[2023-06-27 22:32:04,260] [INFO] DFAST_QC pipeline started.
[2023-06-27 22:32:04,263] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 22:32:04,263] [INFO] DQC Reference Directory: /var/lib/cwl/stg8c4324a4-91b6-4550-ab99-5d8c016880e7/dqc_reference
[2023-06-27 22:32:05,451] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 22:32:05,452] [INFO] Task started: Prodigal
[2023-06-27 22:32:05,452] [INFO] Running command: gunzip -c /var/lib/cwl/stga5449c77-d5f4-44b2-bbb1-0dcca3bf022d/GCA_026339155.1_ASM2633915v1_genomic.fna.gz | prodigal -d GCA_026339155.1_ASM2633915v1_genomic.fna/cds.fna -a GCA_026339155.1_ASM2633915v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 22:32:19,312] [INFO] Task succeeded: Prodigal
[2023-06-27 22:32:19,312] [INFO] Task started: HMMsearch
[2023-06-27 22:32:19,313] [INFO] Running command: hmmsearch --tblout GCA_026339155.1_ASM2633915v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8c4324a4-91b6-4550-ab99-5d8c016880e7/dqc_reference/reference_markers.hmm GCA_026339155.1_ASM2633915v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 22:32:19,561] [INFO] Task succeeded: HMMsearch
[2023-06-27 22:32:19,562] [INFO] Found 6/6 markers.
[2023-06-27 22:32:19,590] [INFO] Query marker FASTA was written to GCA_026339155.1_ASM2633915v1_genomic.fna/markers.fasta
[2023-06-27 22:32:19,590] [INFO] Task started: Blastn
[2023-06-27 22:32:19,590] [INFO] Running command: blastn -query GCA_026339155.1_ASM2633915v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8c4324a4-91b6-4550-ab99-5d8c016880e7/dqc_reference/reference_markers.fasta -out GCA_026339155.1_ASM2633915v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 22:32:20,176] [INFO] Task succeeded: Blastn
[2023-06-27 22:32:20,181] [INFO] Selected 22 target genomes.
[2023-06-27 22:32:20,182] [INFO] Target genome list was writen to GCA_026339155.1_ASM2633915v1_genomic.fna/target_genomes.txt
[2023-06-27 22:32:20,188] [INFO] Task started: fastANI
[2023-06-27 22:32:20,189] [INFO] Running command: fastANI --query /var/lib/cwl/stga5449c77-d5f4-44b2-bbb1-0dcca3bf022d/GCA_026339155.1_ASM2633915v1_genomic.fna.gz --refList GCA_026339155.1_ASM2633915v1_genomic.fna/target_genomes.txt --output GCA_026339155.1_ASM2633915v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 22:32:31,577] [INFO] Task succeeded: fastANI
[2023-06-27 22:32:31,578] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8c4324a4-91b6-4550-ab99-5d8c016880e7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 22:32:31,578] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8c4324a4-91b6-4550-ab99-5d8c016880e7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 22:32:31,580] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 22:32:31,580] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-27 22:32:31,581] [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 22:32:31,583] [INFO] DFAST Taxonomy check result was written to GCA_026339155.1_ASM2633915v1_genomic.fna/tc_result.tsv
[2023-06-27 22:32:31,584] [INFO] ===== Taxonomy check completed =====
[2023-06-27 22:32:31,584] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 22:32:31,584] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8c4324a4-91b6-4550-ab99-5d8c016880e7/dqc_reference/checkm_data
[2023-06-27 22:32:31,589] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 22:32:31,620] [INFO] Task started: CheckM
[2023-06-27 22:32:31,620] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_026339155.1_ASM2633915v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_026339155.1_ASM2633915v1_genomic.fna/checkm_input GCA_026339155.1_ASM2633915v1_genomic.fna/checkm_result
[2023-06-27 22:33:15,197] [INFO] Task succeeded: CheckM
[2023-06-27 22:33:15,199] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 97.92%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 22:33:15,219] [INFO] ===== Completeness check finished =====
[2023-06-27 22:33:15,219] [INFO] ===== Start GTDB Search =====
[2023-06-27 22:33:15,220] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_026339155.1_ASM2633915v1_genomic.fna/markers.fasta)
[2023-06-27 22:33:15,220] [INFO] Task started: Blastn
[2023-06-27 22:33:15,220] [INFO] Running command: blastn -query GCA_026339155.1_ASM2633915v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8c4324a4-91b6-4550-ab99-5d8c016880e7/dqc_reference/reference_markers_gtdb.fasta -out GCA_026339155.1_ASM2633915v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 22:33:15,970] [INFO] Task succeeded: Blastn
[2023-06-27 22:33:15,975] [INFO] Selected 24 target genomes.
