[2023-06-13 20:23:47,724] [INFO] DFAST_QC pipeline started.
[2023-06-13 20:23:47,740] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 20:23:47,740] [INFO] DQC Reference Directory: /var/lib/cwl/stgd263e0f9-725c-4903-a164-d1e4f0a9b443/dqc_reference
[2023-06-13 20:23:49,398] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 20:23:49,399] [INFO] Task started: Prodigal
[2023-06-13 20:23:49,399] [INFO] Running command: gunzip -c /var/lib/cwl/stg0bbba0ca-9f2c-4b1d-af9f-28bea3e96691/GCA_022708145.1_ASM2270814v1_genomic.fna.gz | prodigal -d GCA_022708145.1_ASM2270814v1_genomic.fna/cds.fna -a GCA_022708145.1_ASM2270814v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 20:23:58,831] [INFO] Task succeeded: Prodigal
[2023-06-13 20:23:58,831] [INFO] Task started: HMMsearch
[2023-06-13 20:23:58,831] [INFO] Running command: hmmsearch --tblout GCA_022708145.1_ASM2270814v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd263e0f9-725c-4903-a164-d1e4f0a9b443/dqc_reference/reference_markers.hmm GCA_022708145.1_ASM2270814v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 20:23:59,084] [INFO] Task succeeded: HMMsearch
[2023-06-13 20:23:59,085] [INFO] Found 6/6 markers.
[2023-06-13 20:23:59,109] [INFO] Query marker FASTA was written to GCA_022708145.1_ASM2270814v1_genomic.fna/markers.fasta
[2023-06-13 20:23:59,109] [INFO] Task started: Blastn
[2023-06-13 20:23:59,109] [INFO] Running command: blastn -query GCA_022708145.1_ASM2270814v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd263e0f9-725c-4903-a164-d1e4f0a9b443/dqc_reference/reference_markers.fasta -out GCA_022708145.1_ASM2270814v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 20:23:59,648] [INFO] Task succeeded: Blastn
[2023-06-13 20:23:59,651] [INFO] Selected 24 target genomes.
[2023-06-13 20:23:59,651] [INFO] Target genome list was writen to GCA_022708145.1_ASM2270814v1_genomic.fna/target_genomes.txt
[2023-06-13 20:23:59,653] [INFO] Task started: fastANI
[2023-06-13 20:23:59,653] [INFO] Running command: fastANI --query /var/lib/cwl/stg0bbba0ca-9f2c-4b1d-af9f-28bea3e96691/GCA_022708145.1_ASM2270814v1_genomic.fna.gz --refList GCA_022708145.1_ASM2270814v1_genomic.fna/target_genomes.txt --output GCA_022708145.1_ASM2270814v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 20:24:15,042] [INFO] Task succeeded: fastANI
[2023-06-13 20:24:15,042] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd263e0f9-725c-4903-a164-d1e4f0a9b443/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 20:24:15,043] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd263e0f9-725c-4903-a164-d1e4f0a9b443/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 20:24:15,044] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 20:24:15,044] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-13 20:24:15,044] [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 20:24:15,046] [INFO] DFAST Taxonomy check result was written to GCA_022708145.1_ASM2270814v1_genomic.fna/tc_result.tsv
[2023-06-13 20:24:15,046] [INFO] ===== Taxonomy check completed =====
[2023-06-13 20:24:15,046] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 20:24:15,047] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd263e0f9-725c-4903-a164-d1e4f0a9b443/dqc_reference/checkm_data
[2023-06-13 20:24:15,049] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 20:24:15,078] [INFO] Task started: CheckM
[2023-06-13 20:24:15,078] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022708145.1_ASM2270814v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022708145.1_ASM2270814v1_genomic.fna/checkm_input GCA_022708145.1_ASM2270814v1_genomic.fna/checkm_result
[2023-06-13 20:24:46,235] [INFO] Task succeeded: CheckM
[2023-06-13 20:24:46,236] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 20:24:46,258] [INFO] ===== Completeness check finished =====
[2023-06-13 20:24:46,258] [INFO] ===== Start GTDB Search =====
[2023-06-13 20:24:46,259] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022708145.1_ASM2270814v1_genomic.fna/markers.fasta)
[2023-06-13 20:24:46,259] [INFO] Task started: Blastn
[2023-06-13 20:24:46,259] [INFO] Running command: blastn -query GCA_022708145.1_ASM2270814v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd263e0f9-725c-4903-a164-d1e4f0a9b443/dqc_reference/reference_markers_gtdb.fasta -out GCA_022708145.1_ASM2270814v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 20:24:47,015] [INFO] Task succeeded: Blastn
[2023-06-13 20:24:47,018] [INFO] Selected 25 target genomes.
[2023-06-13 20:24:47,018] [INFO] Target genome list was writen to GCA_022708145.1_ASM2270814v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 20:24:47,025] [INFO] Task started: fastANI
[2023-06-13 20:24:47,025] [INFO] Running command: fastANI --query /var/lib/cwl/stg0bbba0ca-9f2c-4b1d-af9f-28bea3e96691/GCA_022708145.1_ASM2270814v1_genomic.fna.gz --refList GCA_022708145.1_ASM2270814v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022708145.1_ASM2270814v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 20:25:01,971] [INFO] Task succeeded: fastANI
[2023-06-13 20:25:01,979] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 20:25:01,979] [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_012519515.1	s__LD21 sp012519515	98.7291	655	797	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__VadinHA17;g__LD21	95.0	98.49	98.12	0.85	0.77	6	conclusive
GCA_009877105.1	s__LD21 sp009877105	80.9707	100	797	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__VadinHA17;g__LD21	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002428385.1	s__LD21 sp002428385	79.2312	308	797	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__VadinHA17;g__LD21	95.0	99.25	99.22	0.82	0.74	4	-
GCA_016936695.1	s__LD21 sp016936695	79.1365	371	797	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__VadinHA17;g__LD21	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012517605.1	s__LD21 sp012517605	76.6099	106	797	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__VadinHA17;g__LD21	95.0	99.39	99.39	0.94	0.94	2	-
GCA_003520925.1	s__LD21 sp003520925	76.3709	135	797	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__VadinHA17;g__LD21	95.0	99.68	99.68	0.93	0.93	2	-
GCA_003142255.1	s__LD21 sp003142255	76.0749	59	797	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__VadinHA17;g__LD21	95.0	99.86	99.76	0.98	0.97	3	-
GCA_015712185.1	s__LD21 sp015712185	75.8842	54	797	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__VadinHA17;g__LD21	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903844815.1	s__LD21 sp903844815	75.8472	52	797	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__VadinHA17;g__LD21	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002328625.1	s__LD21 sp002328625	75.754	55	797	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__VadinHA17;g__LD21	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002319915.1	s__LD21 sp002319915	75.7374	51	797	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__VadinHA17;g__LD21	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 20:25:01,981] [INFO] GTDB search result was written to GCA_022708145.1_ASM2270814v1_genomic.fna/result_gtdb.tsv
[2023-06-13 20:25:01,981] [INFO] ===== GTDB Search completed =====
[2023-06-13 20:25:01,984] [INFO] DFAST_QC result json was written to GCA_022708145.1_ASM2270814v1_genomic.fna/dqc_result.json
[2023-06-13 20:25:01,984] [INFO] DFAST_QC completed!
[2023-06-13 20:25:01,984] [INFO] Total running time: 0h1m14s