[2023-06-05 00:53:24,465] [INFO] DFAST_QC pipeline started.
[2023-06-05 00:53:24,468] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 00:53:24,468] [INFO] DQC Reference Directory: /var/lib/cwl/stgad1c5aa7-83ac-4466-a149-d7cd1cbf50ee/dqc_reference
[2023-06-05 00:53:26,968] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 00:53:26,969] [INFO] Task started: Prodigal
[2023-06-05 00:53:26,969] [INFO] Running command: gunzip -c /var/lib/cwl/stg82c9c173-e11f-4447-a2bf-858bc53e9954/GCA_934178195.1_ERR7738562_bin.101_genomic.fna.gz | prodigal -d GCA_934178195.1_ERR7738562_bin.101_genomic.fna/cds.fna -a GCA_934178195.1_ERR7738562_bin.101_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 00:53:29,712] [INFO] Task succeeded: Prodigal
[2023-06-05 00:53:29,713] [INFO] Task started: HMMsearch
[2023-06-05 00:53:29,713] [INFO] Running command: hmmsearch --tblout GCA_934178195.1_ERR7738562_bin.101_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgad1c5aa7-83ac-4466-a149-d7cd1cbf50ee/dqc_reference/reference_markers.hmm GCA_934178195.1_ERR7738562_bin.101_genomic.fna/protein.faa > /dev/null
[2023-06-05 00:53:29,924] [INFO] Task succeeded: HMMsearch
[2023-06-05 00:53:29,925] [INFO] Found 6/6 markers.
[2023-06-05 00:53:29,945] [INFO] Query marker FASTA was written to GCA_934178195.1_ERR7738562_bin.101_genomic.fna/markers.fasta
[2023-06-05 00:53:29,945] [INFO] Task started: Blastn
[2023-06-05 00:53:29,945] [INFO] Running command: blastn -query GCA_934178195.1_ERR7738562_bin.101_genomic.fna/markers.fasta -db /var/lib/cwl/stgad1c5aa7-83ac-4466-a149-d7cd1cbf50ee/dqc_reference/reference_markers.fasta -out GCA_934178195.1_ERR7738562_bin.101_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 00:53:31,671] [INFO] Task succeeded: Blastn
[2023-06-05 00:53:31,676] [INFO] Selected 15 target genomes.
[2023-06-05 00:53:31,676] [INFO] Target genome list was writen to GCA_934178195.1_ERR7738562_bin.101_genomic.fna/target_genomes.txt
[2023-06-05 00:53:31,680] [INFO] Task started: fastANI
[2023-06-05 00:53:31,681] [INFO] Running command: fastANI --query /var/lib/cwl/stg82c9c173-e11f-4447-a2bf-858bc53e9954/GCA_934178195.1_ERR7738562_bin.101_genomic.fna.gz --refList GCA_934178195.1_ERR7738562_bin.101_genomic.fna/target_genomes.txt --output GCA_934178195.1_ERR7738562_bin.101_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 00:53:38,415] [INFO] Task succeeded: fastANI
[2023-06-05 00:53:38,416] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgad1c5aa7-83ac-4466-a149-d7cd1cbf50ee/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 00:53:38,416] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgad1c5aa7-83ac-4466-a149-d7cd1cbf50ee/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 00:53:38,418] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 00:53:38,418] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-05 00:53:38,418] [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
--------------------------------------------------------------------------------
[2023-06-05 00:53:38,421] [INFO] DFAST Taxonomy check result was written to GCA_934178195.1_ERR7738562_bin.101_genomic.fna/tc_result.tsv
[2023-06-05 00:53:38,421] [INFO] ===== Taxonomy check completed =====
[2023-06-05 00:53:38,422] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 00:53:38,422] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgad1c5aa7-83ac-4466-a149-d7cd1cbf50ee/dqc_reference/checkm_data
[2023-06-05 00:53:38,426] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 00:53:38,444] [INFO] Task started: CheckM
