[2023-06-13 17:55:53,910] [INFO] DFAST_QC pipeline started.
[2023-06-13 17:55:53,912] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 17:55:53,912] [INFO] DQC Reference Directory: /var/lib/cwl/stg33eed36c-aaf1-4fcd-942c-7899059b544e/dqc_reference
[2023-06-13 17:55:55,120] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 17:55:55,121] [INFO] Task started: Prodigal
[2023-06-13 17:55:55,121] [INFO] Running command: gunzip -c /var/lib/cwl/stg49b52547-3421-4484-ba63-1ee6ad386554/GCA_022508685.1_ASM2250868v1_genomic.fna.gz | prodigal -d GCA_022508685.1_ASM2250868v1_genomic.fna/cds.fna -a GCA_022508685.1_ASM2250868v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 17:56:08,325] [INFO] Task succeeded: Prodigal
[2023-06-13 17:56:08,325] [INFO] Task started: HMMsearch
[2023-06-13 17:56:08,326] [INFO] Running command: hmmsearch --tblout GCA_022508685.1_ASM2250868v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg33eed36c-aaf1-4fcd-942c-7899059b544e/dqc_reference/reference_markers.hmm GCA_022508685.1_ASM2250868v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 17:56:08,531] [INFO] Task succeeded: HMMsearch
[2023-06-13 17:56:08,533] [INFO] Found 6/6 markers.
[2023-06-13 17:56:08,554] [INFO] Query marker FASTA was written to GCA_022508685.1_ASM2250868v1_genomic.fna/markers.fasta
[2023-06-13 17:56:08,554] [INFO] Task started: Blastn
[2023-06-13 17:56:08,554] [INFO] Running command: blastn -query GCA_022508685.1_ASM2250868v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg33eed36c-aaf1-4fcd-942c-7899059b544e/dqc_reference/reference_markers.fasta -out GCA_022508685.1_ASM2250868v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 17:56:09,145] [INFO] Task succeeded: Blastn
[2023-06-13 17:56:09,150] [INFO] Selected 32 target genomes.
[2023-06-13 17:56:09,150] [INFO] Target genome list was writen to GCA_022508685.1_ASM2250868v1_genomic.fna/target_genomes.txt
[2023-06-13 17:56:09,152] [INFO] Task started: fastANI
[2023-06-13 17:56:09,152] [INFO] Running command: fastANI --query /var/lib/cwl/stg49b52547-3421-4484-ba63-1ee6ad386554/GCA_022508685.1_ASM2250868v1_genomic.fna.gz --refList GCA_022508685.1_ASM2250868v1_genomic.fna/target_genomes.txt --output GCA_022508685.1_ASM2250868v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 17:56:26,332] [INFO] Task succeeded: fastANI
[2023-06-13 17:56:26,332] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg33eed36c-aaf1-4fcd-942c-7899059b544e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 17:56:26,333] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg33eed36c-aaf1-4fcd-942c-7899059b544e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 17:56:26,335] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 17:56:26,335] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-13 17:56:26,335] [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
--------------------------------------------------------------------------------
[2023-06-13 17:56:26,337] [INFO] DFAST Taxonomy check result was written to GCA_022508685.1_ASM2250868v1_genomic.fna/tc_result.tsv
[2023-06-13 17:56:26,338] [INFO] ===== Taxonomy check completed =====
[2023-06-13 17:56:26,338] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 17:56:26,339] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg33eed36c-aaf1-4fcd-942c-7899059b544e/dqc_reference/checkm_data
[2023-06-13 17:56:26,341] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 17:56:26,366] [INFO] Task started: CheckM
[2023-06-13 17:56:26,366] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022508685.1_ASM2250868v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022508685.1_ASM2250868v1_genomic.fna/checkm_input GCA_022508685.1_ASM2250868v1_genomic.fna/checkm_result
[2023-06-13 17:57:05,484] [INFO] Task succeeded: CheckM
[2023-06-13 17:57:05,485] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 80.30%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-13 17:57:05,506] [INFO] ===== Completeness check finished =====
[2023-06-13 17:57:05,506] [INFO] ===== Start GTDB Search =====
[2023-06-13 17:57:05,507] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022508685.1_ASM2250868v1_genomic.fna/markers.fasta)
[2023-06-13 17:57:05,507] [INFO] Task started: Blastn
[2023-06-13 17:57:05,507] [INFO] Running command: blastn -query GCA_022508685.1_ASM2250868v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg33eed36c-aaf1-4fcd-942c-7899059b544e/dqc_reference/reference_markers_gtdb.fasta -out GCA_022508685.1_ASM2250868v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 17:57:06,339] [INFO] Task succeeded: Blastn
[2023-06-13 17:57:06,343] [INFO] Selected 25 target genomes.
