[2023-06-13 19:14:47,374] [INFO] DFAST_QC pipeline started.
[2023-06-13 19:14:47,379] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 19:14:47,379] [INFO] DQC Reference Directory: /var/lib/cwl/stg4c46d479-c5d9-4988-b55d-4bef7481f833/dqc_reference
[2023-06-13 19:14:49,205] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 19:14:49,214] [INFO] Task started: Prodigal
[2023-06-13 19:14:49,215] [INFO] Running command: gunzip -c /var/lib/cwl/stg8bdb60f6-7c78-426d-a1dc-e38debd163f9/GCA_022825835.1_ASM2282583v1_genomic.fna.gz | prodigal -d GCA_022825835.1_ASM2282583v1_genomic.fna/cds.fna -a GCA_022825835.1_ASM2282583v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 19:15:05,322] [INFO] Task succeeded: Prodigal
[2023-06-13 19:15:05,322] [INFO] Task started: HMMsearch
[2023-06-13 19:15:05,323] [INFO] Running command: hmmsearch --tblout GCA_022825835.1_ASM2282583v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4c46d479-c5d9-4988-b55d-4bef7481f833/dqc_reference/reference_markers.hmm GCA_022825835.1_ASM2282583v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 19:15:05,607] [INFO] Task succeeded: HMMsearch
[2023-06-13 19:15:05,608] [INFO] Found 6/6 markers.
[2023-06-13 19:15:05,654] [INFO] Query marker FASTA was written to GCA_022825835.1_ASM2282583v1_genomic.fna/markers.fasta
[2023-06-13 19:15:05,655] [INFO] Task started: Blastn
[2023-06-13 19:15:05,655] [INFO] Running command: blastn -query GCA_022825835.1_ASM2282583v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4c46d479-c5d9-4988-b55d-4bef7481f833/dqc_reference/reference_markers.fasta -out GCA_022825835.1_ASM2282583v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 19:15:06,225] [INFO] Task succeeded: Blastn
[2023-06-13 19:15:06,229] [INFO] Selected 37 target genomes.
[2023-06-13 19:15:06,229] [INFO] Target genome list was writen to GCA_022825835.1_ASM2282583v1_genomic.fna/target_genomes.txt
[2023-06-13 19:15:06,234] [INFO] Task started: fastANI
[2023-06-13 19:15:06,235] [INFO] Running command: fastANI --query /var/lib/cwl/stg8bdb60f6-7c78-426d-a1dc-e38debd163f9/GCA_022825835.1_ASM2282583v1_genomic.fna.gz --refList GCA_022825835.1_ASM2282583v1_genomic.fna/target_genomes.txt --output GCA_022825835.1_ASM2282583v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 19:15:33,225] [INFO] Task succeeded: fastANI
[2023-06-13 19:15:33,226] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4c46d479-c5d9-4988-b55d-4bef7481f833/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 19:15:33,227] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4c46d479-c5d9-4988-b55d-4bef7481f833/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 19:15:33,231] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 19:15:33,231] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 19:15:33,231] [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
Haliangium ochraceum	strain=DSM 14365	GCA_000024805.1	80816	80816	type	True	74.8469	85	2024	95	below_threshold
Catellatospora paridis	strain=NEAU-CL2	GCA_009720365.1	1617086	1617086	type	True	74.7557	56	2024	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 19:15:33,233] [INFO] DFAST Taxonomy check result was written to GCA_022825835.1_ASM2282583v1_genomic.fna/tc_result.tsv
[2023-06-13 19:15:33,233] [INFO] ===== Taxonomy check completed =====
[2023-06-13 19:15:33,234] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 19:15:33,234] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4c46d479-c5d9-4988-b55d-4bef7481f833/dqc_reference/checkm_data
[2023-06-13 19:15:33,235] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 19:15:33,300] [INFO] Task started: CheckM
[2023-06-13 19:15:33,301] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022825835.1_ASM2282583v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022825835.1_ASM2282583v1_genomic.fna/checkm_input GCA_022825835.1_ASM2282583v1_genomic.fna/checkm_result
[2023-06-13 19:16:17,827] [INFO] Task succeeded: CheckM
[2023-06-13 19:16:17,828] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 5.09%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 19:16:17,852] [INFO] ===== Completeness check finished =====
[2023-06-13 19:16:17,852] [INFO] ===== Start GTDB Search =====
[2023-06-13 19:16:17,853] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022825835.1_ASM2282583v1_genomic.fna/markers.fasta)
[2023-06-13 19:16:17,853] [INFO] Task started: Blastn
[2023-06-13 19:16:17,853] [INFO] Running command: blastn -query GCA_022825835.1_ASM2282583v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4c46d479-c5d9-4988-b55d-4bef7481f833/dqc_reference/reference_markers_gtdb.fasta -out GCA_022825835.1_ASM2282583v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 19:16:18,690] [INFO] Task succeeded: Blastn
[2023-06-13 19:16:18,693] [INFO] Selected 13 target genomes.
