: Prodigal
[2023-06-29 15:10:16,891] [INFO] Running command: gunzip -c /var/lib/cwl/stg8ea57023-fc18-46c0-b8c7-7cd06a573572/GCA_011375365.1_ASM1137536v1_genomic.fna.gz | prodigal -d GCA_011375365.1_ASM1137536v1_genomic.fna/cds.fna -a GCA_011375365.1_ASM1137536v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 15:10:20,959] [INFO] Task succeeded: Prodigal
[2023-06-29 15:10:20,960] [INFO] Task started: HMMsearch
[2023-06-29 15:10:20,960] [INFO] Running command: hmmsearch --tblout GCA_011375365.1_ASM1137536v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5dc02412-2211-40f3-8b18-891f5e2e19c3/dqc_reference/reference_markers.hmm GCA_011375365.1_ASM1137536v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 15:10:21,267] [INFO] Task succeeded: HMMsearch
[2023-06-29 15:10:21,268] [INFO] Found 6/6 markers.
[2023-06-29 15:10:21,304] [INFO] Query marker FASTA was written to GCA_011375365.1_ASM1137536v1_genomic.fna/markers.fasta
[2023-06-29 15:10:21,304] [INFO] Task started: Blastn
[2023-06-29 15:10:21,304] [INFO] Running command: blastn -query GCA_011375365.1_ASM1137536v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5dc02412-2211-40f3-8b18-891f5e2e19c3/dqc_reference/reference_markers.fasta -out GCA_011375365.1_ASM1137536v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 15:10:22,020] [INFO] Task succeeded: Blastn
[2023-06-29 15:10:22,039] [INFO] Selected 22 target genomes.
[2023-06-29 15:10:22,039] [INFO] Target genome list was writen to GCA_011375365.1_ASM1137536v1_genomic.fna/target_genomes.txt
[2023-06-29 15:10:22,073] [INFO] Task started: fastANI
[2023-06-29 15:10:22,073] [INFO] Running command: fastANI --query /var/lib/cwl/stg8ea57023-fc18-46c0-b8c7-7cd06a573572/GCA_011375365.1_ASM1137536v1_genomic.fna.gz --refList GCA_011375365.1_ASM1137536v1_genomic.fna/target_genomes.txt --output GCA_011375365.1_ASM1137536v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 15:10:37,841] [INFO] Task succeeded: fastANI
[2023-06-29 15:10:37,842] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5dc02412-2211-40f3-8b18-891f5e2e19c3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 15:10:37,842] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5dc02412-2211-40f3-8b18-891f5e2e19c3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 15:10:37,844] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 15:10:37,844] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-29 15:10:37,844] [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
--------------------------------------------------------------------------------
[2023-06-29 15:10:37,850] [INFO] DFAST Taxonomy check result was written to GCA_011375365.1_ASM1137536v1_genomic.fna/tc_result.tsv
[2023-06-29 15:10:37,850] [INFO] ===== Taxonomy check completed =====
[2023-06-29 15:10:37,851] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 15:10:37,851] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5dc02412-2211-40f3-8b18-891f5e2e19c3/dqc_reference/checkm_data
[2023-06-29 15:10:37,854] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 15:10:37,881] [INFO] Task started: CheckM
[2023-06-29 15:10:37,881] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_011375365.1_ASM1137536v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_011375365.1_ASM1137536v1_genomic.fna/checkm_input GCA_011375365.1_ASM1137536v1_genomic.fna/checkm_result
[2023-06-29 15:10:59,050] [INFO] Task succeeded: CheckM
[2023-06-29 15:10:59,051] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 71.99%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 15:10:59,088] [INFO] ===== Completeness check finished =====
[2023-06-29 15:10:59,088] [INFO] ===== Start GTDB Search =====
[2023-06-29 15:10:59,089] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_011375365.1_ASM1137536v1_genomic.fna/markers.fasta)
[2023-06-29 15:10:59,089] [INFO] Task started: Blastn
[2023-06-29 15:10:59,089] [INFO] Running command: blastn -query GCA_011375365.1_ASM1137536v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5dc02412-2211-40f3-8b18-891f5e2e19c3/dqc_reference/reference_markers_gtdb.fasta -out GCA_011375365.1_ASM1137536v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 15:11:00,001] [INFO] Task succeeded: Blastn
[2023-06-29 15:11:00,005] [INFO] Selected 23 target genomes.
[2023-06-29 15:11:00,006] [INFO] Target genome list was writen to GCA_011375365.1_ASM1137536v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 15:11:00,026] [INFO] Task started: fastANI
[2023-06-29 15:11:00,026] [INFO] Running command: fastANI --query /var/lib/cwl/stg8ea57023-fc18-46c0-b8c7-7cd06a573572/GCA_011375365.1_ASM1137536v1_genomic.fna.gz --refList GCA_011375365.1_ASM1137536v1_genomic.fna/target_genomes_gtdb.txt --output GCA_011375365.1_ASM1137536v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 15:11:14,176] [INFO] Task succeeded: fastANI
[2023-06-29 15:11:14,182] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 15:11:14,182] [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_015493745.1	s__J004 sp011051485	83.5377	364	457	d__Bacteria;p__Calditrichota;c__Calditrichia;o__Calditrichales;f__J004;g__J004	95.0	98.79	98.79	0.88	0.88	2	-
GCA_003696775.1	s__J004 sp003696775	77.067	119	457	d__Bacteria;p__Calditrichota;c__Calditrichia;o__Calditrichales;f__J004;g__J004	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 15:11:14,185] [INFO] GTDB search result was written to GCA_011375365.1_ASM1137536v1_genomic.fna/result_gtdb.tsv
[2023-06-29 15:11:14,185] [INFO] ===== GTDB Search completed =====
[2023-06-29 15:11:14,194] [INFO] DFAST_QC result json was written to GCA_011375365.1_ASM1137536v1_genomic.fna/dqc_result.json
[2023-06-29 15:11:14,194] [INFO] DFAST_QC completed!
[2023-06-29 15:11:14,194] [INFO] Total running time: 0h0m59s