[2023-06-28 09:30:13,499] [INFO] DFAST_QC pipeline started.
[2023-06-28 09:30:13,501] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 09:30:13,501] [INFO] DQC Reference Directory: /var/lib/cwl/stg0b879953-d22b-4488-8705-384c3533a25d/dqc_reference
[2023-06-28 09:30:15,039] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 09:30:15,040] [INFO] Task started: Prodigal
[2023-06-28 09:30:15,040] [INFO] Running command: gunzip -c /var/lib/cwl/stgbbe9f65c-aaa1-4e9a-aa9f-b0cd93a7d199/GCA_944359085.1_BRZ_PA_bin23_genomic.fna.gz | prodigal -d GCA_944359085.1_BRZ_PA_bin23_genomic.fna/cds.fna -a GCA_944359085.1_BRZ_PA_bin23_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 09:30:16,568] [INFO] Task succeeded: Prodigal
[2023-06-28 09:30:16,569] [INFO] Task started: HMMsearch
[2023-06-28 09:30:16,569] [INFO] Running command: hmmsearch --tblout GCA_944359085.1_BRZ_PA_bin23_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0b879953-d22b-4488-8705-384c3533a25d/dqc_reference/reference_markers.hmm GCA_944359085.1_BRZ_PA_bin23_genomic.fna/protein.faa > /dev/null
[2023-06-28 09:30:16,783] [INFO] Task succeeded: HMMsearch
[2023-06-28 09:30:16,785] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgbbe9f65c-aaa1-4e9a-aa9f-b0cd93a7d199/GCA_944359085.1_BRZ_PA_bin23_genomic.fna.gz]
[2023-06-28 09:30:16,807] [INFO] Query marker FASTA was written to GCA_944359085.1_BRZ_PA_bin23_genomic.fna/markers.fasta
[2023-06-28 09:30:16,808] [INFO] Task started: Blastn
[2023-06-28 09:30:16,808] [INFO] Running command: blastn -query GCA_944359085.1_BRZ_PA_bin23_genomic.fna/markers.fasta -db /var/lib/cwl/stg0b879953-d22b-4488-8705-384c3533a25d/dqc_reference/reference_markers.fasta -out GCA_944359085.1_BRZ_PA_bin23_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 09:30:17,449] [INFO] Task succeeded: Blastn
[2023-06-28 09:30:17,453] [INFO] Selected 25 target genomes.
[2023-06-28 09:30:17,454] [INFO] Target genome list was writen to GCA_944359085.1_BRZ_PA_bin23_genomic.fna/target_genomes.txt
[2023-06-28 09:30:17,455] [INFO] Task started: fastANI
[2023-06-28 09:30:17,455] [INFO] Running command: fastANI --query /var/lib/cwl/stgbbe9f65c-aaa1-4e9a-aa9f-b0cd93a7d199/GCA_944359085.1_BRZ_PA_bin23_genomic.fna.gz --refList GCA_944359085.1_BRZ_PA_bin23_genomic.fna/target_genomes.txt --output GCA_944359085.1_BRZ_PA_bin23_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 09:30:30,158] [INFO] Task succeeded: fastANI
[2023-06-28 09:30:30,159] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0b879953-d22b-4488-8705-384c3533a25d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 09:30:30,159] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0b879953-d22b-4488-8705-384c3533a25d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 09:30:30,161] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 09:30:30,161] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 09:30:30,161] [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 09:30:30,164] [INFO] DFAST Taxonomy check result was written to GCA_944359085.1_BRZ_PA_bin23_genomic.fna/tc_result.tsv
[2023-06-28 09:30:30,164] [INFO] ===== Taxonomy check completed =====
[2023-06-28 09:30:30,164] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 09:30:30,165] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0b879953-d22b-4488-8705-384c3533a25d/dqc_reference/checkm_data
[2023-06-28 09:30:30,168] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 09:30:30,198] [INFO] Task started: CheckM
[2023-06-28 09:30:30,198] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_944359085.1_BRZ_PA_bin23_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_944359085.1_BRZ_PA_bin23_genomic.fna/checkm_input GCA_944359085.1_BRZ_PA_bin23_genomic.fna/checkm_result
[2023-06-28 09:30:44,207] [INFO] Task succeeded: CheckM
[2023-06-28 09:30:44,208] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 61.57%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 09:30:44,230] [INFO] ===== Completeness check finished =====
[2023-06-28 09:30:44,231] [INFO] ===== Start GTDB Search =====
[2023-06-28 09:30:44,231] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_944359085.1_BRZ_PA_bin23_genomic.fna/markers.fasta)
[2023-06-28 09:30:44,231] [INFO] Task started: Blastn
[2023-06-28 09:30:44,231] [INFO] Running command: blastn -query GCA_944359085.1_BRZ_PA_bin23_genomic.fna/markers.fasta -db /var/lib/cwl/stg0b879953-d22b-4488-8705-384c3533a25d/dqc_reference/reference_markers_gtdb.fasta -out GCA_944359085.1_BRZ_PA_bin23_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 09:30:45,062] [INFO] Task succeeded: Blastn
[2023-06-28 09:30:45,067] [INFO] Selected 17 target genomes.
