[2023-06-17 02:18:33,217] [INFO] DFAST_QC pipeline started.
[2023-06-17 02:18:33,220] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 02:18:33,220] [INFO] DQC Reference Directory: /var/lib/cwl/stg9363ee3b-2314-44ca-976d-f5c233811d29/dqc_reference
[2023-06-17 02:18:35,491] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 02:18:35,492] [INFO] Task started: Prodigal
[2023-06-17 02:18:35,492] [INFO] Running command: gunzip -c /var/lib/cwl/stg8564adc5-7d62-4a13-93c9-695ccee8e25a/GCA_028708235.1_ASM2870823v1_genomic.fna.gz | prodigal -d GCA_028708235.1_ASM2870823v1_genomic.fna/cds.fna -a GCA_028708235.1_ASM2870823v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 02:18:45,277] [INFO] Task succeeded: Prodigal
[2023-06-17 02:18:45,278] [INFO] Task started: HMMsearch
[2023-06-17 02:18:45,278] [INFO] Running command: hmmsearch --tblout GCA_028708235.1_ASM2870823v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9363ee3b-2314-44ca-976d-f5c233811d29/dqc_reference/reference_markers.hmm GCA_028708235.1_ASM2870823v1_genomic.fna/protein.faa > /dev/null
[2023-06-17 02:18:45,534] [INFO] Task succeeded: HMMsearch
[2023-06-17 02:18:45,536] [INFO] Found 6/6 markers.
[2023-06-17 02:18:45,562] [INFO] Query marker FASTA was written to GCA_028708235.1_ASM2870823v1_genomic.fna/markers.fasta
[2023-06-17 02:18:45,562] [INFO] Task started: Blastn
[2023-06-17 02:18:45,563] [INFO] Running command: blastn -query GCA_028708235.1_ASM2870823v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9363ee3b-2314-44ca-976d-f5c233811d29/dqc_reference/reference_markers.fasta -out GCA_028708235.1_ASM2870823v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 02:18:46,126] [INFO] Task succeeded: Blastn
[2023-06-17 02:18:46,131] [INFO] Selected 19 target genomes.
[2023-06-17 02:18:46,131] [INFO] Target genome list was writen to GCA_028708235.1_ASM2870823v1_genomic.fna/target_genomes.txt
[2023-06-17 02:18:46,133] [INFO] Task started: fastANI
[2023-06-17 02:18:46,133] [INFO] Running command: fastANI --query /var/lib/cwl/stg8564adc5-7d62-4a13-93c9-695ccee8e25a/GCA_028708235.1_ASM2870823v1_genomic.fna.gz --refList GCA_028708235.1_ASM2870823v1_genomic.fna/target_genomes.txt --output GCA_028708235.1_ASM2870823v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 02:19:00,333] [INFO] Task succeeded: fastANI
[2023-06-17 02:19:00,334] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9363ee3b-2314-44ca-976d-f5c233811d29/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 02:19:00,334] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9363ee3b-2314-44ca-976d-f5c233811d29/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 02:19:00,336] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 02:19:00,337] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-17 02:19:00,337] [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
--------------------------------------------------------------------------------
[2023-06-17 02:19:00,341] [INFO] DFAST Taxonomy check result was written to GCA_028708235.1_ASM2870823v1_genomic.fna/tc_result.tsv
[2023-06-17 02:19:00,342] [INFO] ===== Taxonomy check completed =====
[2023-06-17 02:19:00,342] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 02:19:00,342] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9363ee3b-2314-44ca-976d-f5c233811d29/dqc_reference/checkm_data
[2023-06-17 02:19:00,347] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 02:19:00,373] [INFO] Task started: CheckM
[2023-06-17 02:19:00,373] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_028708235.1_ASM2870823v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_028708235.1_ASM2870823v1_genomic.fna/checkm_input GCA_028708235.1_ASM2870823v1_genomic.fna/checkm_result
[2023-06-17 02:19:33,071] [INFO] Task succeeded: CheckM
[2023-06-17 02:19:33,072] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 8.33%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-17 02:19:33,093] [INFO] ===== Completeness check finished =====
[2023-06-17 02:19:33,093] [INFO] ===== Start GTDB Search =====
[2023-06-17 02:19:33,094] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_028708235.1_ASM2870823v1_genomic.fna/markers.fasta)
[2023-06-17 02:19:33,094] [INFO] Task started: Blastn
[2023-06-17 02:19:33,094] [INFO] Running command: blastn -query GCA_028708235.1_ASM2870823v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9363ee3b-2314-44ca-976d-f5c233811d29/dqc_reference/reference_markers_gtdb.fasta -out GCA_028708235.1_ASM2870823v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 02:19:33,824] [INFO] Task succeeded: Blastn
[2023-06-17 02:19:33,830] [INFO] Selected 24 target genomes.
[2023-06-17 02:19:33,830] [INFO] Target genome list was writen to GCA_028708235.1_ASM2870823v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 02:19:33,835] [INFO] Task started: fastANI
[2023-06-17 02:19:33,835] [INFO] Running command: fastANI --query /var/lib/cwl/stg8564adc5-7d62-4a13-93c9-695ccee8e25a/GCA_028708235.1_ASM2870823v1_genomic.fna.gz --refList GCA_028708235.1_ASM2870823v1_genomic.fna/target_genomes_gtdb.txt --output GCA_028708235.1_ASM2870823v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 02:19:43,504] [INFO] Task succeeded: fastANI
[2023-06-17 02:19:43,518] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-17 02:19:43,518] [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_002408205.1	s__DMER64 sp002408205	98.2669	538	579	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__DMER64	95.0	98.33	97.78	0.90	0.86	4	conclusive
GCA_001512865.1	s__DMER64 sp001512865	77.8452	90	579	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__DMER64	95.0	99.73	99.73	0.89	0.89	2	-
GCA_001603455.1	s__DMER64 sp001603455	77.5991	91	579	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__DMER64	95.0	99.83	99.68	0.89	0.76	4	-
GCA_002409325.1	s__DMER64 sp002409325	77.5099	94	579	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__DMER64	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002071175.1	s__DMER64 sp002071175	77.4694	76	579	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__DMER64	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002071385.1	s__DMER64 sp002071385	77.419	85	579	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__DMER64	95.0	99.62	99.43	0.93	0.90	7	-
GCA_002070565.1	s__DMER64 sp002070565	77.3867	79	579	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__DMER64	95.0	99.14	99.14	0.85	0.85	2	-
GCA_002427525.1	s__DMER64 sp002427525	77.0616	61	579	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__DMER64	95.0	99.85	99.85	0.93	0.93	2	-
GCA_012510445.1	s__DMER64 sp012510445	76.2577	56	579	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__DMER64	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-17 02:19:43,520] [INFO] GTDB search result was written to GCA_028708235.1_ASM2870823v1_genomic.fna/result_gtdb.tsv
[2023-06-17 02:19:43,520] [INFO] ===== GTDB Search completed =====
[2023-06-17 02:19:43,523] [INFO] DFAST_QC result json was written to GCA_028708235.1_ASM2870823v1_genomic.fna/dqc_result.json
[2023-06-17 02:19:43,523] [INFO] DFAST_QC completed!
[2023-06-17 02:19:43,523] [INFO] Total running time: 0h1m10s