[2023-06-28 14:28:27,015] [INFO] DFAST_QC pipeline started.
[2023-06-28 14:28:27,018] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 14:28:27,018] [INFO] DQC Reference Directory: /var/lib/cwl/stgb6ced9e5-258a-4f37-b1ab-125f0aa0114c/dqc_reference
[2023-06-28 14:28:28,211] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 14:28:28,212] [INFO] Task started: Prodigal
[2023-06-28 14:28:28,212] [INFO] Running command: gunzip -c /var/lib/cwl/stg077d66af-f0cd-4834-9397-d602587b84da/GCA_017464345.1_ASM1746434v1_genomic.fna.gz | prodigal -d GCA_017464345.1_ASM1746434v1_genomic.fna/cds.fna -a GCA_017464345.1_ASM1746434v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 14:28:39,362] [INFO] Task succeeded: Prodigal
[2023-06-28 14:28:39,362] [INFO] Task started: HMMsearch
[2023-06-28 14:28:39,362] [INFO] Running command: hmmsearch --tblout GCA_017464345.1_ASM1746434v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb6ced9e5-258a-4f37-b1ab-125f0aa0114c/dqc_reference/reference_markers.hmm GCA_017464345.1_ASM1746434v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 14:28:39,488] [INFO] Task succeeded: HMMsearch
[2023-06-28 14:28:39,489] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg077d66af-f0cd-4834-9397-d602587b84da/GCA_017464345.1_ASM1746434v1_genomic.fna.gz]
[2023-06-28 14:28:39,509] [INFO] Query marker FASTA was written to GCA_017464345.1_ASM1746434v1_genomic.fna/markers.fasta
[2023-06-28 14:28:39,510] [INFO] Task started: Blastn
[2023-06-28 14:28:39,510] [INFO] Running command: blastn -query GCA_017464345.1_ASM1746434v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb6ced9e5-258a-4f37-b1ab-125f0aa0114c/dqc_reference/reference_markers.fasta -out GCA_017464345.1_ASM1746434v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 14:28:40,048] [INFO] Task succeeded: Blastn
[2023-06-28 14:28:40,052] [INFO] Selected 10 target genomes.
[2023-06-28 14:28:40,052] [INFO] Target genome list was writen to GCA_017464345.1_ASM1746434v1_genomic.fna/target_genomes.txt
[2023-06-28 14:28:40,053] [INFO] Task started: fastANI
[2023-06-28 14:28:40,053] [INFO] Running command: fastANI --query /var/lib/cwl/stg077d66af-f0cd-4834-9397-d602587b84da/GCA_017464345.1_ASM1746434v1_genomic.fna.gz --refList GCA_017464345.1_ASM1746434v1_genomic.fna/target_genomes.txt --output GCA_017464345.1_ASM1746434v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 14:28:45,416] [INFO] Task succeeded: fastANI
[2023-06-28 14:28:45,416] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb6ced9e5-258a-4f37-b1ab-125f0aa0114c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 14:28:45,417] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb6ced9e5-258a-4f37-b1ab-125f0aa0114c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 14:28:45,442] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 14:28:45,442] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 14:28:45,443] [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
--------------------------------------------------------------------------------
[2023-06-28 14:28:45,445] [INFO] DFAST Taxonomy check result was written to GCA_017464345.1_ASM1746434v1_genomic.fna/tc_result.tsv
[2023-06-28 14:28:45,445] [INFO] ===== Taxonomy check completed =====
[2023-06-28 14:28:45,446] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 14:28:45,446] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb6ced9e5-258a-4f37-b1ab-125f0aa0114c/dqc_reference/checkm_data
[2023-06-28 14:28:45,448] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 14:28:45,471] [INFO] Task started: CheckM
[2023-06-28 14:28:45,471] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_017464345.1_ASM1746434v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_017464345.1_ASM1746434v1_genomic.fna/checkm_input GCA_017464345.1_ASM1746434v1_genomic.fna/checkm_result
[2023-06-28 14:29:19,735] [INFO] Task succeeded: CheckM
[2023-06-28 14:29:19,736] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 54.17%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 14:29:19,756] [INFO] ===== Completeness check finished =====
[2023-06-28 14:29:19,756] [INFO] ===== Start GTDB Search =====
[2023-06-28 14:29:19,756] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_017464345.1_ASM1746434v1_genomic.fna/markers.fasta)
[2023-06-28 14:29:19,757] [INFO] Task started: Blastn
[2023-06-28 14:29:19,757] [INFO] Running command: blastn -query GCA_017464345.1_ASM1746434v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb6ced9e5-258a-4f37-b1ab-125f0aa0114c/dqc_reference/reference_markers_gtdb.fasta -out GCA_017464345.1_ASM1746434v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 14:29:20,362] [INFO] Task succeeded: Blastn
[2023-06-28 14:29:20,368] [INFO] Selected 8 target genomes.
[2023-06-28 14:29:20,368] [INFO] Target genome list was writen to GCA_017464345.1_ASM1746434v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 14:29:20,369] [INFO] Task started: fastANI
[2023-06-28 14:29:20,370] [INFO] Running command: fastANI --query /var/lib/cwl/stg077d66af-f0cd-4834-9397-d602587b84da/GCA_017464345.1_ASM1746434v1_genomic.fna.gz --refList GCA_017464345.1_ASM1746434v1_genomic.fna/target_genomes_gtdb.txt --output GCA_017464345.1_ASM1746434v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 14:29:24,657] [INFO] Task succeeded: fastANI
[2023-06-28 14:29:24,665] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 14:29:24,665] [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_017464345.1	s__UBA4372 sp017464345	100.0	613	616	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_017469925.1	s__UBA4372 sp017469925	82.6752	267	616	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017444005.1	s__UBA4372 sp017444005	81.1248	206	616	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017453445.1	s__UBA4372 sp017453445	79.7521	233	616	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372	95.0	98.06	98.06	0.83	0.83	2	-
GCA_002395775.1	s__UBA4372 sp002395775	79.3362	223	616	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372	95.0	96.87	96.87	0.81	0.81	2	-
GCA_902783655.1	s__UBA4372 sp902783655	78.7035	185	616	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002394305.1	s__UBA4372 sp002394305	77.6649	96	616	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372	95.0	97.13	97.13	0.80	0.80	2	-
GCA_017483665.1	s__UBA4372 sp017483665	77.4681	101	616	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 14:29:24,667] [INFO] GTDB search result was written to GCA_017464345.1_ASM1746434v1_genomic.fna/result_gtdb.tsv
[2023-06-28 14:29:24,668] [INFO] ===== GTDB Search completed =====
[2023-06-28 14:29:24,670] [INFO] DFAST_QC result json was written to GCA_017464345.1_ASM1746434v1_genomic.fna/dqc_result.json
[2023-06-28 14:29:24,671] [INFO] DFAST_QC completed!
[2023-06-28 14:29:24,671] [INFO] Total running time: 0h0m58s