[2023-06-29 19:35:39,385] [INFO] DFAST_QC pipeline started.
[2023-06-29 19:35:39,388] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 19:35:39,388] [INFO] DQC Reference Directory: /var/lib/cwl/stga3cd605f-4a65-49f3-b8bb-5572375842d7/dqc_reference
[2023-06-29 19:35:40,825] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 19:35:40,826] [INFO] Task started: Prodigal
[2023-06-29 19:35:40,826] [INFO] Running command: gunzip -c /var/lib/cwl/stg56e7348c-7b95-4e1c-a619-c9b7eb1ecef1/GCA_021413505.1_ASM2141350v1_genomic.fna.gz | prodigal -d GCA_021413505.1_ASM2141350v1_genomic.fna/cds.fna -a GCA_021413505.1_ASM2141350v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 19:35:46,601] [INFO] Task succeeded: Prodigal
[2023-06-29 19:35:46,602] [INFO] Task started: HMMsearch
[2023-06-29 19:35:46,602] [INFO] Running command: hmmsearch --tblout GCA_021413505.1_ASM2141350v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga3cd605f-4a65-49f3-b8bb-5572375842d7/dqc_reference/reference_markers.hmm GCA_021413505.1_ASM2141350v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 19:35:46,849] [INFO] Task succeeded: HMMsearch
[2023-06-29 19:35:46,850] [INFO] Found 6/6 markers.
[2023-06-29 19:35:46,882] [INFO] Query marker FASTA was written to GCA_021413505.1_ASM2141350v1_genomic.fna/markers.fasta
[2023-06-29 19:35:46,883] [INFO] Task started: Blastn
[2023-06-29 19:35:46,883] [INFO] Running command: blastn -query GCA_021413505.1_ASM2141350v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga3cd605f-4a65-49f3-b8bb-5572375842d7/dqc_reference/reference_markers.fasta -out GCA_021413505.1_ASM2141350v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 19:35:47,520] [INFO] Task succeeded: Blastn
[2023-06-29 19:35:47,526] [INFO] Selected 20 target genomes.
[2023-06-29 19:35:47,527] [INFO] Target genome list was writen to GCA_021413505.1_ASM2141350v1_genomic.fna/target_genomes.txt
[2023-06-29 19:35:47,529] [INFO] Task started: fastANI
[2023-06-29 19:35:47,529] [INFO] Running command: fastANI --query /var/lib/cwl/stg56e7348c-7b95-4e1c-a619-c9b7eb1ecef1/GCA_021413505.1_ASM2141350v1_genomic.fna.gz --refList GCA_021413505.1_ASM2141350v1_genomic.fna/target_genomes.txt --output GCA_021413505.1_ASM2141350v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 19:36:05,186] [INFO] Task succeeded: fastANI
[2023-06-29 19:36:05,186] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga3cd605f-4a65-49f3-b8bb-5572375842d7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 19:36:05,187] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga3cd605f-4a65-49f3-b8bb-5572375842d7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 19:36:05,189] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 19:36:05,190] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-29 19:36:05,190] [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
--------------------------------------------------------------------------------
[2023-06-29 19:36:05,193] [INFO] DFAST Taxonomy check result was written to GCA_021413505.1_ASM2141350v1_genomic.fna/tc_result.tsv
[2023-06-29 19:36:05,194] [INFO] ===== Taxonomy check completed =====
[2023-06-29 19:36:05,195] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 19:36:05,196] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga3cd605f-4a65-49f3-b8bb-5572375842d7/dqc_reference/checkm_data
[2023-06-29 19:36:05,201] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 19:36:05,233] [INFO] Task started: CheckM
[2023-06-29 19:36:05,234] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_021413505.1_ASM2141350v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_021413505.1_ASM2141350v1_genomic.fna/checkm_input GCA_021413505.1_ASM2141350v1_genomic.fna/checkm_result
[2023-06-29 19:36:29,464] [INFO] Task succeeded: CheckM
[2023-06-29 19:36:29,465] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 86.38%
Contamintation: 9.26%
Strain heterogeneity: 75.00%
--------------------------------------------------------------------------------
[2023-06-29 19:36:29,492] [INFO] ===== Completeness check finished =====
[2023-06-29 19:36:29,492] [INFO] ===== Start GTDB Search =====
[2023-06-29 19:36:29,493] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_021413505.1_ASM2141350v1_genomic.fna/markers.fasta)
[2023-06-29 19:36:29,494] [INFO] Task started: Blastn
[2023-06-29 19:36:29,494] [INFO] Running command: blastn -query GCA_021413505.1_ASM2141350v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga3cd605f-4a65-49f3-b8bb-5572375842d7/dqc_reference/reference_markers_gtdb.fasta -out GCA_021413505.1_ASM2141350v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 19:36:30,500] [INFO] Task succeeded: Blastn
[2023-06-29 19:36:30,504] [INFO] Selected 12 target genomes.
