[2023-06-27 04:07:39,898] [INFO] DFAST_QC pipeline started.
[2023-06-27 04:07:39,902] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 04:07:39,903] [INFO] DQC Reference Directory: /var/lib/cwl/stg8c70cb02-e400-4c97-9473-eb7cb7e7b642/dqc_reference
[2023-06-27 04:07:41,174] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 04:07:41,176] [INFO] Task started: Prodigal
[2023-06-27 04:07:41,176] [INFO] Running command: gunzip -c /var/lib/cwl/stgc56e864b-74a4-48bf-83bf-cc7932589ee4/GCA_002310035.1_ASM231003v1_genomic.fna.gz | prodigal -d GCA_002310035.1_ASM231003v1_genomic.fna/cds.fna -a GCA_002310035.1_ASM231003v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 04:07:45,343] [INFO] Task succeeded: Prodigal
[2023-06-27 04:07:45,344] [INFO] Task started: HMMsearch
[2023-06-27 04:07:45,344] [INFO] Running command: hmmsearch --tblout GCA_002310035.1_ASM231003v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8c70cb02-e400-4c97-9473-eb7cb7e7b642/dqc_reference/reference_markers.hmm GCA_002310035.1_ASM231003v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 04:07:45,599] [INFO] Task succeeded: HMMsearch
[2023-06-27 04:07:45,600] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgc56e864b-74a4-48bf-83bf-cc7932589ee4/GCA_002310035.1_ASM231003v1_genomic.fna.gz]
[2023-06-27 04:07:45,626] [INFO] Query marker FASTA was written to GCA_002310035.1_ASM231003v1_genomic.fna/markers.fasta
[2023-06-27 04:07:45,626] [INFO] Task started: Blastn
[2023-06-27 04:07:45,626] [INFO] Running command: blastn -query GCA_002310035.1_ASM231003v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8c70cb02-e400-4c97-9473-eb7cb7e7b642/dqc_reference/reference_markers.fasta -out GCA_002310035.1_ASM231003v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 04:07:46,217] [INFO] Task succeeded: Blastn
[2023-06-27 04:07:46,228] [INFO] Selected 16 target genomes.
[2023-06-27 04:07:46,229] [INFO] Target genome list was writen to GCA_002310035.1_ASM231003v1_genomic.fna/target_genomes.txt
[2023-06-27 04:07:46,235] [INFO] Task started: fastANI
[2023-06-27 04:07:46,235] [INFO] Running command: fastANI --query /var/lib/cwl/stgc56e864b-74a4-48bf-83bf-cc7932589ee4/GCA_002310035.1_ASM231003v1_genomic.fna.gz --refList GCA_002310035.1_ASM231003v1_genomic.fna/target_genomes.txt --output GCA_002310035.1_ASM231003v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 04:07:57,003] [INFO] Task succeeded: fastANI
[2023-06-27 04:07:57,004] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8c70cb02-e400-4c97-9473-eb7cb7e7b642/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 04:07:57,004] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8c70cb02-e400-4c97-9473-eb7cb7e7b642/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 04:07:57,006] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 04:07:57,007] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-27 04:07:57,007] [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
--------------------------------------------------------------------------------
[2023-06-27 04:07:57,009] [INFO] DFAST Taxonomy check result was written to GCA_002310035.1_ASM231003v1_genomic.fna/tc_result.tsv
[2023-06-27 04:07:57,010] [INFO] ===== Taxonomy check completed =====
[2023-06-27 04:07:57,010] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 04:07:57,011] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8c70cb02-e400-4c97-9473-eb7cb7e7b642/dqc_reference/checkm_data
[2023-06-27 04:07:57,014] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 04:07:57,078] [INFO] Task started: CheckM
[2023-06-27 04:07:57,079] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_002310035.1_ASM231003v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_002310035.1_ASM231003v1_genomic.fna/checkm_input GCA_002310035.1_ASM231003v1_genomic.fna/checkm_result
[2023-06-27 04:08:17,971] [INFO] Task succeeded: CheckM
[2023-06-27 04:08:17,973] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 88.89%
Contamintation: 11.46%
Strain heterogeneity: 40.00%
--------------------------------------------------------------------------------
[2023-06-27 04:08:18,017] [INFO] ===== Completeness check finished =====
[2023-06-27 04:08:18,017] [INFO] ===== Start GTDB Search =====
[2023-06-27 04:08:18,018] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_002310035.1_ASM231003v1_genomic.fna/markers.fasta)
[2023-06-27 04:08:18,018] [INFO] Task started: Blastn
[2023-06-27 04:08:18,018] [INFO] Running command: blastn -query GCA_002310035.1_ASM231003v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8c70cb02-e400-4c97-9473-eb7cb7e7b642/dqc_reference/reference_markers_gtdb.fasta -out GCA_002310035.1_ASM231003v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 04:08:18,810] [INFO] Task succeeded: Blastn
[2023-06-27 04:08:18,815] [INFO] Selected 13 target genomes.
