[2023-06-13 14:59:17,498] [INFO] DFAST_QC pipeline started.
[2023-06-13 14:59:17,500] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 14:59:17,500] [INFO] DQC Reference Directory: /var/lib/cwl/stga93cd1cc-64f8-4530-9f0a-f33b6e19fe03/dqc_reference
[2023-06-13 14:59:18,756] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 14:59:18,757] [INFO] Task started: Prodigal
[2023-06-13 14:59:18,757] [INFO] Running command: gunzip -c /var/lib/cwl/stged9561e5-2d6f-46f4-beb3-ea743e08e798/GCA_022708165.1_ASM2270816v1_genomic.fna.gz | prodigal -d GCA_022708165.1_ASM2270816v1_genomic.fna/cds.fna -a GCA_022708165.1_ASM2270816v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 14:59:35,829] [INFO] Task succeeded: Prodigal
[2023-06-13 14:59:35,830] [INFO] Task started: HMMsearch
[2023-06-13 14:59:35,830] [INFO] Running command: hmmsearch --tblout GCA_022708165.1_ASM2270816v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga93cd1cc-64f8-4530-9f0a-f33b6e19fe03/dqc_reference/reference_markers.hmm GCA_022708165.1_ASM2270816v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 14:59:36,105] [INFO] Task succeeded: HMMsearch
[2023-06-13 14:59:36,107] [INFO] Found 6/6 markers.
[2023-06-13 14:59:36,144] [INFO] Query marker FASTA was written to GCA_022708165.1_ASM2270816v1_genomic.fna/markers.fasta
[2023-06-13 14:59:36,145] [INFO] Task started: Blastn
[2023-06-13 14:59:36,145] [INFO] Running command: blastn -query GCA_022708165.1_ASM2270816v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga93cd1cc-64f8-4530-9f0a-f33b6e19fe03/dqc_reference/reference_markers.fasta -out GCA_022708165.1_ASM2270816v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 14:59:36,726] [INFO] Task succeeded: Blastn
[2023-06-13 14:59:36,731] [INFO] Selected 22 target genomes.
[2023-06-13 14:59:36,732] [INFO] Target genome list was writen to GCA_022708165.1_ASM2270816v1_genomic.fna/target_genomes.txt
[2023-06-13 14:59:36,736] [INFO] Task started: fastANI
[2023-06-13 14:59:36,736] [INFO] Running command: fastANI --query /var/lib/cwl/stged9561e5-2d6f-46f4-beb3-ea743e08e798/GCA_022708165.1_ASM2270816v1_genomic.fna.gz --refList GCA_022708165.1_ASM2270816v1_genomic.fna/target_genomes.txt --output GCA_022708165.1_ASM2270816v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 14:59:49,963] [INFO] Task succeeded: fastANI
[2023-06-13 14:59:49,964] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga93cd1cc-64f8-4530-9f0a-f33b6e19fe03/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 14:59:49,964] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga93cd1cc-64f8-4530-9f0a-f33b6e19fe03/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 14:59:49,967] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 14:59:49,967] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-13 14:59:49,967] [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 14:59:49,970] [INFO] DFAST Taxonomy check result was written to GCA_022708165.1_ASM2270816v1_genomic.fna/tc_result.tsv
[2023-06-13 14:59:49,970] [INFO] ===== Taxonomy check completed =====
[2023-06-13 14:59:49,971] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 14:59:49,971] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga93cd1cc-64f8-4530-9f0a-f33b6e19fe03/dqc_reference/checkm_data
[2023-06-13 14:59:49,975] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 14:59:50,018] [INFO] Task started: CheckM
[2023-06-13 14:59:50,018] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022708165.1_ASM2270816v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022708165.1_ASM2270816v1_genomic.fna/checkm_input GCA_022708165.1_ASM2270816v1_genomic.fna/checkm_result
[2023-06-13 15:00:42,675] [INFO] Task succeeded: CheckM
[2023-06-13 15:00:42,676] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-13 15:00:42,700] [INFO] ===== Completeness check finished =====
[2023-06-13 15:00:42,701] [INFO] ===== Start GTDB Search =====
[2023-06-13 15:00:42,701] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022708165.1_ASM2270816v1_genomic.fna/markers.fasta)
[2023-06-13 15:00:42,701] [INFO] Task started: Blastn
[2023-06-13 15:00:42,702] [INFO] Running command: blastn -query GCA_022708165.1_ASM2270816v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga93cd1cc-64f8-4530-9f0a-f33b6e19fe03/dqc_reference/reference_markers_gtdb.fasta -out GCA_022708165.1_ASM2270816v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 15:00:43,465] [INFO] Task succeeded: Blastn
[2023-06-13 15:00:43,472] [INFO] Selected 21 target genomes.