[2023-06-13 17:57:06,343] [INFO] Target genome list was writen to GCA_022508685.1_ASM2250868v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 17:57:06,365] [INFO] Task started: fastANI
[2023-06-13 17:57:06,365] [INFO] Running command: fastANI --query /var/lib/cwl/stg49b52547-3421-4484-ba63-1ee6ad386554/GCA_022508685.1_ASM2250868v1_genomic.fna.gz --refList GCA_022508685.1_ASM2250868v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022508685.1_ASM2250868v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 17:57:17,259] [INFO] Task succeeded: fastANI
[2023-06-13 17:57:17,273] [INFO] Found 16 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-13 17:57:17,274] [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_900319385.1	s__UBA3839 sp900319385	78.1093	178	499	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA3839	95.0	99.85	99.85	0.97	0.97	2	-
GCA_900321835.1	s__UBA3839 sp900321835	78.0172	170	499	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA3839	95.0	98.37	97.84	0.86	0.77	6	-
GCA_905234555.1	s__UBA3839 sp905234555	77.5979	144	499	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA3839	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900313845.1	s__UBA3839 sp900313845	77.2426	72	499	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA3839	95.0	96.94	95.74	0.85	0.70	7	-
GCA_002393575.1	s__UBA3839 sp002393575	77.1724	102	499	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA3839	95.0	96.72	96.72	0.83	0.83	2	-
GCA_002350855.1	s__UBA3839 sp002350855	76.8245	64	499	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA3839	95.0	98.51	98.51	0.77	0.77	2	-
GCA_902801475.1	s__UBA4334 sp902801475	76.6661	57	499	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4334	95.0	97.71	97.36	0.83	0.79	15	-
GCA_902798705.1	s__UBA3839 sp902798705	76.6117	96	499	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA3839	95.0	96.86	96.85	0.82	0.82	3	-
GCA_016280445.1	s__UBA4334 sp016280445	76.5643	72	499	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4334	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902768125.1	s__UBA4334 sp902768125	76.4595	58	499	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4334	95.0	98.29	98.29	0.89	0.89	2	-
GCA_017470525.1	s__UBA4334 sp017470525	76.387	64	499	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4334	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017448965.1	s__UBA4334 sp017448965	76.3653	79	499	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4334	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017651245.1	s__UBA4334 sp017651245	76.315	59	499	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4334	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902802265.1	s__UBA4334 sp902802265	76.3026	74	499	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4334	95.0	97.98	97.98	0.87	0.87	2	-
GCA_017529865.1	s__UBA1786 sp017529865	76.0916	58	499	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA1786	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900316505.1	s__UBA4334 sp900316505	75.9655	58	499	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4334	95.0	97.97	97.14	0.89	0.83	54	-
--------------------------------------------------------------------------------
[2023-06-13 17:57:17,277] [INFO] GTDB search result was written to GCA_022508685.1_ASM2250868v1_genomic.fna/result_gtdb.tsv
[2023-06-13 17:57:17,278] [INFO] ===== GTDB Search completed =====
[2023-06-13 17:57:17,282] [INFO] DFAST_QC result json was written to GCA_022508685.1_ASM2250868v1_genomic.fna/dqc_result.json
[2023-06-13 17:57:17,282] [INFO] DFAST_QC completed!
[2023-06-13 17:57:17,282] [INFO] Total running time: 0h1m23s