[2023-06-29 19:36:30,505] [INFO] Target genome list was writen to GCA_021413505.1_ASM2141350v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 19:36:30,509] [INFO] Task started: fastANI
[2023-06-29 19:36:30,509] [INFO] Running command: fastANI --query /var/lib/cwl/stg56e7348c-7b95-4e1c-a619-c9b7eb1ecef1/GCA_021413505.1_ASM2141350v1_genomic.fna.gz --refList GCA_021413505.1_ASM2141350v1_genomic.fna/target_genomes_gtdb.txt --output GCA_021413505.1_ASM2141350v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 19:36:36,775] [INFO] Task succeeded: fastANI
[2023-06-29 19:36:36,791] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 19:36:36,791] [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_005116815.1	s__Palsa-1315 sp005116815	92.1844	173	248	d__Bacteria;p__Nitrospirota;c__Nitrospiria;o__Nitrospirales;f__Nitrospiraceae;g__Palsa-1315	95.0	96.98	96.98	0.59	0.59	2	-
GCA_009885705.1	s__Palsa-1315 sp009885705	91.2328	172	248	d__Bacteria;p__Nitrospirota;c__Nitrospiria;o__Nitrospirales;f__Nitrospiraceae;g__Palsa-1315	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003135435.1	s__Palsa-1315 sp003135435	82.2529	177	248	d__Bacteria;p__Nitrospirota;c__Nitrospiria;o__Nitrospirales;f__Nitrospiraceae;g__Palsa-1315	95.0	95.95	95.95	0.74	0.74	2	-
GCA_018971525.1	s__Palsa-1315 sp018971525	82.2243	197	248	d__Bacteria;p__Nitrospirota;c__Nitrospiria;o__Nitrospirales;f__Nitrospiraceae;g__Palsa-1315	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005239475.1	s__Palsa-1315 sp005239475	81.4691	176	248	d__Bacteria;p__Nitrospirota;c__Nitrospiria;o__Nitrospirales;f__Nitrospiraceae;g__Palsa-1315	95.0	95.15	95.15	0.75	0.75	2	-
GCA_005887945.1	s__Palsa-1315 sp005887945	81.4038	158	248	d__Bacteria;p__Nitrospirota;c__Nitrospiria;o__Nitrospirales;f__Nitrospiraceae;g__Palsa-1315	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002737345.1	s__Palsa-1315 sp002737345	80.8922	119	248	d__Bacteria;p__Nitrospirota;c__Nitrospiria;o__Nitrospirales;f__Nitrospiraceae;g__Palsa-1315	95.0	98.58	98.02	0.94	0.82	12	-
GCA_002869885.2	s__Palsa-1315 sp002869885	80.3759	151	248	d__Bacteria;p__Nitrospirota;c__Nitrospiria;o__Nitrospirales;f__Nitrospiraceae;g__Palsa-1315	95.0	98.36	98.36	0.91	0.91	2	-
GCA_005877535.1	s__Palsa-1315 sp005877535	80.0646	124	248	d__Bacteria;p__Nitrospirota;c__Nitrospiria;o__Nitrospirales;f__Nitrospiraceae;g__Palsa-1315	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002869925.2	s__Palsa-1315 sp002869925	79.6686	136	248	d__Bacteria;p__Nitrospirota;c__Nitrospiria;o__Nitrospirales;f__Nitrospiraceae;g__Palsa-1315	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005116885.1	s__Palsa-1315 sp005116885	79.3044	141	248	d__Bacteria;p__Nitrospirota;c__Nitrospiria;o__Nitrospirales;f__Nitrospiraceae;g__Palsa-1315	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005116835.1	s__Palsa-1315 sp005116835	79.1829	135	248	d__Bacteria;p__Nitrospirota;c__Nitrospiria;o__Nitrospirales;f__Nitrospiraceae;g__Palsa-1315	95.0	97.35	97.35	0.86	0.86	2	-
--------------------------------------------------------------------------------
[2023-06-29 19:36:36,793] [INFO] GTDB search result was written to GCA_021413505.1_ASM2141350v1_genomic.fna/result_gtdb.tsv
[2023-06-29 19:36:36,794] [INFO] ===== GTDB Search completed =====
[2023-06-29 19:36:36,797] [INFO] DFAST_QC result json was written to GCA_021413505.1_ASM2141350v1_genomic.fna/dqc_result.json
[2023-06-29 19:36:36,797] [INFO] DFAST_QC completed!
[2023-06-29 19:36:36,797] [INFO] Total running time: 0h0m57s