[2023-06-18 10:35:31,461] [INFO] DFAST_QC pipeline started.
[2023-06-18 10:35:31,466] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 10:35:31,466] [INFO] DQC Reference Directory: /var/lib/cwl/stg7522722e-83da-4688-9e04-96e093621118/dqc_reference
[2023-06-18 10:35:32,761] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 10:35:32,762] [INFO] Task started: Prodigal
[2023-06-18 10:35:32,762] [INFO] Running command: gunzip -c /var/lib/cwl/stg17e5e275-d29f-4027-9579-816acae32f07/GCA_018435075.1_SL1_genomic.fna.gz | prodigal -d GCA_018435075.1_SL1_genomic.fna/cds.fna -a GCA_018435075.1_SL1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 10:35:43,308] [INFO] Task succeeded: Prodigal
[2023-06-18 10:35:43,308] [INFO] Task started: HMMsearch
[2023-06-18 10:35:43,308] [INFO] Running command: hmmsearch --tblout GCA_018435075.1_SL1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7522722e-83da-4688-9e04-96e093621118/dqc_reference/reference_markers.hmm GCA_018435075.1_SL1_genomic.fna/protein.faa > /dev/null
[2023-06-18 10:35:43,565] [INFO] Task succeeded: HMMsearch
[2023-06-18 10:35:43,566] [INFO] Found 6/6 markers.
[2023-06-18 10:35:43,591] [INFO] Query marker FASTA was written to GCA_018435075.1_SL1_genomic.fna/markers.fasta
[2023-06-18 10:35:43,592] [INFO] Task started: Blastn
[2023-06-18 10:35:43,592] [INFO] Running command: blastn -query GCA_018435075.1_SL1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7522722e-83da-4688-9e04-96e093621118/dqc_reference/reference_markers.fasta -out GCA_018435075.1_SL1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 10:35:44,191] [INFO] Task succeeded: Blastn
[2023-06-18 10:35:44,196] [INFO] Selected 26 target genomes.
[2023-06-18 10:35:44,197] [INFO] Target genome list was writen to GCA_018435075.1_SL1_genomic.fna/target_genomes.txt
[2023-06-18 10:35:44,204] [INFO] Task started: fastANI
[2023-06-18 10:35:44,204] [INFO] Running command: fastANI --query /var/lib/cwl/stg17e5e275-d29f-4027-9579-816acae32f07/GCA_018435075.1_SL1_genomic.fna.gz --refList GCA_018435075.1_SL1_genomic.fna/target_genomes.txt --output GCA_018435075.1_SL1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 10:36:00,702] [INFO] Task succeeded: fastANI
[2023-06-18 10:36:00,703] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7522722e-83da-4688-9e04-96e093621118/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 10:36:00,703] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7522722e-83da-4688-9e04-96e093621118/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 10:36:00,706] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-18 10:36:00,706] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-18 10:36:00,706] [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
--------------------------------------------------------------------------------
[2023-06-18 10:36:00,712] [INFO] DFAST Taxonomy check result was written to GCA_018435075.1_SL1_genomic.fna/tc_result.tsv
[2023-06-18 10:36:00,713] [INFO] ===== Taxonomy check completed =====
[2023-06-18 10:36:00,713] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 10:36:00,714] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7522722e-83da-4688-9e04-96e093621118/dqc_reference/checkm_data
[2023-06-18 10:36:00,719] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 10:36:00,748] [INFO] Task started: CheckM
[2023-06-18 10:36:00,748] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018435075.1_SL1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018435075.1_SL1_genomic.fna/checkm_input GCA_018435075.1_SL1_genomic.fna/checkm_result
[2023-06-18 10:36:36,602] [INFO] Task succeeded: CheckM
[2023-06-18 10:36:36,604] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-18 10:36:36,637] [INFO] ===== Completeness check finished =====
[2023-06-18 10:36:36,637] [INFO] ===== Start GTDB Search =====
[2023-06-18 10:36:36,638] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018435075.1_SL1_genomic.fna/markers.fasta)
[2023-06-18 10:36:36,638] [INFO] Task started: Blastn
[2023-06-18 10:36:36,638] [INFO] Running command: blastn -query GCA_018435075.1_SL1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7522722e-83da-4688-9e04-96e093621118/dqc_reference/reference_markers_gtdb.fasta -out GCA_018435075.1_SL1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 10:36:37,415] [INFO] Task succeeded: Blastn
[2023-06-18 10:36:37,422] [INFO] Selected 12 target genomes.
[2023-06-18 10:36:37,423] [INFO] Target genome list was writen to GCA_018435075.1_SL1_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 10:36:37,428] [INFO] Task started: fastANI
[2023-06-18 10:36:37,429] [INFO] Running command: fastANI --query /var/lib/cwl/stg17e5e275-d29f-4027-9579-816acae32f07/GCA_018435075.1_SL1_genomic.fna.gz --refList GCA_018435075.1_SL1_genomic.fna/target_genomes_gtdb.txt --output GCA_018435075.1_SL1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 10:36:43,231] [INFO] Task succeeded: fastANI
[2023-06-18 10:36:43,245] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-18 10:36:43,245] [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_001603455.1	s__DMER64 sp001603455	99.804	541	655	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__DMER64	95.0	99.83	99.68	0.89	0.76	4	conclusive
GCA_002071175.1	s__DMER64 sp002071175	82.0	358	655	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__DMER64	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002305545.1	s__DMER64 sp002305545	79.6332	280	655	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__DMER64	95.0	99.79	99.75	0.96	0.96	3	-
GCA_002409325.1	s__DMER64 sp002409325	79.1435	289	655	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__DMER64	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001512865.1	s__DMER64 sp001512865	79.0064	279	655	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__DMER64	95.0	99.73	99.73	0.89	0.89	2	-
GCA_002071385.1	s__DMER64 sp002071385	78.9649	262	655	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	78.9007	277	655	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__DMER64	95.0	99.14	99.14	0.85	0.85	2	-
GCA_011620605.1	s__DMER64 sp011620605	78.7733	255	655	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__DMER64	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012515395.1	s__DMER64 sp012515395	77.8702	179	655	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__DMER64	95.0	96.65	96.56	0.76	0.55	3	-
--------------------------------------------------------------------------------
[2023-06-18 10:36:43,249] [INFO] GTDB search result was written to GCA_018435075.1_SL1_genomic.fna/result_gtdb.tsv
[2023-06-18 10:36:43,250] [INFO] ===== GTDB Search completed =====
[2023-06-18 10:36:43,253] [INFO] DFAST_QC result json was written to GCA_018435075.1_SL1_genomic.fna/dqc_result.json
[2023-06-18 10:36:43,253] [INFO] DFAST_QC completed!
[2023-06-18 10:36:43,253] [INFO] Total running time: 0h1m12s