[2023-06-29 22:59:12,515] [INFO] DFAST_QC pipeline started.
[2023-06-29 22:59:12,517] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 22:59:12,517] [INFO] DQC Reference Directory: /var/lib/cwl/stgb454f776-9e66-46bb-815d-b2c6373d55d7/dqc_reference
[2023-06-29 22:59:13,819] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 22:59:13,819] [INFO] Task started: Prodigal
[2023-06-29 22:59:13,820] [INFO] Running command: gunzip -c /var/lib/cwl/stg1d3bd2c2-31fb-46b0-93d9-fcade26d0d83/GCA_024402335.1_ASM2440233v1_genomic.fna.gz | prodigal -d GCA_024402335.1_ASM2440233v1_genomic.fna/cds.fna -a GCA_024402335.1_ASM2440233v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 22:59:25,159] [INFO] Task succeeded: Prodigal
[2023-06-29 22:59:25,159] [INFO] Task started: HMMsearch
[2023-06-29 22:59:25,160] [INFO] Running command: hmmsearch --tblout GCA_024402335.1_ASM2440233v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb454f776-9e66-46bb-815d-b2c6373d55d7/dqc_reference/reference_markers.hmm GCA_024402335.1_ASM2440233v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 22:59:25,463] [INFO] Task succeeded: HMMsearch
[2023-06-29 22:59:25,464] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg1d3bd2c2-31fb-46b0-93d9-fcade26d0d83/GCA_024402335.1_ASM2440233v1_genomic.fna.gz]
[2023-06-29 22:59:25,487] [INFO] Query marker FASTA was written to GCA_024402335.1_ASM2440233v1_genomic.fna/markers.fasta
[2023-06-29 22:59:25,487] [INFO] Task started: Blastn
[2023-06-29 22:59:25,488] [INFO] Running command: blastn -query GCA_024402335.1_ASM2440233v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb454f776-9e66-46bb-815d-b2c6373d55d7/dqc_reference/reference_markers.fasta -out GCA_024402335.1_ASM2440233v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 22:59:26,077] [INFO] Task succeeded: Blastn
[2023-06-29 22:59:26,086] [INFO] Selected 20 target genomes.
[2023-06-29 22:59:26,087] [INFO] Target genome list was writen to GCA_024402335.1_ASM2440233v1_genomic.fna/target_genomes.txt
[2023-06-29 22:59:26,091] [INFO] Task started: fastANI
[2023-06-29 22:59:26,091] [INFO] Running command: fastANI --query /var/lib/cwl/stg1d3bd2c2-31fb-46b0-93d9-fcade26d0d83/GCA_024402335.1_ASM2440233v1_genomic.fna.gz --refList GCA_024402335.1_ASM2440233v1_genomic.fna/target_genomes.txt --output GCA_024402335.1_ASM2440233v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 22:59:40,423] [INFO] Task succeeded: fastANI
[2023-06-29 22:59:40,423] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb454f776-9e66-46bb-815d-b2c6373d55d7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 22:59:40,424] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb454f776-9e66-46bb-815d-b2c6373d55d7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 22:59:40,426] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 22:59:40,426] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-29 22:59:40,426] [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
--------------------------------------------------------------------------------
[2023-06-29 22:59:40,428] [INFO] DFAST Taxonomy check result was written to GCA_024402335.1_ASM2440233v1_genomic.fna/tc_result.tsv
[2023-06-29 22:59:40,428] [INFO] ===== Taxonomy check completed =====
[2023-06-29 22:59:40,428] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 22:59:40,429] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb454f776-9e66-46bb-815d-b2c6373d55d7/dqc_reference/checkm_data
[2023-06-29 22:59:40,432] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 22:59:40,464] [INFO] Task started: CheckM
[2023-06-29 22:59:40,464] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_024402335.1_ASM2440233v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_024402335.1_ASM2440233v1_genomic.fna/checkm_input GCA_024402335.1_ASM2440233v1_genomic.fna/checkm_result
[2023-06-29 23:00:17,582] [INFO] Task succeeded: CheckM
[2023-06-29 23:00:17,584] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 23:00:17,604] [INFO] ===== Completeness check finished =====
[2023-06-29 23:00:17,604] [INFO] ===== Start GTDB Search =====
[2023-06-29 23:00:17,604] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_024402335.1_ASM2440233v1_genomic.fna/markers.fasta)
[2023-06-29 23:00:17,604] [INFO] Task started: Blastn
[2023-06-29 23:00:17,604] [INFO] Running command: blastn -query GCA_024402335.1_ASM2440233v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb454f776-9e66-46bb-815d-b2c6373d55d7/dqc_reference/reference_markers_gtdb.fasta -out GCA_024402335.1_ASM2440233v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 23:00:18,420] [INFO] Task succeeded: Blastn
[2023-06-29 23:00:18,425] [INFO] Selected 19 target genomes.
[2023-06-29 23:00:18,426] [INFO] Target genome list was writen to GCA_024402335.1_ASM2440233v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 23:00:18,433] [INFO] Task started: fastANI
[2023-06-29 23:00:18,433] [INFO] Running command: fastANI --query /var/lib/cwl/stg1d3bd2c2-31fb-46b0-93d9-fcade26d0d83/GCA_024402335.1_ASM2440233v1_genomic.fna.gz --refList GCA_024402335.1_ASM2440233v1_genomic.fna/target_genomes_gtdb.txt --output GCA_024402335.1_ASM2440233v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 23:00:27,694] [INFO] Task succeeded: fastANI
[2023-06-29 23:00:27,705] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 23:00:27,705] [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_002317135.1	s__UBA1715 sp002317135	86.9334	570	786	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA1715;g__UBA1715	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017642535.1	s__UBA1715 sp017642535	78.6364	158	786	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA1715;g__UBA1715	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017552705.1	s__UBA1715 sp017552705	78.2455	154	786	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA1715;g__UBA1715	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017618935.1	s__UBA1715 sp017618935	78.0297	121	786	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA1715;g__UBA1715	95.0	95.58	95.58	0.68	0.68	2	-
GCA_017516865.1	s__UBA1715 sp017516865	77.9324	164	786	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA1715;g__UBA1715	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002371705.1	s__UBA1715 sp002371705	77.6851	135	786	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA1715;g__UBA1715	95.0	97.12	96.45	0.83	0.72	7	-
--------------------------------------------------------------------------------
[2023-06-29 23:00:27,707] [INFO] GTDB search result was written to GCA_024402335.1_ASM2440233v1_genomic.fna/result_gtdb.tsv
[2023-06-29 23:00:27,708] [INFO] ===== GTDB Search completed =====
[2023-06-29 23:00:27,710] [INFO] DFAST_QC result json was written to GCA_024402335.1_ASM2440233v1_genomic.fna/dqc_result.json
[2023-06-29 23:00:27,711] [INFO] DFAST_QC completed!
[2023-06-29 23:00:27,711] [INFO] Total running time: 0h1m15s