[2023-06-13 13:44:18,769] [INFO] DFAST_QC pipeline started.
[2023-06-13 13:44:18,771] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 13:44:18,771] [INFO] DQC Reference Directory: /var/lib/cwl/stg737c540d-fc9b-40d1-b493-a03eb762cf13/dqc_reference
[2023-06-13 13:44:19,975] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 13:44:19,976] [INFO] Task started: Prodigal
[2023-06-13 13:44:19,976] [INFO] Running command: gunzip -c /var/lib/cwl/stg0e6bce8a-37b4-4860-bdce-168de0b581a1/GCA_022764105.1_ASM2276410v1_genomic.fna.gz | prodigal -d GCA_022764105.1_ASM2276410v1_genomic.fna/cds.fna -a GCA_022764105.1_ASM2276410v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 13:44:22,518] [INFO] Task succeeded: Prodigal
[2023-06-13 13:44:22,518] [INFO] Task started: HMMsearch
[2023-06-13 13:44:22,518] [INFO] Running command: hmmsearch --tblout GCA_022764105.1_ASM2276410v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg737c540d-fc9b-40d1-b493-a03eb762cf13/dqc_reference/reference_markers.hmm GCA_022764105.1_ASM2276410v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 13:44:22,757] [INFO] Task succeeded: HMMsearch
[2023-06-13 13:44:22,759] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg0e6bce8a-37b4-4860-bdce-168de0b581a1/GCA_022764105.1_ASM2276410v1_genomic.fna.gz]
[2023-06-13 13:44:22,777] [INFO] Query marker FASTA was written to GCA_022764105.1_ASM2276410v1_genomic.fna/markers.fasta
[2023-06-13 13:44:22,778] [INFO] Task started: Blastn
[2023-06-13 13:44:22,778] [INFO] Running command: blastn -query GCA_022764105.1_ASM2276410v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg737c540d-fc9b-40d1-b493-a03eb762cf13/dqc_reference/reference_markers.fasta -out GCA_022764105.1_ASM2276410v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 13:44:23,332] [INFO] Task succeeded: Blastn
[2023-06-13 13:44:23,337] [INFO] Selected 19 target genomes.
[2023-06-13 13:44:23,337] [INFO] Target genome list was writen to GCA_022764105.1_ASM2276410v1_genomic.fna/target_genomes.txt
[2023-06-13 13:44:23,341] [INFO] Task started: fastANI
[2023-06-13 13:44:23,342] [INFO] Running command: fastANI --query /var/lib/cwl/stg0e6bce8a-37b4-4860-bdce-168de0b581a1/GCA_022764105.1_ASM2276410v1_genomic.fna.gz --refList GCA_022764105.1_ASM2276410v1_genomic.fna/target_genomes.txt --output GCA_022764105.1_ASM2276410v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 13:44:30,558] [INFO] Task succeeded: fastANI
[2023-06-13 13:44:30,559] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg737c540d-fc9b-40d1-b493-a03eb762cf13/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 13:44:30,559] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg737c540d-fc9b-40d1-b493-a03eb762cf13/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 13:44:30,561] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 13:44:30,561] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-13 13:44:30,562] [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
--------------------------------------------------------------------------------
[2023-06-13 13:44:30,564] [INFO] DFAST Taxonomy check result was written to GCA_022764105.1_ASM2276410v1_genomic.fna/tc_result.tsv
[2023-06-13 13:44:30,564] [INFO] ===== Taxonomy check completed =====
[2023-06-13 13:44:30,565] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 13:44:30,565] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg737c540d-fc9b-40d1-b493-a03eb762cf13/dqc_reference/checkm_data
[2023-06-13 13:44:30,570] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 13:44:30,587] [INFO] Task started: CheckM
[2023-06-13 13:44:30,587] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022764105.1_ASM2276410v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022764105.1_ASM2276410v1_genomic.fna/checkm_input GCA_022764105.1_ASM2276410v1_genomic.fna/checkm_result
[2023-06-13 13:44:46,131] [INFO] Task succeeded: CheckM
[2023-06-13 13:44:46,133] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 13:44:46,157] [INFO] ===== Completeness check finished =====
[2023-06-13 13:44:46,158] [INFO] ===== Start GTDB Search =====
[2023-06-13 13:44:46,158] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022764105.1_ASM2276410v1_genomic.fna/markers.fasta)
[2023-06-13 13:44:46,159] [INFO] Task started: Blastn
[2023-06-13 13:44:46,159] [INFO] Running command: blastn -query GCA_022764105.1_ASM2276410v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg737c540d-fc9b-40d1-b493-a03eb762cf13/dqc_reference/reference_markers_gtdb.fasta -out GCA_022764105.1_ASM2276410v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 13:44:46,895] [INFO] Task succeeded: Blastn
[2023-06-13 13:44:46,901] [INFO] Selected 16 target genomes.
[2023-06-13 13:44:46,901] [INFO] Target genome list was writen to GCA_022764105.1_ASM2276410v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 13:44:46,938] [INFO] Task started: fastANI
[2023-06-13 13:44:46,939] [INFO] Running command: fastANI --query /var/lib/cwl/stg0e6bce8a-37b4-4860-bdce-168de0b581a1/GCA_022764105.1_ASM2276410v1_genomic.fna.gz --refList GCA_022764105.1_ASM2276410v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022764105.1_ASM2276410v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 13:44:50,127] [INFO] Task succeeded: fastANI
[2023-06-13 13:44:50,139] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 13:44:50,139] [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_016297915.1	s__UBA11490 sp016297915	99.0677	311	360	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__UBA1242;g__UBA11490	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_003524095.1	s__UBA11490 sp003524095	79.9851	196	360	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__UBA1242;g__UBA11490	95.0	98.85	98.85	0.97	0.97	2	-
GCA_015055815.1	s__UBA11490 sp015055815	78.5843	59	360	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__UBA1242;g__UBA11490	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017453125.1	s__UBA11490 sp017453125	77.7639	56	360	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__UBA1242;g__UBA11490	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015055605.1	s__UBA11490 sp015055605	77.6086	54	360	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__UBA1242;g__UBA11490	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 13:44:50,142] [INFO] GTDB search result was written to GCA_022764105.1_ASM2276410v1_genomic.fna/result_gtdb.tsv
[2023-06-13 13:44:50,142] [INFO] ===== GTDB Search completed =====
[2023-06-13 13:44:50,146] [INFO] DFAST_QC result json was written to GCA_022764105.1_ASM2276410v1_genomic.fna/dqc_result.json
[2023-06-13 13:44:50,146] [INFO] DFAST_QC completed!
[2023-06-13 13:44:50,146] [INFO] Total running time: 0h0m31s