[2023-06-08 16:48:02,923] [INFO] DFAST_QC pipeline started.
[2023-06-08 16:48:02,925] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 16:48:02,925] [INFO] DQC Reference Directory: /var/lib/cwl/stg1c762055-98eb-4d8c-bbc2-18bfeaa13479/dqc_reference
[2023-06-08 16:48:04,384] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 16:48:04,385] [INFO] Task started: Prodigal
[2023-06-08 16:48:04,385] [INFO] Running command: gunzip -c /var/lib/cwl/stg55a6e16b-b91b-4407-9b75-9de393d73642/GCA_945948475.1_SRR11489769_bin.52_metaWRAP_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_945948475.1_SRR11489769_bin.52_metaWRAP_v1.3_MAG_genomic.fna/cds.fna -a GCA_945948475.1_SRR11489769_bin.52_metaWRAP_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 16:48:06,074] [INFO] Task succeeded: Prodigal
[2023-06-08 16:48:06,075] [INFO] Task started: HMMsearch
[2023-06-08 16:48:06,075] [INFO] Running command: hmmsearch --tblout GCA_945948475.1_SRR11489769_bin.52_metaWRAP_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1c762055-98eb-4d8c-bbc2-18bfeaa13479/dqc_reference/reference_markers.hmm GCA_945948475.1_SRR11489769_bin.52_metaWRAP_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-08 16:48:06,347] [INFO] Task succeeded: HMMsearch
[2023-06-08 16:48:06,349] [INFO] Found 6/6 markers.
[2023-06-08 16:48:06,367] [INFO] Query marker FASTA was written to GCA_945948475.1_SRR11489769_bin.52_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-08 16:48:06,368] [INFO] Task started: Blastn
[2023-06-08 16:48:06,368] [INFO] Running command: blastn -query GCA_945948475.1_SRR11489769_bin.52_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg1c762055-98eb-4d8c-bbc2-18bfeaa13479/dqc_reference/reference_markers.fasta -out GCA_945948475.1_SRR11489769_bin.52_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 16:48:06,997] [INFO] Task succeeded: Blastn
[2023-06-08 16:48:07,000] [INFO] Selected 29 target genomes.
[2023-06-08 16:48:07,001] [INFO] Target genome list was writen to GCA_945948475.1_SRR11489769_bin.52_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-08 16:48:07,002] [INFO] Task started: fastANI
[2023-06-08 16:48:07,002] [INFO] Running command: fastANI --query /var/lib/cwl/stg55a6e16b-b91b-4407-9b75-9de393d73642/GCA_945948475.1_SRR11489769_bin.52_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945948475.1_SRR11489769_bin.52_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_945948475.1_SRR11489769_bin.52_metaWRAP_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 16:48:19,790] [INFO] Task succeeded: fastANI
[2023-06-08 16:48:19,790] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1c762055-98eb-4d8c-bbc2-18bfeaa13479/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 16:48:19,791] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1c762055-98eb-4d8c-bbc2-18bfeaa13479/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 16:48:19,793] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 16:48:19,793] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-08 16:48:19,793] [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
--------------------------------------------------------------------------------
[2023-06-08 16:48:19,795] [INFO] DFAST Taxonomy check result was written to GCA_945948475.1_SRR11489769_bin.52_metaWRAP_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-08 16:48:19,796] [INFO] ===== Taxonomy check completed =====
[2023-06-08 16:48:19,796] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 16:48:19,796] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1c762055-98eb-4d8c-bbc2-18bfeaa13479/dqc_reference/checkm_data
[2023-06-08 16:48:19,799] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 16:48:19,817] [INFO] Task started: CheckM
[2023-06-08 16:48:19,817] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_945948475.1_SRR11489769_bin.52_metaWRAP_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_945948475.1_SRR11489769_bin.52_metaWRAP_v1.3_MAG_genomic.fna/checkm_input GCA_945948475.1_SRR11489769_bin.52_metaWRAP_v1.3_MAG_genomic.fna/checkm_result
[2023-06-08 16:48:34,247] [INFO] Task succeeded: CheckM
[2023-06-08 16:48:34,248] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.07%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 16:48:34,270] [INFO] ===== Completeness check finished =====
[2023-06-08 16:48:34,270] [INFO] ===== Start GTDB Search =====
[2023-06-08 16:48:34,271] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_945948475.1_SRR11489769_bin.52_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-08 16:48:34,271] [INFO] Task started: Blastn
[2023-06-08 16:48:34,271] [INFO] Running command: blastn -query GCA_945948475.1_SRR11489769_bin.52_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg1c762055-98eb-4d8c-bbc2-18bfeaa13479/dqc_reference/reference_markers_gtdb.fasta -out GCA_945948475.1_SRR11489769_bin.52_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 16:48:35,181] [INFO] Task succeeded: Blastn
[2023-06-08 16:48:35,185] [INFO] Selected 26 target genomes.
[2023-06-08 16:48:35,186] [INFO] Target genome list was writen to GCA_945948475.1_SRR11489769_bin.52_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 16:48:35,194] [INFO] Task started: fastANI
[2023-06-08 16:48:35,195] [INFO] Running command: fastANI --query /var/lib/cwl/stg55a6e16b-b91b-4407-9b75-9de393d73642/GCA_945948475.1_SRR11489769_bin.52_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945948475.1_SRR11489769_bin.52_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_945948475.1_SRR11489769_bin.52_metaWRAP_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 16:48:41,839] [INFO] Task succeeded: fastANI
[2023-06-08 16:48:41,853] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-08 16:48:41,853] [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	79.6327	140	287	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	-
GCA_900761475.1	s__CAG-245 sp900761475	79.2366	111	287	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_900758165.1	s__CAG-245 sp900758165	79.1835	126	287	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_900552135.1	s__CAG-245 sp900552135	78.7801	111	287	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_000434195.1	s__CAG-245 sp000434195	78.7066	117	287	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_900553755.1	s__UMGS1901 sp900553755	77.8624	91	287	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_900556135.1	s__UMGS1901 sp900556135	77.5903	86	287	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__UMGS1901	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017937285.1	s__CAG-492 sp017937285	77.097	61	287	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_905215935.1	s__CAG-492 sp905215935	76.9841	71	287	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	76.8272	67	287	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_001915995.1	s__CAG-269 sp001915995	76.8139	59	287	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-269	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902406115.1	s__CAG-273 sp902406115	76.8094	55	287	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-273	95.0	97.55	97.49	0.92	0.91	3	-
GCA_900557195.1	s__CAG-492 sp900557195	76.7527	64	287	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	-
--------------------------------------------------------------------------------
[2023-06-08 16:48:41,855] [INFO] GTDB search result was written to GCA_945948475.1_SRR11489769_bin.52_metaWRAP_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-08 16:48:41,856] [INFO] ===== GTDB Search completed =====
[2023-06-08 16:48:41,859] [INFO] DFAST_QC result json was written to GCA_945948475.1_SRR11489769_bin.52_metaWRAP_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-08 16:48:41,859] [INFO] DFAST_QC completed!
[2023-06-08 16:48:41,859] [INFO] Total running time: 0h0m39s