[2023-06-05 06:35:07,827] [INFO] DFAST_QC pipeline started.
[2023-06-05 06:35:07,842] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 06:35:07,842] [INFO] DQC Reference Directory: /var/lib/cwl/stgcb7d0925-0c6a-4c62-973b-fbd4bdd80b95/dqc_reference
[2023-06-05 06:35:09,018] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 06:35:09,019] [INFO] Task started: Prodigal
[2023-06-05 06:35:09,019] [INFO] Running command: gunzip -c /var/lib/cwl/stg55f6ca86-655f-4193-8072-e5f7f2c6a645/GCA_902529795.1_AG-896-P05_genomic.fna.gz | prodigal -d GCA_902529795.1_AG-896-P05_genomic.fna/cds.fna -a GCA_902529795.1_AG-896-P05_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 06:35:11,718] [INFO] Task succeeded: Prodigal
[2023-06-05 06:35:11,718] [INFO] Task started: HMMsearch
[2023-06-05 06:35:11,718] [INFO] Running command: hmmsearch --tblout GCA_902529795.1_AG-896-P05_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcb7d0925-0c6a-4c62-973b-fbd4bdd80b95/dqc_reference/reference_markers.hmm GCA_902529795.1_AG-896-P05_genomic.fna/protein.faa > /dev/null
[2023-06-05 06:35:11,851] [INFO] Task succeeded: HMMsearch
[2023-06-05 06:35:11,852] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg55f6ca86-655f-4193-8072-e5f7f2c6a645/GCA_902529795.1_AG-896-P05_genomic.fna.gz]
[2023-06-05 06:35:11,863] [INFO] Query marker FASTA was written to GCA_902529795.1_AG-896-P05_genomic.fna/markers.fasta
[2023-06-05 06:35:11,864] [INFO] Task started: Blastn
[2023-06-05 06:35:11,864] [INFO] Running command: blastn -query GCA_902529795.1_AG-896-P05_genomic.fna/markers.fasta -db /var/lib/cwl/stgcb7d0925-0c6a-4c62-973b-fbd4bdd80b95/dqc_reference/reference_markers.fasta -out GCA_902529795.1_AG-896-P05_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 06:35:12,321] [INFO] Task succeeded: Blastn
[2023-06-05 06:35:12,324] [INFO] Selected 11 target genomes.
[2023-06-05 06:35:12,325] [INFO] Target genome list was writen to GCA_902529795.1_AG-896-P05_genomic.fna/target_genomes.txt
[2023-06-05 06:35:12,326] [INFO] Task started: fastANI
[2023-06-05 06:35:12,327] [INFO] Running command: fastANI --query /var/lib/cwl/stg55f6ca86-655f-4193-8072-e5f7f2c6a645/GCA_902529795.1_AG-896-P05_genomic.fna.gz --refList GCA_902529795.1_AG-896-P05_genomic.fna/target_genomes.txt --output GCA_902529795.1_AG-896-P05_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 06:35:17,544] [INFO] Task succeeded: fastANI
[2023-06-05 06:35:17,544] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcb7d0925-0c6a-4c62-973b-fbd4bdd80b95/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 06:35:17,545] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcb7d0925-0c6a-4c62-973b-fbd4bdd80b95/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 06:35:17,546] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 06:35:17,546] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-05 06:35:17,546] [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
--------------------------------------------------------------------------------
[2023-06-05 06:35:17,548] [INFO] DFAST Taxonomy check result was written to GCA_902529795.1_AG-896-P05_genomic.fna/tc_result.tsv
[2023-06-05 06:35:17,548] [INFO] ===== Taxonomy check completed =====
[2023-06-05 06:35:17,549] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 06:35:17,549] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcb7d0925-0c6a-4c62-973b-fbd4bdd80b95/dqc_reference/checkm_data
[2023-06-05 06:35:17,551] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 06:35:17,563] [INFO] Task started: CheckM
[2023-06-05 06:35:17,563] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902529795.1_AG-896-P05_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902529795.1_AG-896-P05_genomic.fna/checkm_input GCA_902529795.1_AG-896-P05_genomic.fna/checkm_result
[2023-06-05 06:35:32,871] [INFO] Task succeeded: CheckM
[2023-06-05 06:35:32,872] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 61.36%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 06:35:32,888] [INFO] ===== Completeness check finished =====
[2023-06-05 06:35:32,889] [INFO] ===== Start GTDB Search =====
[2023-06-05 06:35:32,889] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902529795.1_AG-896-P05_genomic.fna/markers.fasta)
[2023-06-05 06:35:32,889] [INFO] Task started: Blastn
[2023-06-05 06:35:32,889] [INFO] Running command: blastn -query GCA_902529795.1_AG-896-P05_genomic.fna/markers.fasta -db /var/lib/cwl/stgcb7d0925-0c6a-4c62-973b-fbd4bdd80b95/dqc_reference/reference_markers_gtdb.fasta -out GCA_902529795.1_AG-896-P05_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 06:35:33,347] [INFO] Task succeeded: Blastn
[2023-06-05 06:35:33,351] [INFO] Selected 8 target genomes.
[2023-06-05 06:35:33,351] [INFO] Target genome list was writen to GCA_902529795.1_AG-896-P05_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 06:35:33,356] [INFO] Task started: fastANI
[2023-06-05 06:35:33,356] [INFO] Running command: fastANI --query /var/lib/cwl/stg55f6ca86-655f-4193-8072-e5f7f2c6a645/GCA_902529795.1_AG-896-P05_genomic.fna.gz --refList GCA_902529795.1_AG-896-P05_genomic.fna/target_genomes_gtdb.txt --output GCA_902529795.1_AG-896-P05_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 06:35:35,047] [INFO] Task succeeded: fastANI
[2023-06-05 06:35:35,057] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 06:35:35,058] [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_902529795.1	s__HIMB59 sp902529795	100.0	291	293	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__HIMB59;g__HIMB59	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_902522585.1	s__HIMB59 sp902522585	89.5247	138	293	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__HIMB59;g__HIMB59	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000299115.1	s__HIMB59 sp000299115	87.3199	244	293	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__HIMB59;g__HIMB59	95.0	N/A	N/A	N/A	N/A	1	-
GCA_008638215.1	s__HIMB59 sp008638215	82.7733	192	293	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__HIMB59;g__HIMB59	95.0	99.46	99.38	0.89	0.85	4	-
GCA_902509695.1	s__HIMB59 sp902509695	79.0425	78	293	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__HIMB59;g__HIMB59	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902611415.1	s__HIMB59 sp902611415	78.1675	102	293	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__HIMB59;g__HIMB59	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902524245.1	s__HIMB59 sp902524245	77.9747	115	293	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__HIMB59;g__HIMB59	95.0	95.30	95.23	0.87	0.86	3	-
GCA_902555695.1	s__HIMB59 sp902555695	77.9338	94	293	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__HIMB59;g__HIMB59	95.0	96.82	95.65	0.73	0.69	4	-
--------------------------------------------------------------------------------
[2023-06-05 06:35:35,060] [INFO] GTDB search result was written to GCA_902529795.1_AG-896-P05_genomic.fna/result_gtdb.tsv
[2023-06-05 06:35:35,060] [INFO] ===== GTDB Search completed =====
[2023-06-05 06:35:35,063] [INFO] DFAST_QC result json was written to GCA_902529795.1_AG-896-P05_genomic.fna/dqc_result.json
[2023-06-05 06:35:35,063] [INFO] DFAST_QC completed!
[2023-06-05 06:35:35,063] [INFO] Total running time: 0h0m27s