[2023-06-30 16:28:39,968] [INFO] DFAST_QC pipeline started.
[2023-06-30 16:28:39,975] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 16:28:39,975] [INFO] DQC Reference Directory: /var/lib/cwl/stg37c03b7c-18cf-48af-8cd8-8ff644454923/dqc_reference
[2023-06-30 16:28:42,501] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 16:28:42,502] [INFO] Task started: Prodigal
[2023-06-30 16:28:42,503] [INFO] Running command: gunzip -c /var/lib/cwl/stg821b5243-f459-4ac4-a594-5e85334ac25e/GCA_024643545.1_ASM2464354v1_genomic.fna.gz | prodigal -d GCA_024643545.1_ASM2464354v1_genomic.fna/cds.fna -a GCA_024643545.1_ASM2464354v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 16:28:54,954] [INFO] Task succeeded: Prodigal
[2023-06-30 16:28:54,954] [INFO] Task started: HMMsearch
[2023-06-30 16:28:54,954] [INFO] Running command: hmmsearch --tblout GCA_024643545.1_ASM2464354v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg37c03b7c-18cf-48af-8cd8-8ff644454923/dqc_reference/reference_markers.hmm GCA_024643545.1_ASM2464354v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 16:28:55,143] [INFO] Task succeeded: HMMsearch
[2023-06-30 16:28:55,144] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg821b5243-f459-4ac4-a594-5e85334ac25e/GCA_024643545.1_ASM2464354v1_genomic.fna.gz]
[2023-06-30 16:28:55,169] [INFO] Query marker FASTA was written to GCA_024643545.1_ASM2464354v1_genomic.fna/markers.fasta
[2023-06-30 16:28:55,169] [INFO] Task started: Blastn
[2023-06-30 16:28:55,169] [INFO] Running command: blastn -query GCA_024643545.1_ASM2464354v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg37c03b7c-18cf-48af-8cd8-8ff644454923/dqc_reference/reference_markers.fasta -out GCA_024643545.1_ASM2464354v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 16:28:55,735] [INFO] Task succeeded: Blastn
[2023-06-30 16:28:55,739] [INFO] Selected 27 target genomes.
[2023-06-30 16:28:55,740] [INFO] Target genome list was writen to GCA_024643545.1_ASM2464354v1_genomic.fna/target_genomes.txt
[2023-06-30 16:28:55,742] [INFO] Task started: fastANI
[2023-06-30 16:28:55,742] [INFO] Running command: fastANI --query /var/lib/cwl/stg821b5243-f459-4ac4-a594-5e85334ac25e/GCA_024643545.1_ASM2464354v1_genomic.fna.gz --refList GCA_024643545.1_ASM2464354v1_genomic.fna/target_genomes.txt --output GCA_024643545.1_ASM2464354v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 16:29:10,456] [INFO] Task succeeded: fastANI
[2023-06-30 16:29:10,456] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg37c03b7c-18cf-48af-8cd8-8ff644454923/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 16:29:10,457] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg37c03b7c-18cf-48af-8cd8-8ff644454923/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 16:29:10,458] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 16:29:10,458] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-30 16:29:10,458] [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
--------------------------------------------------------------------------------
[2023-06-30 16:29:10,460] [INFO] DFAST Taxonomy check result was written to GCA_024643545.1_ASM2464354v1_genomic.fna/tc_result.tsv
[2023-06-30 16:29:10,461] [INFO] ===== Taxonomy check completed =====
[2023-06-30 16:29:10,461] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 16:29:10,461] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg37c03b7c-18cf-48af-8cd8-8ff644454923/dqc_reference/checkm_data
[2023-06-30 16:29:10,464] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 16:29:10,491] [INFO] Task started: CheckM
[2023-06-30 16:29:10,492] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_024643545.1_ASM2464354v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_024643545.1_ASM2464354v1_genomic.fna/checkm_input GCA_024643545.1_ASM2464354v1_genomic.fna/checkm_result
[2023-06-30 16:29:50,363] [INFO] Task succeeded: CheckM
[2023-06-30 16:29:50,364] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 90.91%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 16:29:50,382] [INFO] ===== Completeness check finished =====
[2023-06-30 16:29:50,382] [INFO] ===== Start GTDB Search =====
[2023-06-30 16:29:50,383] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_024643545.1_ASM2464354v1_genomic.fna/markers.fasta)
[2023-06-30 16:29:50,383] [INFO] Task started: Blastn
[2023-06-30 16:29:50,383] [INFO] Running command: blastn -query GCA_024643545.1_ASM2464354v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg37c03b7c-18cf-48af-8cd8-8ff644454923/dqc_reference/reference_markers_gtdb.fasta -out GCA_024643545.1_ASM2464354v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 16:29:51,125] [INFO] Task succeeded: Blastn
[2023-06-30 16:29:51,129] [INFO] Selected 17 target genomes.
[2023-06-30 16:29:51,130] [INFO] Target genome list was writen to GCA_024643545.1_ASM2464354v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 16:29:51,133] [INFO] Task started: fastANI
[2023-06-30 16:29:51,133] [INFO] Running command: fastANI --query /var/lib/cwl/stg821b5243-f459-4ac4-a594-5e85334ac25e/GCA_024643545.1_ASM2464354v1_genomic.fna.gz --refList GCA_024643545.1_ASM2464354v1_genomic.fna/target_genomes_gtdb.txt --output GCA_024643545.1_ASM2464354v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 16:29:58,939] [INFO] Task succeeded: fastANI
[2023-06-30 16:29:58,948] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-30 16:29:58,948] [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_903879765.1	s__UBA952 sp903879765	83.4516	509	901	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__UBA952	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017983465.1	s__UBA952 sp017983465	82.8271	617	901	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__UBA952	95.0	99.99	99.99	0.99	0.99	2	-
GCA_903860985.1	s__UBA952 sp903860985	81.663	513	901	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__UBA952	95.0	99.77	99.68	0.93	0.92	3	-
GCA_903935095.1	s__UBA952 sp903935095	81.0216	546	901	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__UBA952	95.0	99.97	99.95	0.99	0.98	5	-
GCA_017984635.1	s__M0103 sp017984635	76.9518	91	901	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__M0103	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016866415.1	s__UBA952 sp016866415	76.6422	66	901	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__UBA952	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018883325.1	s__UBA952 sp018883325	76.624	132	901	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__UBA952	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016872115.1	s__UBA952 sp016872115	76.5206	50	901	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__UBA952	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903939755.1	s__UBA952 sp903939755	76.3819	50	901	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__UBA952	95.0	99.13	98.32	0.94	0.90	3	-
--------------------------------------------------------------------------------
[2023-06-30 16:29:58,950] [INFO] GTDB search result was written to GCA_024643545.1_ASM2464354v1_genomic.fna/result_gtdb.tsv
[2023-06-30 16:29:58,950] [INFO] ===== GTDB Search completed =====
[2023-06-30 16:29:58,957] [INFO] DFAST_QC result json was written to GCA_024643545.1_ASM2464354v1_genomic.fna/dqc_result.json
[2023-06-30 16:29:58,957] [INFO] DFAST_QC completed!
[2023-06-30 16:29:58,957] [INFO] Total running time: 0h1m19s