[2023-06-30 07:02:07,275] [INFO] DFAST_QC pipeline started.
[2023-06-30 07:02:07,277] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 07:02:07,278] [INFO] DQC Reference Directory: /var/lib/cwl/stg8c48a951-fafa-43be-b841-179e116b55fe/dqc_reference
[2023-06-30 07:02:11,031] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 07:02:11,033] [INFO] Task started: Prodigal
[2023-06-30 07:02:11,034] [INFO] Running command: gunzip -c /var/lib/cwl/stg42c0ce37-5d6e-43ac-869b-84abb807bbf9/GCA_016293535.1_ASM1629353v1_genomic.fna.gz | prodigal -d GCA_016293535.1_ASM1629353v1_genomic.fna/cds.fna -a GCA_016293535.1_ASM1629353v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 07:02:22,836] [INFO] Task succeeded: Prodigal
[2023-06-30 07:02:22,836] [INFO] Task started: HMMsearch
[2023-06-30 07:02:22,836] [INFO] Running command: hmmsearch --tblout GCA_016293535.1_ASM1629353v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8c48a951-fafa-43be-b841-179e116b55fe/dqc_reference/reference_markers.hmm GCA_016293535.1_ASM1629353v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 07:02:23,081] [INFO] Task succeeded: HMMsearch
[2023-06-30 07:02:23,083] [INFO] Found 6/6 markers.
[2023-06-30 07:02:23,111] [INFO] Query marker FASTA was written to GCA_016293535.1_ASM1629353v1_genomic.fna/markers.fasta
[2023-06-30 07:02:23,111] [INFO] Task started: Blastn
[2023-06-30 07:02:23,111] [INFO] Running command: blastn -query GCA_016293535.1_ASM1629353v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8c48a951-fafa-43be-b841-179e116b55fe/dqc_reference/reference_markers.fasta -out GCA_016293535.1_ASM1629353v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 07:02:23,732] [INFO] Task succeeded: Blastn
[2023-06-30 07:02:23,737] [INFO] Selected 24 target genomes.
[2023-06-30 07:02:23,737] [INFO] Target genome list was writen to GCA_016293535.1_ASM1629353v1_genomic.fna/target_genomes.txt
[2023-06-30 07:02:23,739] [INFO] Task started: fastANI
[2023-06-30 07:02:23,740] [INFO] Running command: fastANI --query /var/lib/cwl/stg42c0ce37-5d6e-43ac-869b-84abb807bbf9/GCA_016293535.1_ASM1629353v1_genomic.fna.gz --refList GCA_016293535.1_ASM1629353v1_genomic.fna/target_genomes.txt --output GCA_016293535.1_ASM1629353v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 07:02:36,639] [INFO] Task succeeded: fastANI
[2023-06-30 07:02:36,640] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8c48a951-fafa-43be-b841-179e116b55fe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 07:02:36,640] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8c48a951-fafa-43be-b841-179e116b55fe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 07:02:36,643] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 07:02:36,643] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-30 07:02:36,643] [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 07:02:36,646] [INFO] DFAST Taxonomy check result was written to GCA_016293535.1_ASM1629353v1_genomic.fna/tc_result.tsv
[2023-06-30 07:02:36,647] [INFO] ===== Taxonomy check completed =====
[2023-06-30 07:02:36,647] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 07:02:36,647] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8c48a951-fafa-43be-b841-179e116b55fe/dqc_reference/checkm_data
[2023-06-30 07:02:36,653] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 07:02:36,679] [INFO] Task started: CheckM
[2023-06-30 07:02:36,679] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_016293535.1_ASM1629353v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_016293535.1_ASM1629353v1_genomic.fna/checkm_input GCA_016293535.1_ASM1629353v1_genomic.fna/checkm_result
[2023-06-30 07:03:14,129] [INFO] Task succeeded: CheckM
[2023-06-30 07:03:14,130] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 94.70%
Contamintation: 2.08%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-30 07:03:14,149] [INFO] ===== Completeness check finished =====
[2023-06-30 07:03:14,150] [INFO] ===== Start GTDB Search =====
[2023-06-30 07:03:14,150] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_016293535.1_ASM1629353v1_genomic.fna/markers.fasta)
[2023-06-30 07:03:14,151] [INFO] Task started: Blastn
[2023-06-30 07:03:14,151] [INFO] Running command: blastn -query GCA_016293535.1_ASM1629353v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8c48a951-fafa-43be-b841-179e116b55fe/dqc_reference/reference_markers_gtdb.fasta -out GCA_016293535.1_ASM1629353v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 07:03:15,182] [INFO] Task succeeded: Blastn
[2023-06-30 07:03:15,187] [INFO] Selected 20 target genomes.
[2023-06-30 07:03:15,187] [INFO] Target genome list was writen to GCA_016293535.1_ASM1629353v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 07:03:15,194] [INFO] Task started: fastANI
[2023-06-30 07:03:15,194] [INFO] Running command: fastANI --query /var/lib/cwl/stg42c0ce37-5d6e-43ac-869b-84abb807bbf9/GCA_016293535.1_ASM1629353v1_genomic.fna.gz --refList GCA_016293535.1_ASM1629353v1_genomic.fna/target_genomes_gtdb.txt --output GCA_016293535.1_ASM1629353v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 07:03:22,847] [INFO] Task succeeded: fastANI
[2023-06-30 07:03:22,856] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 07:03:22,856] [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_016293535.1	s__Cryptobacteroides sp016293535	100.0	692	700	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_004554455.1	s__Cryptobacteroides sp004554455	78.7676	134	700	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	98.35	97.49	0.82	0.75	12	-
GCA_004552965.1	s__Cryptobacteroides sp004552965	78.6319	76	700	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	98.55	98.04	0.91	0.85	9	-
GCA_018064725.1	s__Cryptobacteroides sp018064725	78.3868	125	700	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002314885.1	s__Cryptobacteroides sp002314885	77.1323	125	700	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	77.1245	58	700	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	99.45	99.16	0.92	0.88	7	-
GCA_016295455.1	s__Cryptobacteroides sp016295455	76.9545	73	700	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	98.79	98.71	0.83	0.82	3	-
GCA_017452265.1	s__Cryptobacteroides sp017452265	76.566	68	700	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	76.1182	54	700	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 07:03:22,859] [INFO] GTDB search result was written to GCA_016293535.1_ASM1629353v1_genomic.fna/result_gtdb.tsv
[2023-06-30 07:03:22,859] [INFO] ===== GTDB Search completed =====
[2023-06-30 07:03:22,862] [INFO] DFAST_QC result json was written to GCA_016293535.1_ASM1629353v1_genomic.fna/dqc_result.json
[2023-06-30 07:03:22,862] [INFO] DFAST_QC completed!
[2023-06-30 07:03:22,862] [INFO] Total running time: 0h1m16s