[2023-06-28 09:30:45,067] [INFO] Target genome list was writen to GCA_944359085.1_BRZ_PA_bin23_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 09:30:45,070] [INFO] Task started: fastANI
[2023-06-28 09:30:45,071] [INFO] Running command: fastANI --query /var/lib/cwl/stgbbe9f65c-aaa1-4e9a-aa9f-b0cd93a7d199/GCA_944359085.1_BRZ_PA_bin23_genomic.fna.gz --refList GCA_944359085.1_BRZ_PA_bin23_genomic.fna/target_genomes_gtdb.txt --output GCA_944359085.1_BRZ_PA_bin23_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 09:30:48,960] [INFO] Task succeeded: fastANI
[2023-06-28 09:30:48,977] [INFO] Found 15 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 09:30:48,977] [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_018716405.1	s__Faecisoma merdavium	87.648	222	343	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__Faecisoma	95.0	97.86	97.86	0.74	0.74	2	-
GCA_017887425.1	s__Faecisoma sp017887425	80.6228	208	343	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__Faecisoma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900753645.1	s__Faecisoma sp900753645	78.6973	94	343	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__Faecisoma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000432255.1	s__Faecisoma sp000432255	77.4673	99	343	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__Faecisoma	95.0	99.02	98.86	0.88	0.87	4	-
GCA_016288305.1	s__Faecisoma sp016288305	77.4546	111	343	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__Faecisoma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900544605.1	s__SIG204 sp900544605	76.9296	80	343	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__SIG204	95.0	98.54	98.50	0.89	0.86	3	-
GCA_015059285.1	s__SIG208 sp015059285	76.8696	84	343	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__SIG208	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015059545.1	s__UBA5026 sp015059545	76.5679	88	343	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__UBA5026	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015059155.1	s__UMGS1613 sp015059155	76.5542	66	343	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__UMGS1613	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017936845.1	s__UBA5026 sp017936845	76.4081	92	343	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__UBA5026	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017410525.1	s__UMGS1613 sp017410525	76.2032	82	343	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__UMGS1613	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900313725.1	s__UBA5026 sp900313725	76.1745	73	343	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__UBA5026	95.0	99.45	98.91	0.94	0.90	3	-
GCA_002425325.1	s__UBA5578 sp002425325	76.173	82	343	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__UBA5578	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016290195.1	s__UMGS1045 sp016290195	76.1035	75	343	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__UMGS1045	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015059405.1	s__RUG11788 sp015059405	75.6186	52	343	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__RUG11788	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 09:30:48,980] [INFO] GTDB search result was written to GCA_944359085.1_BRZ_PA_bin23_genomic.fna/result_gtdb.tsv
[2023-06-28 09:30:48,981] [INFO] ===== GTDB Search completed =====
[2023-06-28 09:30:48,986] [INFO] DFAST_QC result json was written to GCA_944359085.1_BRZ_PA_bin23_genomic.fna/dqc_result.json
[2023-06-28 09:30:48,986] [INFO] DFAST_QC completed!
[2023-06-28 09:30:48,986] [INFO] Total running time: 0h0m35s