[2023-06-29 15:23:02,996] [INFO] DFAST_QC pipeline started.
[2023-06-29 15:23:02,999] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 15:23:02,999] [INFO] DQC Reference Directory: /var/lib/cwl/stgccee9a3e-3f05-4f57-ab34-67fef8048a60/dqc_reference
[2023-06-29 15:23:04,293] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 15:23:04,294] [INFO] Task started: Prodigal
[2023-06-29 15:23:04,294] [INFO] Running command: gunzip -c /var/lib/cwl/stga8a9c820-1830-4e0f-8de0-45529e1b9a87/GCA_937968725.1_SRR3992965_bin.103_CONCOCT_v1.1_MAG_genomic.fna.gz | prodigal -d GCA_937968725.1_SRR3992965_bin.103_CONCOCT_v1.1_MAG_genomic.fna/cds.fna -a GCA_937968725.1_SRR3992965_bin.103_CONCOCT_v1.1_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 15:23:10,527] [INFO] Task succeeded: Prodigal
[2023-06-29 15:23:10,527] [INFO] Task started: HMMsearch
[2023-06-29 15:23:10,527] [INFO] Running command: hmmsearch --tblout GCA_937968725.1_SRR3992965_bin.103_CONCOCT_v1.1_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgccee9a3e-3f05-4f57-ab34-67fef8048a60/dqc_reference/reference_markers.hmm GCA_937968725.1_SRR3992965_bin.103_CONCOCT_v1.1_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-29 15:23:10,789] [INFO] Task succeeded: HMMsearch
[2023-06-29 15:23:10,791] [INFO] Found 6/6 markers.
[2023-06-29 15:23:10,816] [INFO] Query marker FASTA was written to GCA_937968725.1_SRR3992965_bin.103_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta
[2023-06-29 15:23:10,816] [INFO] Task started: Blastn
[2023-06-29 15:23:10,817] [INFO] Running command: blastn -query GCA_937968725.1_SRR3992965_bin.103_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgccee9a3e-3f05-4f57-ab34-67fef8048a60/dqc_reference/reference_markers.fasta -out GCA_937968725.1_SRR3992965_bin.103_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 15:23:11,456] [INFO] Task succeeded: Blastn
[2023-06-29 15:23:11,461] [INFO] Selected 32 target genomes.
[2023-06-29 15:23:11,461] [INFO] Target genome list was writen to GCA_937968725.1_SRR3992965_bin.103_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt
[2023-06-29 15:23:11,467] [INFO] Task started: fastANI
[2023-06-29 15:23:11,467] [INFO] Running command: fastANI --query /var/lib/cwl/stga8a9c820-1830-4e0f-8de0-45529e1b9a87/GCA_937968725.1_SRR3992965_bin.103_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_937968725.1_SRR3992965_bin.103_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt --output GCA_937968725.1_SRR3992965_bin.103_CONCOCT_v1.1_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 15:23:27,714] [INFO] Task succeeded: fastANI
[2023-06-29 15:23:27,714] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgccee9a3e-3f05-4f57-ab34-67fef8048a60/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 15:23:27,715] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgccee9a3e-3f05-4f57-ab34-67fef8048a60/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 15:23:27,716] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 15:23:27,717] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-29 15:23:27,717] [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 15:23:27,719] [INFO] DFAST Taxonomy check result was written to GCA_937968725.1_SRR3992965_bin.103_CONCOCT_v1.1_MAG_genomic.fna/tc_result.tsv
[2023-06-29 15:23:27,720] [INFO] ===== Taxonomy check completed =====
[2023-06-29 15:23:27,720] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 15:23:27,721] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgccee9a3e-3f05-4f57-ab34-67fef8048a60/dqc_reference/checkm_data
[2023-06-29 15:23:27,726] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 15:23:27,754] [INFO] Task started: CheckM
[2023-06-29 15:23:27,754] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_937968725.1_SRR3992965_bin.103_CONCOCT_v1.1_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_937968725.1_SRR3992965_bin.103_CONCOCT_v1.1_MAG_genomic.fna/checkm_input GCA_937968725.1_SRR3992965_bin.103_CONCOCT_v1.1_MAG_genomic.fna/checkm_result
[2023-06-29 15:23:52,910] [INFO] Task succeeded: CheckM
[2023-06-29 15:23:52,911] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 15:23:52,933] [INFO] ===== Completeness check finished =====
[2023-06-29 15:23:52,933] [INFO] ===== Start GTDB Search =====
[2023-06-29 15:23:52,934] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_937968725.1_SRR3992965_bin.103_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta)
[2023-06-29 15:23:52,934] [INFO] Task started: Blastn
[2023-06-29 15:23:52,934] [INFO] Running command: blastn -query GCA_937968725.1_SRR3992965_bin.103_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgccee9a3e-3f05-4f57-ab34-67fef8048a60/dqc_reference/reference_markers_gtdb.fasta -out GCA_937968725.1_SRR3992965_bin.103_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 15:23:54,000] [INFO] Task succeeded: Blastn
[2023-06-29 15:23:54,004] [INFO] Selected 17 target genomes.
