[2023-06-07 22:55:03,217] [INFO] DFAST_QC pipeline started.
[2023-06-07 22:55:03,219] [INFO] DFAST_QC version: 0.5.7
[2023-06-07 22:55:03,219] [INFO] DQC Reference Directory: /var/lib/cwl/stged16ce44-548d-4c72-8e44-7f7b8d4c1567/dqc_reference
[2023-06-07 22:55:04,464] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-07 22:55:04,465] [INFO] Task started: Prodigal
[2023-06-07 22:55:04,466] [INFO] Running command: gunzip -c /var/lib/cwl/stg3da69b23-749c-4226-975a-6ae658a9269e/GCA_947489095.1_ZE-17mar17-159_genomic.fna.gz | prodigal -d GCA_947489095.1_ZE-17mar17-159_genomic.fna/cds.fna -a GCA_947489095.1_ZE-17mar17-159_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-07 22:55:13,198] [INFO] Task succeeded: Prodigal
[2023-06-07 22:55:13,199] [INFO] Task started: HMMsearch
[2023-06-07 22:55:13,199] [INFO] Running command: hmmsearch --tblout GCA_947489095.1_ZE-17mar17-159_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stged16ce44-548d-4c72-8e44-7f7b8d4c1567/dqc_reference/reference_markers.hmm GCA_947489095.1_ZE-17mar17-159_genomic.fna/protein.faa > /dev/null
[2023-06-07 22:55:13,415] [INFO] Task succeeded: HMMsearch
[2023-06-07 22:55:13,417] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg3da69b23-749c-4226-975a-6ae658a9269e/GCA_947489095.1_ZE-17mar17-159_genomic.fna.gz]
[2023-06-07 22:55:13,436] [INFO] Query marker FASTA was written to GCA_947489095.1_ZE-17mar17-159_genomic.fna/markers.fasta
[2023-06-07 22:55:13,437] [INFO] Task started: Blastn
[2023-06-07 22:55:13,437] [INFO] Running command: blastn -query GCA_947489095.1_ZE-17mar17-159_genomic.fna/markers.fasta -db /var/lib/cwl/stged16ce44-548d-4c72-8e44-7f7b8d4c1567/dqc_reference/reference_markers.fasta -out GCA_947489095.1_ZE-17mar17-159_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-07 22:55:14,032] [INFO] Task succeeded: Blastn
[2023-06-07 22:55:14,036] [INFO] Selected 20 target genomes.
[2023-06-07 22:55:14,036] [INFO] Target genome list was writen to GCA_947489095.1_ZE-17mar17-159_genomic.fna/target_genomes.txt
[2023-06-07 22:55:14,039] [INFO] Task started: fastANI
[2023-06-07 22:55:14,039] [INFO] Running command: fastANI --query /var/lib/cwl/stg3da69b23-749c-4226-975a-6ae658a9269e/GCA_947489095.1_ZE-17mar17-159_genomic.fna.gz --refList GCA_947489095.1_ZE-17mar17-159_genomic.fna/target_genomes.txt --output GCA_947489095.1_ZE-17mar17-159_genomic.fna/fastani_result.tsv --threads 1
[2023-06-07 22:55:26,684] [INFO] Task succeeded: fastANI
[2023-06-07 22:55:26,685] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stged16ce44-548d-4c72-8e44-7f7b8d4c1567/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-07 22:55:26,685] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stged16ce44-548d-4c72-8e44-7f7b8d4c1567/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-07 22:55:26,686] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-07 22:55:26,687] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-07 22:55:26,687] [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
--------------------------------------------------------------------------------
[2023-06-07 22:55:26,689] [INFO] DFAST Taxonomy check result was written to GCA_947489095.1_ZE-17mar17-159_genomic.fna/tc_result.tsv
[2023-06-07 22:55:26,689] [INFO] ===== Taxonomy check completed =====
[2023-06-07 22:55:26,689] [INFO] ===== Start completeness check using CheckM =====
[2023-06-07 22:55:26,690] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stged16ce44-548d-4c72-8e44-7f7b8d4c1567/dqc_reference/checkm_data