[2023-06-13 19:16:18,694] [INFO] Target genome list was writen to GCA_022825835.1_ASM2282583v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 19:16:18,701] [INFO] Task started: fastANI
[2023-06-13 19:16:18,701] [INFO] Running command: fastANI --query /var/lib/cwl/stg8bdb60f6-7c78-426d-a1dc-e38debd163f9/GCA_022825835.1_ASM2282583v1_genomic.fna.gz --refList GCA_022825835.1_ASM2282583v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022825835.1_ASM2282583v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 19:16:31,664] [INFO] Task succeeded: fastANI
[2023-06-13 19:16:31,671] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-13 19:16:31,671] [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_009840005.1	s__GCA-2724215 sp009840005	91.9001	1672	2024	d__Bacteria;p__Latescibacterota;c__UBA2968;o__UBA8231;f__UBA8231;g__GCA-2724215	95.0	99.94	99.94	0.99	0.99	2	-
GCA_009841115.1	s__GCA-2724215 sp009841115	91.426	1575	2024	d__Bacteria;p__Latescibacterota;c__UBA2968;o__UBA8231;f__UBA8231;g__GCA-2724215	95.0	99.89	99.89	0.98	0.96	3	-
GCA_009845645.1	s__GCA-2724215 sp009845645	90.8526	909	2024	d__Bacteria;p__Latescibacterota;c__UBA2968;o__UBA8231;f__UBA8231;g__GCA-2724215	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007571365.1	s__GCA-2724215 sp007571365	87.8521	1330	2024	d__Bacteria;p__Latescibacterota;c__UBA2968;o__UBA8231;f__UBA8231;g__GCA-2724215	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002724215.1	s__GCA-2724215 sp002724215	77.7495	442	2024	d__Bacteria;p__Latescibacterota;c__UBA2968;o__UBA8231;f__UBA8231;g__GCA-2724215	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015660315.1	s__GCA-2724215 sp015660315	77.1227	269	2024	d__Bacteria;p__Latescibacterota;c__UBA2968;o__UBA8231;f__UBA8231;g__GCA-2724215	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016187725.1	s__SICG01 sp016187725	76.4404	140	2024	d__Bacteria;p__Latescibacterota;c__UBA2968;o__UBA8231;f__UBA8231;g__SICG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002725915.1	s__GCA-2725915 sp002725915	75.9187	68	2024	d__Bacteria;p__Latescibacterota;c__UBA2968;o__UBA8231;f__UBA8231;g__GCA-2725915	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 19:16:31,673] [INFO] GTDB search result was written to GCA_022825835.1_ASM2282583v1_genomic.fna/result_gtdb.tsv
[2023-06-13 19:16:31,674] [INFO] ===== GTDB Search completed =====
[2023-06-13 19:16:31,676] [INFO] DFAST_QC result json was written to GCA_022825835.1_ASM2282583v1_genomic.fna/dqc_result.json
[2023-06-13 19:16:31,676] [INFO] DFAST_QC completed!
[2023-06-13 19:16:31,676] [INFO] Total running time: 0h1m44s