[2023-06-18 20:56:39,156] [INFO] DFAST_QC pipeline started.
[2023-06-18 20:56:39,157] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 20:56:39,158] [INFO] DQC Reference Directory: /var/lib/cwl/stgc194bd56-75ee-4f12-9f4f-d192addbafe0/dqc_reference
[2023-06-18 20:56:40,323] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 20:56:40,323] [INFO] Task started: Prodigal
[2023-06-18 20:56:40,324] [INFO] Running command: gunzip -c /var/lib/cwl/stg5d8efd9d-c83d-4a8c-a21b-c05170728795/GCA_018897095.1_ASM1889709v1_genomic.fna.gz | prodigal -d GCA_018897095.1_ASM1889709v1_genomic.fna/cds.fna -a GCA_018897095.1_ASM1889709v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 20:56:42,484] [INFO] Task succeeded: Prodigal
[2023-06-18 20:56:42,484] [INFO] Task started: HMMsearch
[2023-06-18 20:56:42,484] [INFO] Running command: hmmsearch --tblout GCA_018897095.1_ASM1889709v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc194bd56-75ee-4f12-9f4f-d192addbafe0/dqc_reference/reference_markers.hmm GCA_018897095.1_ASM1889709v1_genomic.fna/protein.faa > /dev/null
[2023-06-18 20:56:42,625] [INFO] Task succeeded: HMMsearch
[2023-06-18 20:56:42,626] [INFO] Found 6/6 markers.
[2023-06-18 20:56:42,641] [INFO] Query marker FASTA was written to GCA_018897095.1_ASM1889709v1_genomic.fna/markers.fasta
[2023-06-18 20:56:42,641] [INFO] Task started: Blastn
[2023-06-18 20:56:42,641] [INFO] Running command: blastn -query GCA_018897095.1_ASM1889709v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc194bd56-75ee-4f12-9f4f-d192addbafe0/dqc_reference/reference_markers.fasta -out GCA_018897095.1_ASM1889709v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 20:56:43,605] [INFO] Task succeeded: Blastn
[2023-06-18 20:56:43,608] [INFO] Selected 12 target genomes.
[2023-06-18 20:56:43,609] [INFO] Target genome list was writen to GCA_018897095.1_ASM1889709v1_genomic.fna/target_genomes.txt
[2023-06-18 20:56:43,613] [INFO] Task started: fastANI
[2023-06-18 20:56:43,613] [INFO] Running command: fastANI --query /var/lib/cwl/stg5d8efd9d-c83d-4a8c-a21b-c05170728795/GCA_018897095.1_ASM1889709v1_genomic.fna.gz --refList GCA_018897095.1_ASM1889709v1_genomic.fna/target_genomes.txt --output GCA_018897095.1_ASM1889709v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 20:56:49,852] [INFO] Task succeeded: fastANI
[2023-06-18 20:56:49,852] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc194bd56-75ee-4f12-9f4f-d192addbafe0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 20:56:49,852] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc194bd56-75ee-4f12-9f4f-d192addbafe0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 20:56:49,856] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-18 20:56:49,856] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-18 20:56:49,856] [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 20:56:49,859] [INFO] DFAST Taxonomy check result was written to GCA_018897095.1_ASM1889709v1_genomic.fna/tc_result.tsv
[2023-06-18 20:56:49,859] [INFO] ===== Taxonomy check completed =====
[2023-06-18 20:56:49,859] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 20:56:49,860] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc194bd56-75ee-4f12-9f4f-d192addbafe0/dqc_reference/checkm_data
[2023-06-18 20:56:49,862] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 20:56:49,876] [INFO] Task started: CheckM
[2023-06-18 20:56:49,876] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018897095.1_ASM1889709v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018897095.1_ASM1889709v1_genomic.fna/checkm_input GCA_018897095.1_ASM1889709v1_genomic.fna/checkm_result
[2023-06-18 20:57:03,596] [INFO] Task succeeded: CheckM
[2023-06-18 20:57:03,597] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-18 20:57:03,615] [INFO] ===== Completeness check finished =====
[2023-06-18 20:57:03,615] [INFO] ===== Start GTDB Search =====
[2023-06-18 20:57:03,615] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018897095.1_ASM1889709v1_genomic.fna/markers.fasta)
[2023-06-18 20:57:03,615] [INFO] Task started: Blastn
[2023-06-18 20:57:03,615] [INFO] Running command: blastn -query GCA_018897095.1_ASM1889709v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc194bd56-75ee-4f12-9f4f-d192addbafe0/dqc_reference/reference_markers_gtdb.fasta -out GCA_018897095.1_ASM1889709v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 20:57:04,401] [INFO] Task succeeded: Blastn
[2023-06-18 20:57:04,404] [INFO] Selected 13 target genomes.
[2023-06-18 20:57:04,404] [INFO] Target genome list was writen to GCA_018897095.1_ASM1889709v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 20:57:04,412] [INFO] Task started: fastANI
[2023-06-18 20:57:04,412] [INFO] Running command: fastANI --query /var/lib/cwl/stg5d8efd9d-c83d-4a8c-a21b-c05170728795/GCA_018897095.1_ASM1889709v1_genomic.fna.gz --refList GCA_018897095.1_ASM1889709v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018897095.1_ASM1889709v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 20:57:07,453] [INFO] Task succeeded: fastANI
[2023-06-18 20:57:07,460] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-18 20:57:07,460] [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_018897555.1	s__UBA6249 sp018897555	99.7753	347	377	d__Bacteria;p__Omnitrophota;c__Koll11;o__GIF10;f__UBA6249;g__UBA6249	95.0	99.78	99.78	0.93	0.92	3	conclusive
GCA_002796135.1	s__UBA6249 sp002796135	78.7082	153	377	d__Bacteria;p__Omnitrophota;c__Koll11;o__GIF10;f__UBA6249;g__UBA6249	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018812825.1	s__UBA6249 sp018812825	78.5529	130	377	d__Bacteria;p__Omnitrophota;c__Koll11;o__GIF10;f__UBA6249;g__UBA6249	95.0	99.89	99.89	0.90	0.90	2	-
GCA_903852325.1	s__UBA6249 sp903852325	78.1211	126	377	d__Bacteria;p__Omnitrophota;c__Koll11;o__GIF10;f__UBA6249;g__UBA6249	95.0	99.74	99.73	0.84	0.84	3	-
GCA_002441245.1	s__UBA6249 sp002441245	77.6112	147	377	d__Bacteria;p__Omnitrophota;c__Koll11;o__GIF10;f__UBA6249;g__UBA6249	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004298075.1	s__UBA6249 sp004298075	76.7799	56	377	d__Bacteria;p__Omnitrophota;c__Koll11;o__GIF10;f__UBA6249;g__UBA6249	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-18 20:57:07,461] [INFO] GTDB search result was written to GCA_018897095.1_ASM1889709v1_genomic.fna/result_gtdb.tsv
[2023-06-18 20:57:07,462] [INFO] ===== GTDB Search completed =====
[2023-06-18 20:57:07,464] [INFO] DFAST_QC result json was written to GCA_018897095.1_ASM1889709v1_genomic.fna/dqc_result.json
[2023-06-18 20:57:07,464] [INFO] DFAST_QC completed!
[2023-06-18 20:57:07,464] [INFO] Total running time: 0h0m28s