[2023-06-08 02:39:19,196] [INFO] DFAST_QC pipeline started.
[2023-06-08 02:39:19,199] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 02:39:19,200] [INFO] DQC Reference Directory: /var/lib/cwl/stg215910d2-2b17-4553-a9d0-608e0f7a15fd/dqc_reference
[2023-06-08 02:39:21,995] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 02:39:21,996] [INFO] Task started: Prodigal
[2023-06-08 02:39:21,996] [INFO] Running command: gunzip -c /var/lib/cwl/stg912012b1-5ee1-4a1a-837a-7721be188495/GCA_945879095.1_TrH-25oct19-145_genomic.fna.gz | prodigal -d GCA_945879095.1_TrH-25oct19-145_genomic.fna/cds.fna -a GCA_945879095.1_TrH-25oct19-145_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 02:39:31,358] [INFO] Task succeeded: Prodigal
[2023-06-08 02:39:31,358] [INFO] Task started: HMMsearch
[2023-06-08 02:39:31,358] [INFO] Running command: hmmsearch --tblout GCA_945879095.1_TrH-25oct19-145_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg215910d2-2b17-4553-a9d0-608e0f7a15fd/dqc_reference/reference_markers.hmm GCA_945879095.1_TrH-25oct19-145_genomic.fna/protein.faa > /dev/null
[2023-06-08 02:39:31,635] [INFO] Task succeeded: HMMsearch
[2023-06-08 02:39:31,636] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg912012b1-5ee1-4a1a-837a-7721be188495/GCA_945879095.1_TrH-25oct19-145_genomic.fna.gz]
[2023-06-08 02:39:31,684] [INFO] Query marker FASTA was written to GCA_945879095.1_TrH-25oct19-145_genomic.fna/markers.fasta
[2023-06-08 02:39:31,684] [INFO] Task started: Blastn
[2023-06-08 02:39:31,684] [INFO] Running command: blastn -query GCA_945879095.1_TrH-25oct19-145_genomic.fna/markers.fasta -db /var/lib/cwl/stg215910d2-2b17-4553-a9d0-608e0f7a15fd/dqc_reference/reference_markers.fasta -out GCA_945879095.1_TrH-25oct19-145_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 02:39:32,360] [INFO] Task succeeded: Blastn
[2023-06-08 02:39:32,364] [INFO] Selected 19 target genomes.
[2023-06-08 02:39:32,364] [INFO] Target genome list was writen to GCA_945879095.1_TrH-25oct19-145_genomic.fna/target_genomes.txt
[2023-06-08 02:39:32,368] [INFO] Task started: fastANI
[2023-06-08 02:39:32,368] [INFO] Running command: fastANI --query /var/lib/cwl/stg912012b1-5ee1-4a1a-837a-7721be188495/GCA_945879095.1_TrH-25oct19-145_genomic.fna.gz --refList GCA_945879095.1_TrH-25oct19-145_genomic.fna/target_genomes.txt --output GCA_945879095.1_TrH-25oct19-145_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 02:39:46,405] [INFO] Task succeeded: fastANI
[2023-06-08 02:39:46,405] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg215910d2-2b17-4553-a9d0-608e0f7a15fd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 02:39:46,406] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg215910d2-2b17-4553-a9d0-608e0f7a15fd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 02:39:46,411] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 02:39:46,412] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-08 02:39:46,412] [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
Fluviicola taffensis	strain=DSM 16823	GCA_000194605.1	191579	191579	type	True	76.3955	82	711	95	below_threshold
Brumimicrobium aurantiacum	strain=N62	GCA_003402975.1	1737063	1737063	type	True	76.0134	53	711	95	below_threshold
Brumimicrobium mesophilum	strain=JCM 14063	GCA_003025005.1	392717	392717	type	True	75.8132	50	711	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 02:39:46,414] [INFO] DFAST Taxonomy check result was written to GCA_945879095.1_TrH-25oct19-145_genomic.fna/tc_result.tsv
[2023-06-08 02:39:46,414] [INFO] ===== Taxonomy check completed =====
[2023-06-08 02:39:46,414] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 02:39:46,415] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg215910d2-2b17-4553-a9d0-608e0f7a15fd/dqc_reference/checkm_data
[2023-06-08 02:39:46,416] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 02:39:46,455] [INFO] Task started: CheckM