[2023-06-27 22:33:15,975] [INFO] Target genome list was writen to GCA_026339155.1_ASM2633915v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 22:33:15,992] [INFO] Task started: fastANI
[2023-06-27 22:33:15,992] [INFO] Running command: fastANI --query /var/lib/cwl/stga5449c77-d5f4-44b2-bbb1-0dcca3bf022d/GCA_026339155.1_ASM2633915v1_genomic.fna.gz --refList GCA_026339155.1_ASM2633915v1_genomic.fna/target_genomes_gtdb.txt --output GCA_026339155.1_ASM2633915v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 22:33:25,246] [INFO] Task succeeded: fastANI
[2023-06-27 22:33:25,271] [INFO] Found 24 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-27 22:33:25,272] [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_009774765.1	s__Cryptobacteroides sp009774765	99.9083	755	859	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	97.21	97.21	0.84	0.84	2	conclusive
GCA_900760425.1	s__Cryptobacteroides sp900760425	78.3569	211	859	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017695025.1	s__Cryptobacteroides excrementavium	77.5217	82	859	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017695015.1	s__Cryptobacteroides faecigallinarum	77.4965	125	859	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900546395.1	s__Cryptobacteroides sp900546395	77.3899	103	859	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015060455.1	s__Cryptobacteroides sp015060455	77.2554	89	859	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017546585.1	s__Cryptobacteroides sp017546585	77.1466	87	859	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017555445.1	s__Cryptobacteroides sp017555445	77.1426	74	859	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017695065.1	s__Cryptobacteroides excrementipullorum	77.1311	100	859	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017695115.1	s__Cryptobacteroides avicola	77.1174	116	859	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015060325.1	s__Cryptobacteroides sp015060325	77.0959	90	859	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017694885.1	s__Cryptobacteroides faecipullorum	76.9922	111	859	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017694845.1	s__Cryptobacteroides intestinavium	76.9912	124	859	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017694755.1	s__Cryptobacteroides merdavium	76.9641	122	859	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015060385.1	s__Cryptobacteroides sp015060385	76.9255	77	859	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017626355.1	s__Cryptobacteroides sp017626355	76.8852	83	859	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017555965.1	s__Cryptobacteroides sp017555965	76.8426	69	859	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017398335.1	s__Cryptobacteroides sp017398335	76.7762	98	859	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017502125.1	s__Cryptobacteroides sp017502125	76.7327	80	859	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017550025.1	s__Cryptobacteroides sp017550025	76.6299	90	859	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017399905.1	s__Cryptobacteroides sp017399905	76.5736	95	859	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	97.58	97.58	0.79	0.79	2	-
GCA_017546275.1	s__Cryptobacteroides sp017546275	76.4771	57	859	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017474265.1	s__Cryptobacteroides sp017474265	76.3612	59	859	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017461285.1	s__Cryptobacteroides sp017461285	75.944	76	859	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-27 22:33:25,294] [INFO] GTDB search result was written to GCA_026339155.1_ASM2633915v1_genomic.fna/result_gtdb.tsv
[2023-06-27 22:33:25,295] [INFO] ===== GTDB Search completed =====
[2023-06-27 22:33:25,300] [INFO] DFAST_QC result json was written to GCA_026339155.1_ASM2633915v1_genomic.fna/dqc_result.json
[2023-06-27 22:33:25,300] [INFO] DFAST_QC completed!
[2023-06-27 22:33:25,300] [INFO] Total running time: 0h1m21s