[2023-06-28 18:45:21,991] [INFO] DFAST_QC pipeline started.
[2023-06-28 18:45:21,993] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 18:45:21,993] [INFO] DQC Reference Directory: /var/lib/cwl/stgb2c195d4-c962-4701-9c91-5cf04bc51886/dqc_reference
[2023-06-28 18:45:23,351] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 18:45:23,352] [INFO] Task started: Prodigal
[2023-06-28 18:45:23,352] [INFO] Running command: gunzip -c /var/lib/cwl/stg378ac7ec-3d49-43d0-94d4-a9c2438601fd/GCA_012517605.1_ASM1251760v1_genomic.fna.gz | prodigal -d GCA_012517605.1_ASM1251760v1_genomic.fna/cds.fna -a GCA_012517605.1_ASM1251760v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 18:45:36,327] [INFO] Task succeeded: Prodigal
[2023-06-28 18:45:36,328] [INFO] Task started: HMMsearch
[2023-06-28 18:45:36,328] [INFO] Running command: hmmsearch --tblout GCA_012517605.1_ASM1251760v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb2c195d4-c962-4701-9c91-5cf04bc51886/dqc_reference/reference_markers.hmm GCA_012517605.1_ASM1251760v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 18:45:36,560] [INFO] Task succeeded: HMMsearch
[2023-06-28 18:45:36,561] [INFO] Found 6/6 markers.
[2023-06-28 18:45:36,594] [INFO] Query marker FASTA was written to GCA_012517605.1_ASM1251760v1_genomic.fna/markers.fasta
[2023-06-28 18:45:36,595] [INFO] Task started: Blastn
[2023-06-28 18:45:36,595] [INFO] Running command: blastn -query GCA_012517605.1_ASM1251760v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb2c195d4-c962-4701-9c91-5cf04bc51886/dqc_reference/reference_markers.fasta -out GCA_012517605.1_ASM1251760v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 18:45:37,171] [INFO] Task succeeded: Blastn
[2023-06-28 18:45:37,175] [INFO] Selected 25 target genomes.
[2023-06-28 18:45:37,175] [INFO] Target genome list was writen to GCA_012517605.1_ASM1251760v1_genomic.fna/target_genomes.txt
[2023-06-28 18:45:37,180] [INFO] Task started: fastANI
[2023-06-28 18:45:37,180] [INFO] Running command: fastANI --query /var/lib/cwl/stg378ac7ec-3d49-43d0-94d4-a9c2438601fd/GCA_012517605.1_ASM1251760v1_genomic.fna.gz --refList GCA_012517605.1_ASM1251760v1_genomic.fna/target_genomes.txt --output GCA_012517605.1_ASM1251760v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 18:45:53,584] [INFO] Task succeeded: fastANI
[2023-06-28 18:45:53,585] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb2c195d4-c962-4701-9c91-5cf04bc51886/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 18:45:53,585] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb2c195d4-c962-4701-9c91-5cf04bc51886/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 18:45:53,587] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 18:45:53,587] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 18:45:53,587] [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
--------------------------------------------------------------------------------
[2023-06-28 18:45:53,590] [INFO] DFAST Taxonomy check result was written to GCA_012517605.1_ASM1251760v1_genomic.fna/tc_result.tsv
[2023-06-28 18:45:53,591] [INFO] ===== Taxonomy check completed =====
[2023-06-28 18:45:53,591] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 18:45:53,591] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb2c195d4-c962-4701-9c91-5cf04bc51886/dqc_reference/checkm_data
[2023-06-28 18:45:53,594] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 18:45:53,649] [INFO] Task started: CheckM
[2023-06-28 18:45:53,650] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_012517605.1_ASM1251760v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_012517605.1_ASM1251760v1_genomic.fna/checkm_input GCA_012517605.1_ASM1251760v1_genomic.fna/checkm_result
[2023-06-28 18:46:35,385] [INFO] Task succeeded: CheckM
[2023-06-28 18:46:35,386] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 97.22%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 18:46:35,405] [INFO] ===== Completeness check finished =====
[2023-06-28 18:46:35,405] [INFO] ===== Start GTDB Search =====
[2023-06-28 18:46:35,405] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_012517605.1_ASM1251760v1_genomic.fna/markers.fasta)
[2023-06-28 18:46:35,405] [INFO] Task started: Blastn
[2023-06-28 18:46:35,406] [INFO] Running command: blastn -query GCA_012517605.1_ASM1251760v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb2c195d4-c962-4701-9c91-5cf04bc51886/dqc_reference/reference_markers_gtdb.fasta -out GCA_012517605.1_ASM1251760v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 18:46:36,145] [INFO] Task succeeded: Blastn
[2023-06-28 18:46:36,151] [INFO] Selected 25 target genomes.