[2023-06-13 15:00:43,472] [INFO] Target genome list was writen to GCA_022708165.1_ASM2270816v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 15:00:43,479] [INFO] Task started: fastANI
[2023-06-13 15:00:43,479] [INFO] Running command: fastANI --query /var/lib/cwl/stged9561e5-2d6f-46f4-beb3-ea743e08e798/GCA_022708165.1_ASM2270816v1_genomic.fna.gz --refList GCA_022708165.1_ASM2270816v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022708165.1_ASM2270816v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 15:00:56,388] [INFO] Task succeeded: fastANI
[2023-06-13 15:00:56,404] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 15:00:56,405] [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_009877105.1	s__LD21 sp009877105	99.9832	1220	1255	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__VadinHA17;g__LD21	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_012519515.1	s__LD21 sp012519515	79.3204	124	1255	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__VadinHA17;g__LD21	95.0	98.49	98.12	0.85	0.77	6	-
GCA_012517605.1	s__LD21 sp012517605	76.1493	105	1255	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__VadinHA17;g__LD21	95.0	99.39	99.39	0.94	0.94	2	-
GCA_016715075.1	s__LD21 sp016715075	75.9797	64	1255	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__VadinHA17;g__LD21	95.0	98.94	98.94	0.93	0.93	2	-
GCA_003141525.1	s__LD21 sp003141525	75.9047	62	1255	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__VadinHA17;g__LD21	95.0	99.74	99.74	0.88	0.88	2	-
GCA_016709865.1	s__LD21 sp016709865	75.9014	70	1255	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__VadinHA17;g__LD21	95.0	98.60	98.60	0.94	0.94	2	-
GCA_016936435.1	s__LD21 sp016936435	75.8585	55	1255	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__VadinHA17;g__LD21	95.0	99.88	99.88	0.95	0.95	2	-
GCA_001768195.1	s__LD21 sp001768195	75.7774	81	1255	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__VadinHA17;g__LD21	95.0	99.84	99.74	0.96	0.95	8	-
GCA_002319885.1	s__LD21 sp002319885	75.6893	50	1255	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__VadinHA17;g__LD21	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002424525.1	s__LD21 sp002424525	75.6305	63	1255	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	75.6244	55	1255	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__VadinHA17;g__LD21	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903824785.1	s__LD21 sp903824785	75.4742	58	1255	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__VadinHA17;g__LD21	95.0	99.94	99.93	0.97	0.96	4	-
GCA_003141415.1	s__LD21 sp003141415	75.2257	62	1255	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 15:00:56,407] [INFO] GTDB search result was written to GCA_022708165.1_ASM2270816v1_genomic.fna/result_gtdb.tsv
[2023-06-13 15:00:56,407] [INFO] ===== GTDB Search completed =====
[2023-06-13 15:00:56,410] [INFO] DFAST_QC result json was written to GCA_022708165.1_ASM2270816v1_genomic.fna/dqc_result.json
[2023-06-13 15:00:56,411] [INFO] DFAST_QC completed!
[2023-06-13 15:00:56,411] [INFO] Total running time: 0h1m39s