[2023-06-27 04:08:18,815] [INFO] Target genome list was writen to GCA_002310035.1_ASM231003v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 04:08:18,828] [INFO] Task started: fastANI
[2023-06-27 04:08:18,828] [INFO] Running command: fastANI --query /var/lib/cwl/stgc56e864b-74a4-48bf-83bf-cc7932589ee4/GCA_002310035.1_ASM231003v1_genomic.fna.gz --refList GCA_002310035.1_ASM231003v1_genomic.fna/target_genomes_gtdb.txt --output GCA_002310035.1_ASM231003v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 04:08:25,710] [INFO] Task succeeded: fastANI
[2023-06-27 04:08:25,726] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-27 04:08:25,726] [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_002310035.1	s__UBA1177 sp002310035	100.0	593	597	d__Bacteria;p__UBP6;c__UBA1177;o__UBA1177;f__UBA1177;g__UBA1177	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_905233945.1	s__UBA1177 sp905233945	84.2436	402	597	d__Bacteria;p__UBP6;c__UBA1177;o__UBA1177;f__UBA1177;g__UBA1177	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017963125.1	s__UBA1177 sp017963125	83.7303	403	597	d__Bacteria;p__UBP6;c__UBA1177;o__UBA1177;f__UBA1177;g__UBA1177	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017645765.1	s__UBA1177 sp017645765	83.5263	414	597	d__Bacteria;p__UBP6;c__UBA1177;o__UBA1177;f__UBA1177;g__UBA1177	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902774115.1	s__UBA1177 sp902774115	83.5168	424	597	d__Bacteria;p__UBP6;c__UBA1177;o__UBA1177;f__UBA1177;g__UBA1177	95.0	96.80	96.80	0.84	0.84	2	-
GCA_902780365.1	s__UBA1177 sp902780365	83.512	318	597	d__Bacteria;p__UBP6;c__UBA1177;o__UBA1177;f__UBA1177;g__UBA1177	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002310995.1	s__UBA1177 sp002310995	83.3558	369	597	d__Bacteria;p__UBP6;c__UBA1177;o__UBA1177;f__UBA1177;g__UBA1177	95.0	99.84	99.84	0.93	0.93	2	-
GCA_017405875.1	s__UBA1177 sp017405875	81.8936	381	597	d__Bacteria;p__UBP6;c__UBA1177;o__UBA1177;f__UBA1177;g__UBA1177	95.0	97.50	97.50	0.88	0.88	2	-
GCA_905235605.1	s__UBA1177 sp905235605	81.7088	368	597	d__Bacteria;p__UBP6;c__UBA1177;o__UBA1177;f__UBA1177;g__UBA1177	95.0	99.00	99.00	0.87	0.87	2	-
GCA_017961325.1	s__UBA1177 sp017961325	81.5087	377	597	d__Bacteria;p__UBP6;c__UBA1177;o__UBA1177;f__UBA1177;g__UBA1177	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017538365.1	s__UBA1177 sp017538365	81.4224	357	597	d__Bacteria;p__UBP6;c__UBA1177;o__UBA1177;f__UBA1177;g__UBA1177	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017615095.1	s__UBA1177 sp017615095	78.5982	119	597	d__Bacteria;p__UBP6;c__UBA1177;o__UBA1177;f__UBA1177;g__UBA1177	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-27 04:08:25,728] [INFO] GTDB search result was written to GCA_002310035.1_ASM231003v1_genomic.fna/result_gtdb.tsv
[2023-06-27 04:08:25,728] [INFO] ===== GTDB Search completed =====
[2023-06-27 04:08:25,731] [INFO] DFAST_QC result json was written to GCA_002310035.1_ASM231003v1_genomic.fna/dqc_result.json
[2023-06-27 04:08:25,731] [INFO] DFAST_QC completed!
[2023-06-27 04:08:25,732] [INFO] Total running time: 0h0m46s