[2023-06-28 13:31:21,284] [INFO] DFAST_QC pipeline started.
[2023-06-28 13:31:21,286] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 13:31:21,286] [INFO] DQC Reference Directory: /var/lib/cwl/stge3e038d7-4338-4a94-a74c-22980cab555c/dqc_reference
[2023-06-28 13:31:22,437] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 13:31:22,438] [INFO] Task started: Prodigal
[2023-06-28 13:31:22,438] [INFO] Running command: gunzip -c /var/lib/cwl/stgbefb6603-b418-4001-875a-95a57b73008f/GCA_017511065.1_ASM1751106v1_genomic.fna.gz | prodigal -d GCA_017511065.1_ASM1751106v1_genomic.fna/cds.fna -a GCA_017511065.1_ASM1751106v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 13:31:28,375] [INFO] Task succeeded: Prodigal
[2023-06-28 13:31:28,375] [INFO] Task started: HMMsearch
[2023-06-28 13:31:28,375] [INFO] Running command: hmmsearch --tblout GCA_017511065.1_ASM1751106v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge3e038d7-4338-4a94-a74c-22980cab555c/dqc_reference/reference_markers.hmm GCA_017511065.1_ASM1751106v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 13:31:28,595] [INFO] Task succeeded: HMMsearch
[2023-06-28 13:31:28,596] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgbefb6603-b418-4001-875a-95a57b73008f/GCA_017511065.1_ASM1751106v1_genomic.fna.gz]
[2023-06-28 13:31:28,623] [INFO] Query marker FASTA was written to GCA_017511065.1_ASM1751106v1_genomic.fna/markers.fasta
[2023-06-28 13:31:28,623] [INFO] Task started: Blastn
[2023-06-28 13:31:28,623] [INFO] Running command: blastn -query GCA_017511065.1_ASM1751106v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge3e038d7-4338-4a94-a74c-22980cab555c/dqc_reference/reference_markers.fasta -out GCA_017511065.1_ASM1751106v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 13:31:29,188] [INFO] Task succeeded: Blastn
[2023-06-28 13:31:29,191] [INFO] Selected 25 target genomes.
[2023-06-28 13:31:29,191] [INFO] Target genome list was writen to GCA_017511065.1_ASM1751106v1_genomic.fna/target_genomes.txt
[2023-06-28 13:31:29,192] [INFO] Task started: fastANI
[2023-06-28 13:31:29,192] [INFO] Running command: fastANI --query /var/lib/cwl/stgbefb6603-b418-4001-875a-95a57b73008f/GCA_017511065.1_ASM1751106v1_genomic.fna.gz --refList GCA_017511065.1_ASM1751106v1_genomic.fna/target_genomes.txt --output GCA_017511065.1_ASM1751106v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 13:31:43,611] [INFO] Task succeeded: fastANI
[2023-06-28 13:31:43,611] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge3e038d7-4338-4a94-a74c-22980cab555c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 13:31:43,611] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge3e038d7-4338-4a94-a74c-22980cab555c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 13:31:43,613] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 13:31:43,613] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 13:31:43,613] [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
--------------------------------------------------------------------------------
[2023-06-28 13:31:43,615] [INFO] DFAST Taxonomy check result was written to GCA_017511065.1_ASM1751106v1_genomic.fna/tc_result.tsv
[2023-06-28 13:31:43,615] [INFO] ===== Taxonomy check completed =====
[2023-06-28 13:31:43,615] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 13:31:43,615] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge3e038d7-4338-4a94-a74c-22980cab555c/dqc_reference/checkm_data
[2023-06-28 13:31:43,618] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 13:31:43,650] [INFO] Task started: CheckM
[2023-06-28 13:31:43,650] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_017511065.1_ASM1751106v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_017511065.1_ASM1751106v1_genomic.fna/checkm_input GCA_017511065.1_ASM1751106v1_genomic.fna/checkm_result
[2023-06-28 13:32:06,903] [INFO] Task succeeded: CheckM
[2023-06-28 13:32:06,905] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 77.27%
Contamintation: 6.25%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 13:32:06,931] [INFO] ===== Completeness check finished =====
[2023-06-28 13:32:06,931] [INFO] ===== Start GTDB Search =====
[2023-06-28 13:32:06,932] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_017511065.1_ASM1751106v1_genomic.fna/markers.fasta)
[2023-06-28 13:32:06,932] [INFO] Task started: Blastn
[2023-06-28 13:32:06,932] [INFO] Running command: blastn -query GCA_017511065.1_ASM1751106v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge3e038d7-4338-4a94-a74c-22980cab555c/dqc_reference/reference_markers_gtdb.fasta -out GCA_017511065.1_ASM1751106v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 13:32:07,807] [INFO] Task succeeded: Blastn
[2023-06-28 13:32:07,810] [INFO] Selected 18 target genomes.
[2023-06-28 13:32:07,810] [INFO] Target genome list was writen to GCA_017511065.1_ASM1751106v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 13:32:07,837] [INFO] Task started: fastANI
[2023-06-28 13:32:07,837] [INFO] Running command: fastANI --query /var/lib/cwl/stgbefb6603-b418-4001-875a-95a57b73008f/GCA_017511065.1_ASM1751106v1_genomic.fna.gz --refList GCA_017511065.1_ASM1751106v1_genomic.fna/target_genomes_gtdb.txt --output GCA_017511065.1_ASM1751106v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 13:32:15,676] [INFO] Task succeeded: fastANI
[2023-06-28 13:32:15,682] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 13:32:15,682] [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_902788035.1	s__UBA1066 sp902788035	98.494	343	699	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA1066	95.0	97.60	97.29	0.74	0.68	4	conclusive
GCA_017514845.1	s__UBA1066 sp017514845	87.5963	326	699	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA1066	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017404585.1	s__UBA1066 sp017404585	86.784	203	699	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA1066	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900314565.1	s__UBA1066 sp900314565	77.6881	84	699	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA1066	95.0	98.26	96.12	0.90	0.66	19	-
GCA_902776305.1	s__UBA1066 sp902776305	77.6501	88	699	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA1066	95.0	97.81	95.96	0.86	0.75	9	-
GCA_017433725.1	s__UBA1066 sp017433725	77.4797	67	699	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA1066	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902785985.1	s__UBA1066 sp902785985	77.0796	60	699	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA1066	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900317515.1	s__UBA1066 sp900317515	77.0119	67	699	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA1066	95.0	98.06	96.06	0.86	0.79	9	-
--------------------------------------------------------------------------------
[2023-06-28 13:32:15,684] [INFO] GTDB search result was written to GCA_017511065.1_ASM1751106v1_genomic.fna/result_gtdb.tsv
[2023-06-28 13:32:15,684] [INFO] ===== GTDB Search completed =====
[2023-06-28 13:32:15,686] [INFO] DFAST_QC result json was written to GCA_017511065.1_ASM1751106v1_genomic.fna/dqc_result.json
[2023-06-28 13:32:15,687] [INFO] DFAST_QC completed!
[2023-06-28 13:32:15,687] [INFO] Total running time: 0h0m54s