[2023-06-29 01:04:23,174] [INFO] DFAST_QC pipeline started.
[2023-06-29 01:04:23,176] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 01:04:23,176] [INFO] DQC Reference Directory: /var/lib/cwl/stgb257c26f-75d1-4a57-bb53-ec030147d877/dqc_reference
[2023-06-29 01:04:24,557] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 01:04:24,558] [INFO] Task started: Prodigal
[2023-06-29 01:04:24,558] [INFO] Running command: gunzip -c /var/lib/cwl/stg781aa5b4-bcbd-463c-ac87-fe3768eabee3/GCA_020403185.1_ASM2040318v1_genomic.fna.gz | prodigal -d GCA_020403185.1_ASM2040318v1_genomic.fna/cds.fna -a GCA_020403185.1_ASM2040318v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 01:04:45,728] [INFO] Task succeeded: Prodigal
[2023-06-29 01:04:45,729] [INFO] Task started: HMMsearch
[2023-06-29 01:04:45,729] [INFO] Running command: hmmsearch --tblout GCA_020403185.1_ASM2040318v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb257c26f-75d1-4a57-bb53-ec030147d877/dqc_reference/reference_markers.hmm GCA_020403185.1_ASM2040318v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 01:04:46,023] [INFO] Task succeeded: HMMsearch
[2023-06-29 01:04:46,024] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg781aa5b4-bcbd-463c-ac87-fe3768eabee3/GCA_020403185.1_ASM2040318v1_genomic.fna.gz]
[2023-06-29 01:04:46,072] [INFO] Query marker FASTA was written to GCA_020403185.1_ASM2040318v1_genomic.fna/markers.fasta
[2023-06-29 01:04:46,073] [INFO] Task started: Blastn
[2023-06-29 01:04:46,073] [INFO] Running command: blastn -query GCA_020403185.1_ASM2040318v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb257c26f-75d1-4a57-bb53-ec030147d877/dqc_reference/reference_markers.fasta -out GCA_020403185.1_ASM2040318v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 01:04:46,672] [INFO] Task succeeded: Blastn
[2023-06-29 01:04:46,678] [INFO] Selected 24 target genomes.
[2023-06-29 01:04:46,679] [INFO] Target genome list was writen to GCA_020403185.1_ASM2040318v1_genomic.fna/target_genomes.txt
[2023-06-29 01:04:46,684] [INFO] Task started: fastANI
[2023-06-29 01:04:46,684] [INFO] Running command: fastANI --query /var/lib/cwl/stg781aa5b4-bcbd-463c-ac87-fe3768eabee3/GCA_020403185.1_ASM2040318v1_genomic.fna.gz --refList GCA_020403185.1_ASM2040318v1_genomic.fna/target_genomes.txt --output GCA_020403185.1_ASM2040318v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 01:05:08,969] [INFO] Task succeeded: fastANI
[2023-06-29 01:05:08,969] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb257c26f-75d1-4a57-bb53-ec030147d877/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 01:05:08,970] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb257c26f-75d1-4a57-bb53-ec030147d877/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 01:05:08,971] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 01:05:08,971] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-29 01:05:08,971] [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 01:05:08,973] [INFO] DFAST Taxonomy check result was written to GCA_020403185.1_ASM2040318v1_genomic.fna/tc_result.tsv
[2023-06-29 01:05:08,973] [INFO] ===== Taxonomy check completed =====
[2023-06-29 01:05:08,974] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 01:05:08,974] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb257c26f-75d1-4a57-bb53-ec030147d877/dqc_reference/checkm_data
[2023-06-29 01:05:08,976] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 01:05:09,028] [INFO] Task started: CheckM
[2023-06-29 01:05:09,028] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_020403185.1_ASM2040318v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_020403185.1_ASM2040318v1_genomic.fna/checkm_input GCA_020403185.1_ASM2040318v1_genomic.fna/checkm_result
[2023-06-29 01:06:09,970] [INFO] Task succeeded: CheckM
[2023-06-29 01:06:09,971] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 01:06:09,997] [INFO] ===== Completeness check finished =====
[2023-06-29 01:06:09,997] [INFO] ===== Start GTDB Search =====
[2023-06-29 01:06:09,997] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_020403185.1_ASM2040318v1_genomic.fna/markers.fasta)
[2023-06-29 01:06:09,998] [INFO] Task started: Blastn
[2023-06-29 01:06:09,998] [INFO] Running command: blastn -query GCA_020403185.1_ASM2040318v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb257c26f-75d1-4a57-bb53-ec030147d877/dqc_reference/reference_markers_gtdb.fasta -out GCA_020403185.1_ASM2040318v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 01:06:10,763] [INFO] Task succeeded: Blastn
[2023-06-29 01:06:10,768] [INFO] Selected 28 target genomes.
[2023-06-29 01:06:10,769] [INFO] Target genome list was writen to GCA_020403185.1_ASM2040318v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 01:06:10,783] [INFO] Task started: fastANI
[2023-06-29 01:06:10,783] [INFO] Running command: fastANI --query /var/lib/cwl/stg781aa5b4-bcbd-463c-ac87-fe3768eabee3/GCA_020403185.1_ASM2040318v1_genomic.fna.gz --refList GCA_020403185.1_ASM2040318v1_genomic.fna/target_genomes_gtdb.txt --output GCA_020403185.1_ASM2040318v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 01:06:27,438] [INFO] Task succeeded: fastANI
[2023-06-29 01:06:27,453] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 01:06:27,453] [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_013140395.1	s__ELB16-189 sp013140395	89.329	568	1383	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_018267275.1	s__ELB16-189 sp018267275	78.4621	145	1383	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_013140555.1	s__ELB16-189 sp013140555	77.2853	176	1383	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_002398365.1	s__ELB16-189 sp002398365	76.9839	199	1383	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_016191555.1	s__ELB16-189 sp016191555	76.8461	173	1383	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_018267285.1	s__ELB16-189 sp018267285	76.0031	61	1383	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	75.8478	54	1383	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_002425185.1	s__UBA2336 sp002425185	75.7777	52	1383	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__UBA2336	95.0	99.97	99.94	0.98	0.97	4	-
GCA_003537495.1	s__ELB16-189 sp003537495	75.7769	60	1383	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	75.7244	67	1383	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_018267135.1	s__ELB16-189 sp018267135	75.5658	59	1383	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__ELB16-189	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 01:06:27,455] [INFO] GTDB search result was written to GCA_020403185.1_ASM2040318v1_genomic.fna/result_gtdb.tsv
[2023-06-29 01:06:27,455] [INFO] ===== GTDB Search completed =====
[2023-06-29 01:06:27,458] [INFO] DFAST_QC result json was written to GCA_020403185.1_ASM2040318v1_genomic.fna/dqc_result.json
[2023-06-29 01:06:27,458] [INFO] DFAST_QC completed!
[2023-06-29 01:06:27,459] [INFO] Total running time: 0h2m4s