[2023-06-29 15:23:54,004] [INFO] Target genome list was writen to GCA_937968725.1_SRR3992965_bin.103_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 15:23:54,013] [INFO] Task started: fastANI
[2023-06-29 15:23:54,013] [INFO] Running command: fastANI --query /var/lib/cwl/stga8a9c820-1830-4e0f-8de0-45529e1b9a87/GCA_937968725.1_SRR3992965_bin.103_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_937968725.1_SRR3992965_bin.103_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_937968725.1_SRR3992965_bin.103_CONCOCT_v1.1_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 15:23:59,721] [INFO] Task succeeded: fastANI
[2023-06-29 15:23:59,737] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 15:23:59,738] [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_900545185.1	s__UMGS755 sp900545185	100.0	649	725	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__UBA1381;f__UBA9506;g__UMGS755	95.0	99.96	99.96	0.89	0.89	2	conclusive
GCA_015068855.1	s__UMGS755 sp015068855	77.8951	81	725	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__UBA1381;f__UBA9506;g__UMGS755	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017507525.1	s__UMGS755 sp017507525	77.8273	89	725	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__UBA1381;f__UBA9506;g__UMGS755	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017416855.1	s__UMGS755 sp017416855	77.8024	98	725	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__UBA1381;f__UBA9506;g__UMGS755	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017549205.1	s__UMGS755 sp017549205	77.6962	118	725	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__UBA1381;f__UBA9506;g__UMGS755	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015069045.1	s__UMGS755 sp015069045	77.5999	78	725	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__UBA1381;f__UBA9506;g__UMGS755	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015068865.1	s__UMGS755 sp015068865	77.3389	75	725	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__UBA1381;f__UBA9506;g__UMGS755	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015068555.1	s__UMGS755 sp015068555	77.2818	72	725	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__UBA1381;f__UBA9506;g__UMGS755	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015068905.1	s__UMGS755 sp015068905	77.2225	96	725	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__UBA1381;f__UBA9506;g__UMGS755	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017407515.1	s__UMGS755 sp017407515	76.9512	71	725	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__UBA1381;f__UBA9506;g__UMGS755	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 15:23:59,740] [INFO] GTDB search result was written to GCA_937968725.1_SRR3992965_bin.103_CONCOCT_v1.1_MAG_genomic.fna/result_gtdb.tsv
[2023-06-29 15:23:59,740] [INFO] ===== GTDB Search completed =====
[2023-06-29 15:23:59,743] [INFO] DFAST_QC result json was written to GCA_937968725.1_SRR3992965_bin.103_CONCOCT_v1.1_MAG_genomic.fna/dqc_result.json
[2023-06-29 15:23:59,743] [INFO] DFAST_QC completed!
[2023-06-29 15:23:59,743] [INFO] Total running time: 0h0m57s