[2023-06-19 03:05:44,997] [INFO] DFAST_QC pipeline started.
[2023-06-19 03:05:45,001] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 03:05:45,001] [INFO] DQC Reference Directory: /var/lib/cwl/stg5bdb114a-d565-4326-9638-24eb69e3c857/dqc_reference
[2023-06-19 03:05:46,274] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 03:05:46,275] [INFO] Task started: Prodigal
[2023-06-19 03:05:46,275] [INFO] Running command: gunzip -c /var/lib/cwl/stg53b95ab7-dfe9-4bb7-9793-1743e19cce18/GCA_018266435.1_ASM1826643v1_genomic.fna.gz | prodigal -d GCA_018266435.1_ASM1826643v1_genomic.fna/cds.fna -a GCA_018266435.1_ASM1826643v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 03:06:03,841] [INFO] Task succeeded: Prodigal
[2023-06-19 03:06:03,842] [INFO] Task started: HMMsearch
[2023-06-19 03:06:03,842] [INFO] Running command: hmmsearch --tblout GCA_018266435.1_ASM1826643v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5bdb114a-d565-4326-9638-24eb69e3c857/dqc_reference/reference_markers.hmm GCA_018266435.1_ASM1826643v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 03:06:04,160] [INFO] Task succeeded: HMMsearch
[2023-06-19 03:06:04,161] [INFO] Found 6/6 markers.
[2023-06-19 03:06:04,194] [INFO] Query marker FASTA was written to GCA_018266435.1_ASM1826643v1_genomic.fna/markers.fasta
[2023-06-19 03:06:04,194] [INFO] Task started: Blastn
[2023-06-19 03:06:04,194] [INFO] Running command: blastn -query GCA_018266435.1_ASM1826643v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5bdb114a-d565-4326-9638-24eb69e3c857/dqc_reference/reference_markers.fasta -out GCA_018266435.1_ASM1826643v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 03:06:04,775] [INFO] Task succeeded: Blastn
[2023-06-19 03:06:04,821] [INFO] Selected 26 target genomes.
[2023-06-19 03:06:04,821] [INFO] Target genome list was writen to GCA_018266435.1_ASM1826643v1_genomic.fna/target_genomes.txt
[2023-06-19 03:06:04,829] [INFO] Task started: fastANI
[2023-06-19 03:06:04,829] [INFO] Running command: fastANI --query /var/lib/cwl/stg53b95ab7-dfe9-4bb7-9793-1743e19cce18/GCA_018266435.1_ASM1826643v1_genomic.fna.gz --refList GCA_018266435.1_ASM1826643v1_genomic.fna/target_genomes.txt --output GCA_018266435.1_ASM1826643v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 03:06:26,972] [INFO] Task succeeded: fastANI
[2023-06-19 03:06:26,973] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5bdb114a-d565-4326-9638-24eb69e3c857/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 03:06:26,974] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5bdb114a-d565-4326-9638-24eb69e3c857/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 03:06:26,976] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 03:06:26,976] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-19 03:06:26,976] [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
--------------------------------------------------------------------------------
[2023-06-19 03:06:26,978] [INFO] DFAST Taxonomy check result was written to GCA_018266435.1_ASM1826643v1_genomic.fna/tc_result.tsv
[2023-06-19 03:06:26,979] [INFO] ===== Taxonomy check completed =====
[2023-06-19 03:06:26,979] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 03:06:26,979] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5bdb114a-d565-4326-9638-24eb69e3c857/dqc_reference/checkm_data
[2023-06-19 03:06:26,983] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 03:06:27,025] [INFO] Task started: CheckM
[2023-06-19 03:06:27,025] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018266435.1_ASM1826643v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018266435.1_ASM1826643v1_genomic.fna/checkm_input GCA_018266435.1_ASM1826643v1_genomic.fna/checkm_result
[2023-06-19 03:07:20,053] [INFO] Task succeeded: CheckM
[2023-06-19 03:07:20,055] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 03:07:20,082] [INFO] ===== Completeness check finished =====
[2023-06-19 03:07:20,083] [INFO] ===== Start GTDB Search =====
[2023-06-19 03:07:20,083] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018266435.1_ASM1826643v1_genomic.fna/markers.fasta)
[2023-06-19 03:07:20,083] [INFO] Task started: Blastn
[2023-06-19 03:07:20,084] [INFO] Running command: blastn -query GCA_018266435.1_ASM1826643v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5bdb114a-d565-4326-9638-24eb69e3c857/dqc_reference/reference_markers_gtdb.fasta -out GCA_018266435.1_ASM1826643v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 03:07:20,881] [INFO] Task succeeded: Blastn
[2023-06-19 03:07:20,886] [INFO] Selected 16 target genomes.
[2023-06-19 03:07:20,886] [INFO] Target genome list was writen to GCA_018266435.1_ASM1826643v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 03:07:20,898] [INFO] Task started: fastANI
[2023-06-19 03:07:20,898] [INFO] Running command: fastANI --query /var/lib/cwl/stg53b95ab7-dfe9-4bb7-9793-1743e19cce18/GCA_018266435.1_ASM1826643v1_genomic.fna.gz --refList GCA_018266435.1_ASM1826643v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018266435.1_ASM1826643v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 03:07:31,893] [INFO] Task succeeded: fastANI
[2023-06-19 03:07:31,914] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 03:07:31,915] [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_018266435.1	s__ELB16-189 sp018266435	100.0	1150	1150	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__ELB16-189	95.0	99.94	99.94	0.96	0.96	2	conclusive
GCA_018267285.1	s__ELB16-189 sp018267285	80.245	237	1150	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__ELB16-189	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018267135.1	s__ELB16-189 sp018267135	78.3337	401	1150	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__ELB16-189	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018267195.1	s__ELB16-189 sp018267195	77.9014	359	1150	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__ELB16-189	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018267215.1	s__ELB16-189 sp018267215	77.4728	382	1150	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__ELB16-189	95.0	99.99	99.99	0.96	0.96	2	-
GCA_016178785.1	s__ELB16-189 sp016178785	76.6249	159	1150	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__ELB16-189	95.0	99.88	99.88	0.90	0.90	2	-
GCA_018266055.1	s__ELB16-189 sp018266055	76.3494	161	1150	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__ELB16-189	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002352225.1	s__ELB16-189 sp002352225	76.0826	91	1150	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__ELB16-189	95.0	99.83	99.75	0.94	0.90	4	-
GCA_002398365.1	s__ELB16-189 sp002398365	75.9662	99	1150	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__ELB16-189	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013298505.1	s__ELB16-189 sp013298505	75.8253	97	1150	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__ELB16-189	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016787755.1	s__ELB16-189 sp016787755	75.4827	89	1150	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__ELB16-189	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-19 03:07:31,917] [INFO] GTDB search result was written to GCA_018266435.1_ASM1826643v1_genomic.fna/result_gtdb.tsv
[2023-06-19 03:07:31,918] [INFO] ===== GTDB Search completed =====
[2023-06-19 03:07:31,921] [INFO] DFAST_QC result json was written to GCA_018266435.1_ASM1826643v1_genomic.fna/dqc_result.json
[2023-06-19 03:07:31,921] [INFO] DFAST_QC completed!
[2023-06-19 03:07:31,922] [INFO] Total running time: 0h1m47s