[2023-06-13 05:12:52,708] [INFO] DFAST_QC pipeline started.
[2023-06-13 05:12:52,712] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 05:12:52,712] [INFO] DQC Reference Directory: /var/lib/cwl/stg0b9f7c35-2597-4bf9-8c88-21e90e9c0544/dqc_reference
[2023-06-13 05:12:54,056] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 05:12:54,057] [INFO] Task started: Prodigal
[2023-06-13 05:12:54,057] [INFO] Running command: gunzip -c /var/lib/cwl/stg71030fd7-90ec-442f-bd32-50aebb5b1032/GCA_022771715.1_ASM2277171v1_genomic.fna.gz | prodigal -d GCA_022771715.1_ASM2277171v1_genomic.fna/cds.fna -a GCA_022771715.1_ASM2277171v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 05:12:55,507] [INFO] Task succeeded: Prodigal
[2023-06-13 05:12:55,507] [INFO] Task started: HMMsearch
[2023-06-13 05:12:55,507] [INFO] Running command: hmmsearch --tblout GCA_022771715.1_ASM2277171v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0b9f7c35-2597-4bf9-8c88-21e90e9c0544/dqc_reference/reference_markers.hmm GCA_022771715.1_ASM2277171v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 05:12:55,765] [INFO] Task succeeded: HMMsearch
[2023-06-13 05:12:55,766] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg71030fd7-90ec-442f-bd32-50aebb5b1032/GCA_022771715.1_ASM2277171v1_genomic.fna.gz]
[2023-06-13 05:12:55,795] [INFO] Query marker FASTA was written to GCA_022771715.1_ASM2277171v1_genomic.fna/markers.fasta
[2023-06-13 05:12:55,795] [INFO] Task started: Blastn
[2023-06-13 05:12:55,795] [INFO] Running command: blastn -query GCA_022771715.1_ASM2277171v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0b9f7c35-2597-4bf9-8c88-21e90e9c0544/dqc_reference/reference_markers.fasta -out GCA_022771715.1_ASM2277171v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 05:12:56,425] [INFO] Task succeeded: Blastn
[2023-06-13 05:12:56,429] [INFO] Selected 25 target genomes.
[2023-06-13 05:12:56,429] [INFO] Target genome list was writen to GCA_022771715.1_ASM2277171v1_genomic.fna/target_genomes.txt
[2023-06-13 05:12:56,441] [INFO] Task started: fastANI
[2023-06-13 05:12:56,441] [INFO] Running command: fastANI --query /var/lib/cwl/stg71030fd7-90ec-442f-bd32-50aebb5b1032/GCA_022771715.1_ASM2277171v1_genomic.fna.gz --refList GCA_022771715.1_ASM2277171v1_genomic.fna/target_genomes.txt --output GCA_022771715.1_ASM2277171v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 05:13:06,103] [INFO] Task succeeded: fastANI
[2023-06-13 05:13:06,103] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0b9f7c35-2597-4bf9-8c88-21e90e9c0544/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 05:13:06,104] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0b9f7c35-2597-4bf9-8c88-21e90e9c0544/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 05:13:06,105] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 05:13:06,105] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-13 05:13:06,105] [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
--------------------------------------------------------------------------------
[2023-06-13 05:13:06,108] [INFO] DFAST Taxonomy check result was written to GCA_022771715.1_ASM2277171v1_genomic.fna/tc_result.tsv
[2023-06-13 05:13:06,108] [INFO] ===== Taxonomy check completed =====
[2023-06-13 05:13:06,108] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 05:13:06,109] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0b9f7c35-2597-4bf9-8c88-21e90e9c0544/dqc_reference/checkm_data
[2023-06-13 05:13:06,111] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 05:13:06,127] [INFO] Task started: CheckM
[2023-06-13 05:13:06,127] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022771715.1_ASM2277171v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022771715.1_ASM2277171v1_genomic.fna/checkm_input GCA_022771715.1_ASM2277171v1_genomic.fna/checkm_result
[2023-06-13 05:13:20,223] [INFO] Task succeeded: CheckM
[2023-06-13 05:13:20,225] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 05:13:20,243] [INFO] ===== Completeness check finished =====
[2023-06-13 05:13:20,244] [INFO] ===== Start GTDB Search =====
[2023-06-13 05:13:20,245] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022771715.1_ASM2277171v1_genomic.fna/markers.fasta)
[2023-06-13 05:13:20,245] [INFO] Task started: Blastn
[2023-06-13 05:13:20,245] [INFO] Running command: blastn -query GCA_022771715.1_ASM2277171v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0b9f7c35-2597-4bf9-8c88-21e90e9c0544/dqc_reference/reference_markers_gtdb.fasta -out GCA_022771715.1_ASM2277171v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 05:13:21,086] [INFO] Task succeeded: Blastn
[2023-06-13 05:13:21,090] [INFO] Selected 29 target genomes.
[2023-06-13 05:13:21,090] [INFO] Target genome list was writen to GCA_022771715.1_ASM2277171v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 05:13:21,109] [INFO] Task started: fastANI
[2023-06-13 05:13:21,109] [INFO] Running command: fastANI --query /var/lib/cwl/stg71030fd7-90ec-442f-bd32-50aebb5b1032/GCA_022771715.1_ASM2277171v1_genomic.fna.gz --refList GCA_022771715.1_ASM2277171v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022771715.1_ASM2277171v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 05:13:26,806] [INFO] Task succeeded: fastANI
[2023-06-13 05:13:26,817] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-13 05:13:26,817] [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_015059285.1	s__SIG208 sp015059285	77.6633	66	310	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__SIG208	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018716405.1	s__Faecisoma merdavium	77.4272	73	310	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__Faecisoma	95.0	97.86	97.86	0.74	0.74	2	-
GCA_017936845.1	s__UBA5026 sp017936845	77.2729	80	310	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__UBA5026	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900544605.1	s__SIG204 sp900544605	77.1439	64	310	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__SIG204	95.0	98.54	98.50	0.89	0.86	3	-
GCA_905206805.1	s__CAJLIR01 sp905206805	76.9906	70	310	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__CAJLIR01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016282155.1	s__RGIG4266 sp016282155	76.6168	50	310	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__RGIG4266	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002425325.1	s__UBA5578 sp002425325	76.4305	64	310	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__UBA5578	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000432255.1	s__Faecisoma sp000432255	76.4003	57	310	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__Faecisoma	95.0	99.02	98.86	0.88	0.87	4	-
GCA_016290195.1	s__UMGS1045 sp016290195	76.3927	57	310	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__UMGS1045	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012520435.1	s__JAAYOI01 sp012520435	76.3641	53	310	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__JAAYOI01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000433875.1	s__CAG-884 sp000433875	76.3515	60	310	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__CAG-884	95.0	99.19	99.19	0.82	0.82	2	-
--------------------------------------------------------------------------------
[2023-06-13 05:13:26,820] [INFO] GTDB search result was written to GCA_022771715.1_ASM2277171v1_genomic.fna/result_gtdb.tsv
[2023-06-13 05:13:26,821] [INFO] ===== GTDB Search completed =====
[2023-06-13 05:13:26,824] [INFO] DFAST_QC result json was written to GCA_022771715.1_ASM2277171v1_genomic.fna/dqc_result.json
[2023-06-13 05:13:26,824] [INFO] DFAST_QC completed!
[2023-06-13 05:13:26,825] [INFO] Total running time: 0h0m34s