[2023-06-05 00:53:38,444] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_934178195.1_ERR7738562_bin.101_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_934178195.1_ERR7738562_bin.101_genomic.fna/checkm_input GCA_934178195.1_ERR7738562_bin.101_genomic.fna/checkm_result
[2023-06-05 00:53:54,416] [INFO] Task succeeded: CheckM
[2023-06-05 00:53:54,418] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 00:53:54,439] [INFO] ===== Completeness check finished =====
[2023-06-05 00:53:54,439] [INFO] ===== Start GTDB Search =====
[2023-06-05 00:53:54,439] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_934178195.1_ERR7738562_bin.101_genomic.fna/markers.fasta)
[2023-06-05 00:53:54,440] [INFO] Task started: Blastn
[2023-06-05 00:53:54,440] [INFO] Running command: blastn -query GCA_934178195.1_ERR7738562_bin.101_genomic.fna/markers.fasta -db /var/lib/cwl/stgad1c5aa7-83ac-4466-a149-d7cd1cbf50ee/dqc_reference/reference_markers_gtdb.fasta -out GCA_934178195.1_ERR7738562_bin.101_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 00:53:55,232] [INFO] Task succeeded: Blastn
[2023-06-05 00:53:55,237] [INFO] Selected 10 target genomes.
[2023-06-05 00:53:55,238] [INFO] Target genome list was writen to GCA_934178195.1_ERR7738562_bin.101_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 00:53:55,244] [INFO] Task started: fastANI
[2023-06-05 00:53:55,245] [INFO] Running command: fastANI --query /var/lib/cwl/stg82c9c173-e11f-4447-a2bf-858bc53e9954/GCA_934178195.1_ERR7738562_bin.101_genomic.fna.gz --refList GCA_934178195.1_ERR7738562_bin.101_genomic.fna/target_genomes_gtdb.txt --output GCA_934178195.1_ERR7738562_bin.101_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 00:53:58,114] [INFO] Task succeeded: fastANI
[2023-06-05 00:53:58,133] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 00:53:58,133] [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_000435175.1	s__CAG-245 sp000435175	98.7377	409	481	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-245	95.0	96.85	96.24	0.85	0.78	7	conclusive
GCA_900761475.1	s__CAG-245 sp900761475	93.6207	272	481	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-245	95.0	98.04	98.04	0.75	0.75	2	-
GCA_900552135.1	s__CAG-245 sp900552135	83.1058	246	481	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-245	95.0	98.23	98.19	0.87	0.85	3	-
GCA_900758165.1	s__CAG-245 sp900758165	79.474	157	481	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-245	95.0	98.95	98.95	0.76	0.76	2	-
GCA_900553755.1	s__UMGS1901 sp900553755	79.2391	143	481	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__UMGS1901	95.0	98.71	98.71	0.86	0.86	2	-
GCA_000434195.1	s__CAG-245 sp000434195	79.0489	167	481	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-245	95.0	97.93	97.77	0.87	0.84	3	-
GCA_003507395.1	s__CAG-273 sp003507395	78.0935	79	481	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-273	95.0	99.04	98.89	0.89	0.87	5	-
GCA_900557195.1	s__CAG-492 sp900557195	77.4391	103	481	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-492	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000434015.1	s__CAG-492 sp000434015	77.1165	116	481	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-492	95.0	99.68	99.35	0.94	0.91	3	-
GCA_017470645.1	s__CAG-492 sp017470645	76.9759	66	481	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-492	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-05 00:53:58,136] [INFO] GTDB search result was written to GCA_934178195.1_ERR7738562_bin.101_genomic.fna/result_gtdb.tsv
[2023-06-05 00:53:58,137] [INFO] ===== GTDB Search completed =====
[2023-06-05 00:53:58,140] [INFO] DFAST_QC result json was written to GCA_934178195.1_ERR7738562_bin.101_genomic.fna/dqc_result.json
[2023-06-05 00:53:58,141] [INFO] DFAST_QC completed!
[2023-06-05 00:53:58,141] [INFO] Total running time: 0h0m34s