[2023-06-13 08:07:24,806] [INFO] DFAST_QC pipeline started.
[2023-06-13 08:07:24,808] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 08:07:24,808] [INFO] DQC Reference Directory: /var/lib/cwl/stg44665f95-2de8-4fe8-8087-950a6cab2caf/dqc_reference
[2023-06-13 08:07:26,074] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 08:07:26,075] [INFO] Task started: Prodigal
[2023-06-13 08:07:26,075] [INFO] Running command: gunzip -c /var/lib/cwl/stg75ebdbbf-032a-4b9d-9c14-410160faac08/GCA_022778295.1_ASM2277829v1_genomic.fna.gz | prodigal -d GCA_022778295.1_ASM2277829v1_genomic.fna/cds.fna -a GCA_022778295.1_ASM2277829v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 08:07:34,348] [INFO] Task succeeded: Prodigal
[2023-06-13 08:07:34,348] [INFO] Task started: HMMsearch
[2023-06-13 08:07:34,348] [INFO] Running command: hmmsearch --tblout GCA_022778295.1_ASM2277829v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg44665f95-2de8-4fe8-8087-950a6cab2caf/dqc_reference/reference_markers.hmm GCA_022778295.1_ASM2277829v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 08:07:34,609] [INFO] Task succeeded: HMMsearch
[2023-06-13 08:07:34,611] [INFO] Found 6/6 markers.
[2023-06-13 08:07:34,632] [INFO] Query marker FASTA was written to GCA_022778295.1_ASM2277829v1_genomic.fna/markers.fasta
[2023-06-13 08:07:34,632] [INFO] Task started: Blastn
[2023-06-13 08:07:34,632] [INFO] Running command: blastn -query GCA_022778295.1_ASM2277829v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg44665f95-2de8-4fe8-8087-950a6cab2caf/dqc_reference/reference_markers.fasta -out GCA_022778295.1_ASM2277829v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 08:07:35,193] [INFO] Task succeeded: Blastn
[2023-06-13 08:07:35,197] [INFO] Selected 22 target genomes.
[2023-06-13 08:07:35,197] [INFO] Target genome list was writen to GCA_022778295.1_ASM2277829v1_genomic.fna/target_genomes.txt
[2023-06-13 08:07:35,201] [INFO] Task started: fastANI
[2023-06-13 08:07:35,202] [INFO] Running command: fastANI --query /var/lib/cwl/stg75ebdbbf-032a-4b9d-9c14-410160faac08/GCA_022778295.1_ASM2277829v1_genomic.fna.gz --refList GCA_022778295.1_ASM2277829v1_genomic.fna/target_genomes.txt --output GCA_022778295.1_ASM2277829v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 08:07:50,381] [INFO] Task succeeded: fastANI
[2023-06-13 08:07:50,382] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg44665f95-2de8-4fe8-8087-950a6cab2caf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 08:07:50,382] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg44665f95-2de8-4fe8-8087-950a6cab2caf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 08:07:50,384] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 08:07:50,384] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-13 08:07:50,384] [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 08:07:50,386] [INFO] DFAST Taxonomy check result was written to GCA_022778295.1_ASM2277829v1_genomic.fna/tc_result.tsv
[2023-06-13 08:07:50,386] [INFO] ===== Taxonomy check completed =====
[2023-06-13 08:07:50,386] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 08:07:50,387] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg44665f95-2de8-4fe8-8087-950a6cab2caf/dqc_reference/checkm_data
[2023-06-13 08:07:50,390] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 08:07:50,413] [INFO] Task started: CheckM
[2023-06-13 08:07:50,414] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022778295.1_ASM2277829v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022778295.1_ASM2277829v1_genomic.fna/checkm_input GCA_022778295.1_ASM2277829v1_genomic.fna/checkm_result
[2023-06-13 08:08:19,302] [INFO] Task succeeded: CheckM
[2023-06-13 08:08:19,304] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 08:08:19,325] [INFO] ===== Completeness check finished =====
[2023-06-13 08:08:19,325] [INFO] ===== Start GTDB Search =====
[2023-06-13 08:08:19,325] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022778295.1_ASM2277829v1_genomic.fna/markers.fasta)
[2023-06-13 08:08:19,326] [INFO] Task started: Blastn
[2023-06-13 08:08:19,326] [INFO] Running command: blastn -query GCA_022778295.1_ASM2277829v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg44665f95-2de8-4fe8-8087-950a6cab2caf/dqc_reference/reference_markers_gtdb.fasta -out GCA_022778295.1_ASM2277829v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 08:08:20,094] [INFO] Task succeeded: Blastn
[2023-06-13 08:08:20,099] [INFO] Selected 22 target genomes.
[2023-06-13 08:08:20,099] [INFO] Target genome list was writen to GCA_022778295.1_ASM2277829v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 08:08:20,125] [INFO] Task started: fastANI
[2023-06-13 08:08:20,125] [INFO] Running command: fastANI --query /var/lib/cwl/stg75ebdbbf-032a-4b9d-9c14-410160faac08/GCA_022778295.1_ASM2277829v1_genomic.fna.gz --refList GCA_022778295.1_ASM2277829v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022778295.1_ASM2277829v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 08:08:27,748] [INFO] Task succeeded: fastANI
[2023-06-13 08:08:27,759] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 08:08:27,759] [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_900546445.1	s__Cryptobacteroides sp900546445	98.4945	450	551	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	97.53	96.27	0.86	0.83	5	conclusive
GCA_002438635.1	s__Cryptobacteroides sp002438635	78.4803	142	551	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	99.38	99.25	0.92	0.82	10	-
GCA_905234485.1	s__Cryptobacteroides sp905234485	77.461	56	551	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	99.26	99.26	0.82	0.82	2	-
GCA_017615435.1	s__Cryptobacteroides sp017615435	77.2483	51	551	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900769905.1	s__Cryptobacteroides sp900769905	77.1049	55	551	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	98.32	98.32	0.78	0.78	2	-
--------------------------------------------------------------------------------
[2023-06-13 08:08:27,761] [INFO] GTDB search result was written to GCA_022778295.1_ASM2277829v1_genomic.fna/result_gtdb.tsv
[2023-06-13 08:08:27,762] [INFO] ===== GTDB Search completed =====
[2023-06-13 08:08:27,764] [INFO] DFAST_QC result json was written to GCA_022778295.1_ASM2277829v1_genomic.fna/dqc_result.json
[2023-06-13 08:08:27,765] [INFO] DFAST_QC completed!
[2023-06-13 08:08:27,765] [INFO] Total running time: 0h1m3s