[2023-06-13 00:09:34,097] [INFO] DFAST_QC pipeline started.
[2023-06-13 00:09:34,099] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 00:09:34,100] [INFO] DQC Reference Directory: /var/lib/cwl/stgf13626aa-5aa7-449a-ba53-b66e729fdb14/dqc_reference
[2023-06-13 00:09:35,358] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 00:09:35,359] [INFO] Task started: Prodigal
[2023-06-13 00:09:35,359] [INFO] Running command: gunzip -c /var/lib/cwl/stg06692757-0c86-4eab-a89e-7120a79326fa/GCA_022708125.1_ASM2270812v1_genomic.fna.gz | prodigal -d GCA_022708125.1_ASM2270812v1_genomic.fna/cds.fna -a GCA_022708125.1_ASM2270812v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 00:09:45,953] [INFO] Task succeeded: Prodigal
[2023-06-13 00:09:45,954] [INFO] Task started: HMMsearch
[2023-06-13 00:09:45,954] [INFO] Running command: hmmsearch --tblout GCA_022708125.1_ASM2270812v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf13626aa-5aa7-449a-ba53-b66e729fdb14/dqc_reference/reference_markers.hmm GCA_022708125.1_ASM2270812v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 00:09:46,204] [INFO] Task succeeded: HMMsearch
[2023-06-13 00:09:46,212] [INFO] Found 6/6 markers.
[2023-06-13 00:09:46,248] [INFO] Query marker FASTA was written to GCA_022708125.1_ASM2270812v1_genomic.fna/markers.fasta
[2023-06-13 00:09:46,248] [INFO] Task started: Blastn
[2023-06-13 00:09:46,248] [INFO] Running command: blastn -query GCA_022708125.1_ASM2270812v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf13626aa-5aa7-449a-ba53-b66e729fdb14/dqc_reference/reference_markers.fasta -out GCA_022708125.1_ASM2270812v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 00:09:46,819] [INFO] Task succeeded: Blastn
[2023-06-13 00:09:46,828] [INFO] Selected 23 target genomes.
[2023-06-13 00:09:46,829] [INFO] Target genome list was writen to GCA_022708125.1_ASM2270812v1_genomic.fna/target_genomes.txt
[2023-06-13 00:09:46,864] [INFO] Task started: fastANI
[2023-06-13 00:09:46,865] [INFO] Running command: fastANI --query /var/lib/cwl/stg06692757-0c86-4eab-a89e-7120a79326fa/GCA_022708125.1_ASM2270812v1_genomic.fna.gz --refList GCA_022708125.1_ASM2270812v1_genomic.fna/target_genomes.txt --output GCA_022708125.1_ASM2270812v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 00:10:00,576] [INFO] Task succeeded: fastANI
[2023-06-13 00:10:00,577] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf13626aa-5aa7-449a-ba53-b66e729fdb14/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 00:10:00,577] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf13626aa-5aa7-449a-ba53-b66e729fdb14/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 00:10:00,579] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 00:10:00,579] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-13 00:10:00,580] [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
--------------------------------------------------------------------------------
[2023-06-13 00:10:00,586] [INFO] DFAST Taxonomy check result was written to GCA_022708125.1_ASM2270812v1_genomic.fna/tc_result.tsv
[2023-06-13 00:10:00,588] [INFO] ===== Taxonomy check completed =====
[2023-06-13 00:10:00,588] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 00:10:00,588] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf13626aa-5aa7-449a-ba53-b66e729fdb14/dqc_reference/checkm_data
[2023-06-13 00:10:00,592] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 00:10:00,631] [INFO] Task started: CheckM
[2023-06-13 00:10:00,632] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022708125.1_ASM2270812v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022708125.1_ASM2270812v1_genomic.fna/checkm_input GCA_022708125.1_ASM2270812v1_genomic.fna/checkm_result
[2023-06-13 00:10:37,256] [INFO] Task succeeded: CheckM
[2023-06-13 00:10:37,258] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 70.31%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 00:10:37,282] [INFO] ===== Completeness check finished =====
[2023-06-13 00:10:37,282] [INFO] ===== Start GTDB Search =====
[2023-06-13 00:10:37,283] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022708125.1_ASM2270812v1_genomic.fna/markers.fasta)
[2023-06-13 00:10:37,283] [INFO] Task started: Blastn
[2023-06-13 00:10:37,283] [INFO] Running command: blastn -query GCA_022708125.1_ASM2270812v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf13626aa-5aa7-449a-ba53-b66e729fdb14/dqc_reference/reference_markers_gtdb.fasta -out GCA_022708125.1_ASM2270812v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 00:10:38,052] [INFO] Task succeeded: Blastn
[2023-06-13 00:10:38,056] [INFO] Selected 11 target genomes.
[2023-06-13 00:10:38,056] [INFO] Target genome list was writen to GCA_022708125.1_ASM2270812v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 00:10:38,061] [INFO] Task started: fastANI
[2023-06-13 00:10:38,062] [INFO] Running command: fastANI --query /var/lib/cwl/stg06692757-0c86-4eab-a89e-7120a79326fa/GCA_022708125.1_ASM2270812v1_genomic.fna.gz --refList GCA_022708125.1_ASM2270812v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022708125.1_ASM2270812v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 00:10:44,099] [INFO] Task succeeded: fastANI
[2023-06-13 00:10:44,112] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 00:10:44,112] [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_009881065.1	s__SR-FBR-E99 sp009881065	99.7635	597	636	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__VadinHA17;g__SR-FBR-E99	95.0	99.27	99.14	0.89	0.83	7	conclusive
GCA_018262715.1	s__SR-FBR-E99 sp018262715	88.3886	536	636	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__VadinHA17;g__SR-FBR-E99	95.0	99.48	99.48	0.89	0.86	3	-
GCA_002409145.1	s__SR-FBR-E99 sp002409145	83.1084	522	636	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__VadinHA17;g__SR-FBR-E99	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012513795.1	s__SR-FBR-E99 sp012513795	79.1079	284	636	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__VadinHA17;g__SR-FBR-E99	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002402965.1	s__SR-FBR-E99 sp002402965	78.7995	307	636	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__VadinHA17;g__SR-FBR-E99	95.0	N/A	N/A	N/A	N/A	1	-
GCA_006227095.1	s__SR-FBR-E99 sp006227095	78.6575	185	636	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__VadinHA17;g__SR-FBR-E99	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012514255.1	s__SR-FBR-E99 sp012514255	78.2878	276	636	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__VadinHA17;g__SR-FBR-E99	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002383485.1	s__SR-FBR-E99 sp002383485	78.1594	310	636	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__VadinHA17;g__SR-FBR-E99	95.0	99.98	99.98	0.99	0.99	2	-
GCA_002325785.1	s__SR-FBR-E99 sp002325785	77.5813	169	636	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__VadinHA17;g__SR-FBR-E99	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 00:10:44,114] [INFO] GTDB search result was written to GCA_022708125.1_ASM2270812v1_genomic.fna/result_gtdb.tsv
[2023-06-13 00:10:44,115] [INFO] ===== GTDB Search completed =====
[2023-06-13 00:10:44,117] [INFO] DFAST_QC result json was written to GCA_022708125.1_ASM2270812v1_genomic.fna/dqc_result.json
[2023-06-13 00:10:44,117] [INFO] DFAST_QC completed!
[2023-06-13 00:10:44,118] [INFO] Total running time: 0h1m10s