[2023-06-28 18:46:36,151] [INFO] Target genome list was writen to GCA_012517605.1_ASM1251760v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 18:46:36,162] [INFO] Task started: fastANI
[2023-06-28 18:46:36,162] [INFO] Running command: fastANI --query /var/lib/cwl/stg378ac7ec-3d49-43d0-94d4-a9c2438601fd/GCA_012517605.1_ASM1251760v1_genomic.fna.gz --refList GCA_012517605.1_ASM1251760v1_genomic.fna/target_genomes_gtdb.txt --output GCA_012517605.1_ASM1251760v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 18:46:51,318] [INFO] Task succeeded: fastANI
[2023-06-28 18:46:51,333] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 18:46:51,334] [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_012517605.1	s__LD21 sp012517605	100.0	991	999	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__VadinHA17;g__LD21	95.0	99.39	99.39	0.94	0.94	2	conclusive
GCA_003520925.1	s__LD21 sp003520925	76.9248	188	999	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__VadinHA17;g__LD21	95.0	99.68	99.68	0.93	0.93	2	-
GCA_002428385.1	s__LD21 sp002428385	76.8392	112	999	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__VadinHA17;g__LD21	95.0	99.25	99.22	0.82	0.74	4	-
GCA_012519515.1	s__LD21 sp012519515	76.5258	116	999	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__VadinHA17;g__LD21	95.0	98.49	98.12	0.85	0.77	6	-
GCA_003141895.1	s__LD21 sp003141895	76.451	68	999	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__VadinHA17;g__LD21	95.0	99.95	99.95	0.99	0.99	2	-
GCA_003157015.1	s__LD21 sp003157015	76.4343	60	999	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__VadinHA17;g__LD21	95.0	99.74	99.74	0.96	0.96	2	-
GCA_003141525.1	s__LD21 sp003141525	76.3327	76	999	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__VadinHA17;g__LD21	95.0	99.74	99.74	0.88	0.88	2	-
GCA_003501665.1	s__LD21 sp003501665	76.2022	67	999	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__VadinHA17;g__LD21	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016718875.1	s__LD21 sp016718875	76.1538	78	999	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	76.1384	85	999	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__VadinHA17;g__LD21	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003142255.1	s__LD21 sp003142255	76.0993	89	999	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__VadinHA17;g__LD21	95.0	99.86	99.76	0.98	0.97	3	-
GCA_003162595.1	s__LD21 sp003162595	76.0289	59	999	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__VadinHA17;g__LD21	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009877105.1	s__LD21 sp009877105	75.9206	113	999	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__VadinHA17;g__LD21	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012729475.1	s__LD21 sp012729475	75.8728	56	999	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	75.7985	101	999	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__VadinHA17;g__LD21	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013314865.1	s__LD21 sp013314865	75.7328	72	999	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__VadinHA17;g__LD21	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003157055.1	s__LD21 sp003157055	75.645	50	999	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__VadinHA17;g__LD21	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015712185.1	s__LD21 sp015712185	75.582	82	999	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__VadinHA17;g__LD21	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 18:46:51,336] [INFO] GTDB search result was written to GCA_012517605.1_ASM1251760v1_genomic.fna/result_gtdb.tsv
[2023-06-28 18:46:51,336] [INFO] ===== GTDB Search completed =====
[2023-06-28 18:46:51,347] [INFO] DFAST_QC result json was written to GCA_012517605.1_ASM1251760v1_genomic.fna/dqc_result.json
[2023-06-28 18:46:51,347] [INFO] DFAST_QC completed!
[2023-06-28 18:46:51,347] [INFO] Total running time: 0h1m29s