[2023-06-28 00:55:19,318] [INFO] DFAST_QC pipeline started.
[2023-06-28 00:55:19,320] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 00:55:19,321] [INFO] DQC Reference Directory: /var/lib/cwl/stg5b5b8f28-b184-41b3-ad8d-d576a346a897/dqc_reference
[2023-06-28 00:55:21,182] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 00:55:21,183] [INFO] Task started: Prodigal
[2023-06-28 00:55:21,183] [INFO] Running command: gunzip -c /var/lib/cwl/stg00d60065-c307-44b3-8394-8a07ad1f237c/GCA_017884445.1_ASM1788444v1_genomic.fna.gz | prodigal -d GCA_017884445.1_ASM1788444v1_genomic.fna/cds.fna -a GCA_017884445.1_ASM1788444v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 00:55:53,925] [INFO] Task succeeded: Prodigal
[2023-06-28 00:55:53,926] [INFO] Task started: HMMsearch
[2023-06-28 00:55:53,926] [INFO] Running command: hmmsearch --tblout GCA_017884445.1_ASM1788444v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5b5b8f28-b184-41b3-ad8d-d576a346a897/dqc_reference/reference_markers.hmm GCA_017884445.1_ASM1788444v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 00:55:54,380] [INFO] Task succeeded: HMMsearch
[2023-06-28 00:55:54,381] [INFO] Found 6/6 markers.
[2023-06-28 00:55:54,458] [INFO] Query marker FASTA was written to GCA_017884445.1_ASM1788444v1_genomic.fna/markers.fasta
[2023-06-28 00:55:54,459] [INFO] Task started: Blastn
[2023-06-28 00:55:54,459] [INFO] Running command: blastn -query GCA_017884445.1_ASM1788444v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5b5b8f28-b184-41b3-ad8d-d576a346a897/dqc_reference/reference_markers.fasta -out GCA_017884445.1_ASM1788444v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 00:55:55,054] [INFO] Task succeeded: Blastn
[2023-06-28 00:55:55,059] [INFO] Selected 52 target genomes.
[2023-06-28 00:55:55,059] [INFO] Target genome list was writen to GCA_017884445.1_ASM1788444v1_genomic.fna/target_genomes.txt
[2023-06-28 00:55:55,070] [INFO] Task started: fastANI
[2023-06-28 00:55:55,070] [INFO] Running command: fastANI --query /var/lib/cwl/stg00d60065-c307-44b3-8394-8a07ad1f237c/GCA_017884445.1_ASM1788444v1_genomic.fna.gz --refList GCA_017884445.1_ASM1788444v1_genomic.fna/target_genomes.txt --output GCA_017884445.1_ASM1788444v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 00:56:28,253] [INFO] Task succeeded: fastANI
[2023-06-28 00:56:28,253] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5b5b8f28-b184-41b3-ad8d-d576a346a897/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 00:56:28,254] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5b5b8f28-b184-41b3-ad8d-d576a346a897/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 00:56:28,256] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 00:56:28,256] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 00:56:28,256] [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 00:56:28,259] [INFO] DFAST Taxonomy check result was written to GCA_017884445.1_ASM1788444v1_genomic.fna/tc_result.tsv
[2023-06-28 00:56:28,259] [INFO] ===== Taxonomy check completed =====
[2023-06-28 00:56:28,259] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 00:56:28,260] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5b5b8f28-b184-41b3-ad8d-d576a346a897/dqc_reference/checkm_data
[2023-06-28 00:56:28,263] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 00:56:28,353] [INFO] Task started: CheckM
[2023-06-28 00:56:28,353] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_017884445.1_ASM1788444v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_017884445.1_ASM1788444v1_genomic.fna/checkm_input GCA_017884445.1_ASM1788444v1_genomic.fna/checkm_result
[2023-06-28 00:58:01,863] [INFO] Task succeeded: CheckM
[2023-06-28 00:58:01,865] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.80%
Contamintation: 89.35%
Strain heterogeneity: 17.95%
--------------------------------------------------------------------------------
[2023-06-28 00:58:01,900] [INFO] ===== Completeness check finished =====
[2023-06-28 00:58:01,901] [INFO] ===== Start GTDB Search =====
[2023-06-28 00:58:01,901] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_017884445.1_ASM1788444v1_genomic.fna/markers.fasta)
[2023-06-28 00:58:01,901] [INFO] Task started: Blastn
[2023-06-28 00:58:01,901] [INFO] Running command: blastn -query GCA_017884445.1_ASM1788444v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5b5b8f28-b184-41b3-ad8d-d576a346a897/dqc_reference/reference_markers_gtdb.fasta -out GCA_017884445.1_ASM1788444v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 00:58:02,740] [INFO] Task succeeded: Blastn
[2023-06-28 00:58:02,747] [INFO] Selected 69 target genomes.