[2023-06-08 02:39:46,455] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_945879095.1_TrH-25oct19-145_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_945879095.1_TrH-25oct19-145_genomic.fna/checkm_input GCA_945879095.1_TrH-25oct19-145_genomic.fna/checkm_result
[2023-06-08 02:40:19,530] [INFO] Task succeeded: CheckM
[2023-06-08 02:40:19,532] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 56.77%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 02:40:19,558] [INFO] ===== Completeness check finished =====
[2023-06-08 02:40:19,559] [INFO] ===== Start GTDB Search =====
[2023-06-08 02:40:19,559] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_945879095.1_TrH-25oct19-145_genomic.fna/markers.fasta)
[2023-06-08 02:40:19,560] [INFO] Task started: Blastn
[2023-06-08 02:40:19,560] [INFO] Running command: blastn -query GCA_945879095.1_TrH-25oct19-145_genomic.fna/markers.fasta -db /var/lib/cwl/stg215910d2-2b17-4553-a9d0-608e0f7a15fd/dqc_reference/reference_markers_gtdb.fasta -out GCA_945879095.1_TrH-25oct19-145_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 02:40:20,385] [INFO] Task succeeded: Blastn
[2023-06-08 02:40:20,390] [INFO] Selected 21 target genomes.
[2023-06-08 02:40:20,390] [INFO] Target genome list was writen to GCA_945879095.1_TrH-25oct19-145_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 02:40:20,402] [INFO] Task started: fastANI
[2023-06-08 02:40:20,402] [INFO] Running command: fastANI --query /var/lib/cwl/stg912012b1-5ee1-4a1a-837a-7721be188495/GCA_945879095.1_TrH-25oct19-145_genomic.fna.gz --refList GCA_945879095.1_TrH-25oct19-145_genomic.fna/target_genomes_gtdb.txt --output GCA_945879095.1_TrH-25oct19-145_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 02:40:30,479] [INFO] Task succeeded: fastANI
[2023-06-08 02:40:30,493] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-08 02:40:30,494] [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_009885545.1	s__M0103 sp009885545	83.5563	437	711	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__M0103	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903945495.1	s__M0103 sp903945495	77.721	226	711	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__M0103	95.0	99.87	99.80	0.95	0.92	6	-
GCA_017984635.1	s__M0103 sp017984635	77.5111	127	711	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__M0103	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903930085.1	s__M0103 sp903930085	77.4856	114	711	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__M0103	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018883325.1	s__UBA952 sp018883325	76.6211	83	711	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__UBA952	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000194605.1	s__Fluviicola taffensis	76.3661	82	711	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__Fluviicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905182335.1	s__UBA4466 sp905182335	76.3048	56	711	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__UBA4466	95.0	99.88	99.88	0.98	0.98	2	-
GCA_905480145.1	s__UBA4466 sp905480145	76.1516	55	711	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__UBA4466	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016866415.1	s__UBA952 sp016866415	76.0244	54	711	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__UBA952	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903873915.1	s__M0103 sp903873915	76.0002	60	711	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__M0103	95.0	99.96	99.96	0.94	0.94	3	-
GCA_016183815.1	s__M2408 sp016183815	75.8228	51	711	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__M2408	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-08 02:40:30,496] [INFO] GTDB search result was written to GCA_945879095.1_TrH-25oct19-145_genomic.fna/result_gtdb.tsv
[2023-06-08 02:40:30,496] [INFO] ===== GTDB Search completed =====
[2023-06-08 02:40:30,499] [INFO] DFAST_QC result json was written to GCA_945879095.1_TrH-25oct19-145_genomic.fna/dqc_result.json
[2023-06-08 02:40:30,499] [INFO] DFAST_QC completed!
[2023-06-08 02:40:30,499] [INFO] Total running time: 0h1m11s