[2023-06-13 13:00:26,133] [INFO] DFAST_QC pipeline started.
[2023-06-13 13:00:26,135] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 13:00:26,135] [INFO] DQC Reference Directory: /var/lib/cwl/stg1692116d-6430-4d74-9a6f-d2bf063a2c33/dqc_reference
[2023-06-13 13:00:27,364] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 13:00:27,365] [INFO] Task started: Prodigal
[2023-06-13 13:00:27,366] [INFO] Running command: gunzip -c /var/lib/cwl/stg90b983a3-40d2-42f7-ae5c-f2ac31ef21da/GCA_022771245.1_ASM2277124v1_genomic.fna.gz | prodigal -d GCA_022771245.1_ASM2277124v1_genomic.fna/cds.fna -a GCA_022771245.1_ASM2277124v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 13:00:38,699] [INFO] Task succeeded: Prodigal
[2023-06-13 13:00:38,699] [INFO] Task started: HMMsearch
[2023-06-13 13:00:38,699] [INFO] Running command: hmmsearch --tblout GCA_022771245.1_ASM2277124v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1692116d-6430-4d74-9a6f-d2bf063a2c33/dqc_reference/reference_markers.hmm GCA_022771245.1_ASM2277124v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 13:00:38,919] [INFO] Task succeeded: HMMsearch
[2023-06-13 13:00:38,921] [INFO] Found 6/6 markers.
[2023-06-13 13:00:38,957] [INFO] Query marker FASTA was written to GCA_022771245.1_ASM2277124v1_genomic.fna/markers.fasta
[2023-06-13 13:00:38,957] [INFO] Task started: Blastn
[2023-06-13 13:00:38,957] [INFO] Running command: blastn -query GCA_022771245.1_ASM2277124v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1692116d-6430-4d74-9a6f-d2bf063a2c33/dqc_reference/reference_markers.fasta -out GCA_022771245.1_ASM2277124v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 13:00:39,615] [INFO] Task succeeded: Blastn
[2023-06-13 13:00:39,620] [INFO] Selected 29 target genomes.
[2023-06-13 13:00:39,620] [INFO] Target genome list was writen to GCA_022771245.1_ASM2277124v1_genomic.fna/target_genomes.txt
[2023-06-13 13:00:39,626] [INFO] Task started: fastANI
[2023-06-13 13:00:39,627] [INFO] Running command: fastANI --query /var/lib/cwl/stg90b983a3-40d2-42f7-ae5c-f2ac31ef21da/GCA_022771245.1_ASM2277124v1_genomic.fna.gz --refList GCA_022771245.1_ASM2277124v1_genomic.fna/target_genomes.txt --output GCA_022771245.1_ASM2277124v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 13:00:59,495] [INFO] Task succeeded: fastANI
[2023-06-13 13:00:59,496] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1692116d-6430-4d74-9a6f-d2bf063a2c33/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 13:00:59,496] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1692116d-6430-4d74-9a6f-d2bf063a2c33/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 13:00:59,498] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 13:00:59,498] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-13 13:00:59,498] [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 13:00:59,501] [INFO] DFAST Taxonomy check result was written to GCA_022771245.1_ASM2277124v1_genomic.fna/tc_result.tsv
[2023-06-13 13:00:59,501] [INFO] ===== Taxonomy check completed =====
[2023-06-13 13:00:59,501] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 13:00:59,502] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1692116d-6430-4d74-9a6f-d2bf063a2c33/dqc_reference/checkm_data
[2023-06-13 13:00:59,505] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 13:00:59,533] [INFO] Task started: CheckM
[2023-06-13 13:00:59,533] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022771245.1_ASM2277124v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022771245.1_ASM2277124v1_genomic.fna/checkm_input GCA_022771245.1_ASM2277124v1_genomic.fna/checkm_result
[2023-06-13 13:01:36,380] [INFO] Task succeeded: CheckM
[2023-06-13 13:01:36,381] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 96.97%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 13:01:36,401] [INFO] ===== Completeness check finished =====
[2023-06-13 13:01:36,401] [INFO] ===== Start GTDB Search =====
[2023-06-13 13:01:36,401] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022771245.1_ASM2277124v1_genomic.fna/markers.fasta)
[2023-06-13 13:01:36,402] [INFO] Task started: Blastn
[2023-06-13 13:01:36,402] [INFO] Running command: blastn -query GCA_022771245.1_ASM2277124v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1692116d-6430-4d74-9a6f-d2bf063a2c33/dqc_reference/reference_markers_gtdb.fasta -out GCA_022771245.1_ASM2277124v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 13:01:37,301] [INFO] Task succeeded: Blastn
[2023-06-13 13:01:37,306] [INFO] Selected 30 target genomes.
[2023-06-13 13:01:37,306] [INFO] Target genome list was writen to GCA_022771245.1_ASM2277124v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 13:01:37,323] [INFO] Task started: fastANI
[2023-06-13 13:01:37,324] [INFO] Running command: fastANI --query /var/lib/cwl/stg90b983a3-40d2-42f7-ae5c-f2ac31ef21da/GCA_022771245.1_ASM2277124v1_genomic.fna.gz --refList GCA_022771245.1_ASM2277124v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022771245.1_ASM2277124v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 13:01:48,069] [INFO] Task succeeded: fastANI
[2023-06-13 13:01:48,083] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-13 13:01:48,083] [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_900545245.1	s__Cryptobacteroides sp900545245	78.98	117	602	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	96.89	96.83	0.80	0.79	3	-
GCA_002440085.1	s__Cryptobacteroides sp002440085	78.482	107	602	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002439805.1	s__Cryptobacteroides sp002439805	78.307	106	602	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	99.45	99.16	0.92	0.88	7	-
GCA_002438905.1	s__Cryptobacteroides sp002438905	77.9979	88	602	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910585445.1	s__Cryptobacteroides sp910585445	77.8027	60	602	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	96.74	96.72	0.88	0.88	3	-
GCA_009774765.1	s__Cryptobacteroides sp009774765	77.6582	55	602	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	97.21	97.21	0.84	0.84	2	-
GCA_004554455.1	s__Cryptobacteroides sp004554455	77.4443	72	602	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	98.35	97.49	0.82	0.75	12	-
GCA_017938925.1	s__Cryptobacteroides sp017938925	77.0676	75	602	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	97.18	96.33	0.77	0.70	3	-
GCA_017694845.1	s__Cryptobacteroides intestinavium	76.7091	51	602	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900760425.1	s__Cryptobacteroides sp900760425	76.6588	62	602	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017560825.1	s__Cryptobacteroides sp017560825	76.3826	58	602	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	95.79	95.07	0.79	0.69	4	-
--------------------------------------------------------------------------------
[2023-06-13 13:01:48,085] [INFO] GTDB search result was written to GCA_022771245.1_ASM2277124v1_genomic.fna/result_gtdb.tsv
[2023-06-13 13:01:48,085] [INFO] ===== GTDB Search completed =====
[2023-06-13 13:01:48,088] [INFO] DFAST_QC result json was written to GCA_022771245.1_ASM2277124v1_genomic.fna/dqc_result.json
[2023-06-13 13:01:48,088] [INFO] DFAST_QC completed!
[2023-06-13 13:01:48,088] [INFO] Total running time: 0h1m22s