[2023-06-28 00:58:02,747] [INFO] Target genome list was writen to GCA_017884445.1_ASM1788444v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 00:58:02,781] [INFO] Task started: fastANI
[2023-06-28 00:58:02,781] [INFO] Running command: fastANI --query /var/lib/cwl/stg00d60065-c307-44b3-8394-8a07ad1f237c/GCA_017884445.1_ASM1788444v1_genomic.fna.gz --refList GCA_017884445.1_ASM1788444v1_genomic.fna/target_genomes_gtdb.txt --output GCA_017884445.1_ASM1788444v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 00:58:42,907] [INFO] Task succeeded: fastANI
[2023-06-28 00:58:42,932] [INFO] Found 25 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 00:58:42,932] [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_003520925.1	s__LD21 sp003520925	77.8884	312	2429	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__VadinHA17;g__LD21	95.0	99.68	99.68	0.93	0.93	2	-
GCA_003152835.1	s__LD21 sp003152835	76.6046	152	2429	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__VadinHA17;g__LD21	95.0	99.43	99.38	0.90	0.89	3	-
GCA_002328625.1	s__LD21 sp002328625	76.5936	171	2429	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__VadinHA17;g__LD21	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003141495.1	s__LD21 sp003141495	76.5639	126	2429	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__VadinHA17;g__LD21	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017882345.1	s__LD21 sp017882345	76.5421	128	2429	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	76.4886	160	2429	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__VadinHA17;g__LD21	95.0	99.39	99.39	0.94	0.94	2	-
GCA_016936695.1	s__LD21 sp016936695	76.4135	115	2429	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__VadinHA17;g__LD21	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017882305.1	s__LD21 sp017882305	76.4125	127	2429	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	76.3793	89	2429	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__VadinHA17;g__LD21	95.0	99.25	99.22	0.82	0.74	4	-
GCA_003141415.1	s__LD21 sp003141415	76.3314	153	2429	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	76.3202	148	2429	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__VadinHA17;g__LD21	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012519515.1	s__LD21 sp012519515	76.176	94	2429	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__VadinHA17;g__LD21	95.0	98.49	98.12	0.85	0.77	6	-
GCA_003157055.1	s__LD21 sp003157055	76.1601	93	2429	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	76.1201	82	2429	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__VadinHA17;g__LD21	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003141895.1	s__LD21 sp003141895	76.0469	130	2429	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__VadinHA17;g__LD21	95.0	99.95	99.95	0.99	0.99	2	-
GCA_016936435.1	s__LD21 sp016936435	75.9837	76	2429	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__VadinHA17;g__LD21	95.0	99.88	99.88	0.95	0.95	2	-
GCA_003501665.1	s__LD21 sp003501665	75.9203	116	2429	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	75.8838	62	2429	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	75.7956	109	2429	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__VadinHA17;g__LD21	95.0	99.94	99.93	0.97	0.96	4	-
GCA_016709865.1	s__LD21 sp016709865	75.7807	125	2429	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__VadinHA17;g__LD21	95.0	98.60	98.60	0.94	0.94	2	-
GCA_016715075.1	s__LD21 sp016715075	75.7484	110	2429	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__VadinHA17;g__LD21	95.0	98.94	98.94	0.93	0.93	2	-
GCA_003157075.1	s__LD21 sp003157075	75.7111	130	2429	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__VadinHA17;g__LD21	95.0	99.24	99.24	0.86	0.86	2	-
GCA_001304505.1	s__LJUQ01 sp001304505	75.7073	106	2429	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__SM23-62;g__LJUQ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002319885.1	s__LD21 sp002319885	75.6937	106	2429	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	75.6166	95	2429	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 00:58:42,934] [INFO] GTDB search result was written to GCA_017884445.1_ASM1788444v1_genomic.fna/result_gtdb.tsv
[2023-06-28 00:58:42,935] [INFO] ===== GTDB Search completed =====
[2023-06-28 00:58:42,938] [INFO] DFAST_QC result json was written to GCA_017884445.1_ASM1788444v1_genomic.fna/dqc_result.json
[2023-06-28 00:58:42,938] [INFO] DFAST_QC completed!
[2023-06-28 00:58:42,939] [INFO] Total running time: 0h3m24s