[2023-06-30 22:46:23,662] [INFO] DFAST_QC pipeline started.
[2023-06-30 22:46:23,665] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 22:46:23,665] [INFO] DQC Reference Directory: /var/lib/cwl/stg1c8f1b77-3e07-4bb0-a3f1-3baa05a9b268/dqc_reference
[2023-06-30 22:46:25,635] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 22:46:25,637] [INFO] Task started: Prodigal
[2023-06-30 22:46:25,637] [INFO] Running command: gunzip -c /var/lib/cwl/stgc88ac2ce-e9e8-45a5-a110-e65589ae64d3/GCA_016290095.1_ASM1629009v1_genomic.fna.gz | prodigal -d GCA_016290095.1_ASM1629009v1_genomic.fna/cds.fna -a GCA_016290095.1_ASM1629009v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 22:46:28,112] [INFO] Task succeeded: Prodigal
[2023-06-30 22:46:28,112] [INFO] Task started: HMMsearch
[2023-06-30 22:46:28,112] [INFO] Running command: hmmsearch --tblout GCA_016290095.1_ASM1629009v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1c8f1b77-3e07-4bb0-a3f1-3baa05a9b268/dqc_reference/reference_markers.hmm GCA_016290095.1_ASM1629009v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 22:46:28,349] [INFO] Task succeeded: HMMsearch
[2023-06-30 22:46:28,350] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgc88ac2ce-e9e8-45a5-a110-e65589ae64d3/GCA_016290095.1_ASM1629009v1_genomic.fna.gz]
[2023-06-30 22:46:28,420] [INFO] Query marker FASTA was written to GCA_016290095.1_ASM1629009v1_genomic.fna/markers.fasta
[2023-06-30 22:46:28,420] [INFO] Task started: Blastn
[2023-06-30 22:46:28,421] [INFO] Running command: blastn -query GCA_016290095.1_ASM1629009v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1c8f1b77-3e07-4bb0-a3f1-3baa05a9b268/dqc_reference/reference_markers.fasta -out GCA_016290095.1_ASM1629009v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 22:46:30,077] [INFO] Task succeeded: Blastn
[2023-06-30 22:46:30,081] [INFO] Selected 15 target genomes.
[2023-06-30 22:46:30,082] [INFO] Target genome list was writen to GCA_016290095.1_ASM1629009v1_genomic.fna/target_genomes.txt
[2023-06-30 22:46:30,086] [INFO] Task started: fastANI
[2023-06-30 22:46:30,087] [INFO] Running command: fastANI --query /var/lib/cwl/stgc88ac2ce-e9e8-45a5-a110-e65589ae64d3/GCA_016290095.1_ASM1629009v1_genomic.fna.gz --refList GCA_016290095.1_ASM1629009v1_genomic.fna/target_genomes.txt --output GCA_016290095.1_ASM1629009v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 22:46:37,715] [INFO] Task succeeded: fastANI
[2023-06-30 22:46:37,716] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1c8f1b77-3e07-4bb0-a3f1-3baa05a9b268/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 22:46:37,716] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1c8f1b77-3e07-4bb0-a3f1-3baa05a9b268/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 22:46:37,718] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 22:46:37,718] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-30 22:46:37,718] [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
--------------------------------------------------------------------------------
[2023-06-30 22:46:37,720] [INFO] DFAST Taxonomy check result was written to GCA_016290095.1_ASM1629009v1_genomic.fna/tc_result.tsv
[2023-06-30 22:46:37,720] [INFO] ===== Taxonomy check completed =====
[2023-06-30 22:46:37,721] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 22:46:37,721] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1c8f1b77-3e07-4bb0-a3f1-3baa05a9b268/dqc_reference/checkm_data
[2023-06-30 22:46:37,723] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 22:46:37,745] [INFO] Task started: CheckM
[2023-06-30 22:46:37,746] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_016290095.1_ASM1629009v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_016290095.1_ASM1629009v1_genomic.fna/checkm_input GCA_016290095.1_ASM1629009v1_genomic.fna/checkm_result
[2023-06-30 22:46:53,766] [INFO] Task succeeded: CheckM
[2023-06-30 22:46:53,767] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 93.98%
Contamintation: 0.38%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-30 22:46:53,788] [INFO] ===== Completeness check finished =====
[2023-06-30 22:46:53,789] [INFO] ===== Start GTDB Search =====
[2023-06-30 22:46:53,789] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_016290095.1_ASM1629009v1_genomic.fna/markers.fasta)
[2023-06-30 22:46:53,789] [INFO] Task started: Blastn
[2023-06-30 22:46:53,790] [INFO] Running command: blastn -query GCA_016290095.1_ASM1629009v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1c8f1b77-3e07-4bb0-a3f1-3baa05a9b268/dqc_reference/reference_markers_gtdb.fasta -out GCA_016290095.1_ASM1629009v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 22:46:54,277] [INFO] Task succeeded: Blastn
[2023-06-30 22:46:54,282] [INFO] Selected 11 target genomes.
[2023-06-30 22:46:54,282] [INFO] Target genome list was writen to GCA_016290095.1_ASM1629009v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 22:46:54,287] [INFO] Task started: fastANI
[2023-06-30 22:46:54,287] [INFO] Running command: fastANI --query /var/lib/cwl/stgc88ac2ce-e9e8-45a5-a110-e65589ae64d3/GCA_016290095.1_ASM1629009v1_genomic.fna.gz --refList GCA_016290095.1_ASM1629009v1_genomic.fna/target_genomes_gtdb.txt --output GCA_016290095.1_ASM1629009v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 22:46:59,063] [INFO] Task succeeded: fastANI
[2023-06-30 22:46:59,074] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 22:46:59,075] [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_016290095.1	s__Scatovivens sp016290095	100.0	488	489	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__Scatovivens	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_017456555.1	s__Scatovivens sp017456555	79.6746	200	489	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__Scatovivens	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017536685.1	s__Scatovivens sp017536685	79.3369	199	489	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__Scatovivens	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017517685.1	s__Scatovivens sp017517685	79.1173	191	489	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__Scatovivens	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900553685.1	s__Scatovivens faecipullorum	79.0534	206	489	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__Scatovivens	95.0	98.76	98.76	0.86	0.86	2	-
GCA_002449785.1	s__Scatovivens sp002449785	78.7383	177	489	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__Scatovivens	95.0	99.11	99.11	0.87	0.87	2	-
GCA_017625465.1	s__Scatovivens sp017625465	78.3129	137	489	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__Scatovivens	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900768805.1	s__Scatovivens sp900768805	77.5212	120	489	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__Scatovivens	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900555075.1	s__UMGS1781 sp900555075	76.6636	60	489	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__UMGS1781	95.0	99.58	99.24	0.86	0.82	3	-
GCA_017621295.1	s__CAG-492 sp017621295	76.4748	68	489	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-492	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 22:46:59,077] [INFO] GTDB search result was written to GCA_016290095.1_ASM1629009v1_genomic.fna/result_gtdb.tsv
[2023-06-30 22:46:59,078] [INFO] ===== GTDB Search completed =====
[2023-06-30 22:46:59,081] [INFO] DFAST_QC result json was written to GCA_016290095.1_ASM1629009v1_genomic.fna/dqc_result.json
[2023-06-30 22:46:59,081] [INFO] DFAST_QC completed!
[2023-06-30 22:46:59,081] [INFO] Total running time: 0h0m35s