[2023-06-07 22:55:26,693] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-07 22:55:26,718] [INFO] Task started: CheckM
[2023-06-07 22:55:26,719] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_947489095.1_ZE-17mar17-159_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_947489095.1_ZE-17mar17-159_genomic.fna/checkm_input GCA_947489095.1_ZE-17mar17-159_genomic.fna/checkm_result
[2023-06-07 22:55:57,785] [INFO] Task succeeded: CheckM
[2023-06-07 22:55:57,787] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 67.99%
Contamintation: 0.46%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-07 22:55:57,809] [INFO] ===== Completeness check finished =====
[2023-06-07 22:55:57,809] [INFO] ===== Start GTDB Search =====
[2023-06-07 22:55:57,810] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_947489095.1_ZE-17mar17-159_genomic.fna/markers.fasta)
[2023-06-07 22:55:57,810] [INFO] Task started: Blastn
[2023-06-07 22:55:57,810] [INFO] Running command: blastn -query GCA_947489095.1_ZE-17mar17-159_genomic.fna/markers.fasta -db /var/lib/cwl/stged16ce44-548d-4c72-8e44-7f7b8d4c1567/dqc_reference/reference_markers_gtdb.fasta -out GCA_947489095.1_ZE-17mar17-159_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-07 22:55:58,676] [INFO] Task succeeded: Blastn
[2023-06-07 22:55:58,681] [INFO] Selected 12 target genomes.
[2023-06-07 22:55:58,681] [INFO] Target genome list was writen to GCA_947489095.1_ZE-17mar17-159_genomic.fna/target_genomes_gtdb.txt
[2023-06-07 22:55:58,714] [INFO] Task started: fastANI
[2023-06-07 22:55:58,715] [INFO] Running command: fastANI --query /var/lib/cwl/stg3da69b23-749c-4226-975a-6ae658a9269e/GCA_947489095.1_ZE-17mar17-159_genomic.fna.gz --refList GCA_947489095.1_ZE-17mar17-159_genomic.fna/target_genomes_gtdb.txt --output GCA_947489095.1_ZE-17mar17-159_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-07 22:56:03,625] [INFO] Task succeeded: fastANI
[2023-06-07 22:56:03,637] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-07 22:56:03,637] [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_002737625.1	s__UBA955 sp002737625	97.7877	293	454	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__NS11-12g;f__UBA955;g__UBA955	95.0	97.97	95.99	0.82	0.69	3	conclusive
GCA_903959115.1	s__UBA955 sp903959115	86.5777	325	454	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__NS11-12g;f__UBA955;g__UBA955	95.0	98.58	98.30	0.81	0.78	5	-
GCA_002347985.1	s__UBA955 sp002347985	82.6107	334	454	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__NS11-12g;f__UBA955;g__UBA955	95.0	99.54	99.54	0.88	0.88	2	-
GCA_002293105.1	s__UBA955 sp002293105	78.7075	139	454	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__NS11-12g;f__UBA955;g__UBA955	95.0	98.32	98.13	0.83	0.80	10	-
GCA_016868785.1	s__UBA955 sp016868785	78.0266	157	454	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__NS11-12g;f__UBA955;g__UBA955	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005788145.1	s__UBA955 sp005788145	77.8346	119	454	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__NS11-12g;f__UBA955;g__UBA955	95.0	96.27	95.94	0.80	0.76	5	-
--------------------------------------------------------------------------------
[2023-06-07 22:56:03,639] [INFO] GTDB search result was written to GCA_947489095.1_ZE-17mar17-159_genomic.fna/result_gtdb.tsv
[2023-06-07 22:56:03,640] [INFO] ===== GTDB Search completed =====
[2023-06-07 22:56:03,644] [INFO] DFAST_QC result json was written to GCA_947489095.1_ZE-17mar17-159_genomic.fna/dqc_result.json
[2023-06-07 22:56:03,644] [INFO] DFAST_QC completed!
[2023-06-07 22:56:03,644] [INFO] Total running time: 0h1m0s