[2023-06-19 13:42:21,751] [INFO] DFAST_QC pipeline started.
[2023-06-19 13:42:21,753] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 13:42:21,753] [INFO] DQC Reference Directory: /var/lib/cwl/stgbe719378-a26c-4cff-ad86-13cc64469f58/dqc_reference
[2023-06-19 13:42:24,081] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 13:42:24,082] [INFO] Task started: Prodigal
[2023-06-19 13:42:24,082] [INFO] Running command: gunzip -c /var/lib/cwl/stg2fb67c9f-d59c-4388-83dd-c7497ad09abf/GCA_937996775.1_SRR7658653_bin.35_CONCOCT_v1.1_MAG_genomic.fna.gz | prodigal -d GCA_937996775.1_SRR7658653_bin.35_CONCOCT_v1.1_MAG_genomic.fna/cds.fna -a GCA_937996775.1_SRR7658653_bin.35_CONCOCT_v1.1_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 13:42:33,032] [INFO] Task succeeded: Prodigal
[2023-06-19 13:42:33,033] [INFO] Task started: HMMsearch
[2023-06-19 13:42:33,033] [INFO] Running command: hmmsearch --tblout GCA_937996775.1_SRR7658653_bin.35_CONCOCT_v1.1_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbe719378-a26c-4cff-ad86-13cc64469f58/dqc_reference/reference_markers.hmm GCA_937996775.1_SRR7658653_bin.35_CONCOCT_v1.1_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-19 13:42:33,292] [INFO] Task succeeded: HMMsearch
[2023-06-19 13:42:33,294] [INFO] Found 6/6 markers.
[2023-06-19 13:42:33,324] [INFO] Query marker FASTA was written to GCA_937996775.1_SRR7658653_bin.35_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta
[2023-06-19 13:42:33,325] [INFO] Task started: Blastn
[2023-06-19 13:42:33,325] [INFO] Running command: blastn -query GCA_937996775.1_SRR7658653_bin.35_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgbe719378-a26c-4cff-ad86-13cc64469f58/dqc_reference/reference_markers.fasta -out GCA_937996775.1_SRR7658653_bin.35_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 13:42:34,001] [INFO] Task succeeded: Blastn
[2023-06-19 13:42:34,007] [INFO] Selected 23 target genomes.
[2023-06-19 13:42:34,008] [INFO] Target genome list was writen to GCA_937996775.1_SRR7658653_bin.35_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt
[2023-06-19 13:42:34,014] [INFO] Task started: fastANI
[2023-06-19 13:42:34,015] [INFO] Running command: fastANI --query /var/lib/cwl/stg2fb67c9f-d59c-4388-83dd-c7497ad09abf/GCA_937996775.1_SRR7658653_bin.35_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_937996775.1_SRR7658653_bin.35_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt --output GCA_937996775.1_SRR7658653_bin.35_CONCOCT_v1.1_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 13:42:49,939] [INFO] Task succeeded: fastANI
[2023-06-19 13:42:49,940] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbe719378-a26c-4cff-ad86-13cc64469f58/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 13:42:49,940] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbe719378-a26c-4cff-ad86-13cc64469f58/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 13:42:49,942] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 13:42:49,943] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-19 13:42:49,943] [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
--------------------------------------------------------------------------------
[2023-06-19 13:42:49,945] [INFO] DFAST Taxonomy check result was written to GCA_937996775.1_SRR7658653_bin.35_CONCOCT_v1.1_MAG_genomic.fna/tc_result.tsv
[2023-06-19 13:42:49,946] [INFO] ===== Taxonomy check completed =====
[2023-06-19 13:42:49,946] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 13:42:49,947] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbe719378-a26c-4cff-ad86-13cc64469f58/dqc_reference/checkm_data
[2023-06-19 13:42:49,951] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 13:42:49,988] [INFO] Task started: CheckM
[2023-06-19 13:42:49,989] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_937996775.1_SRR7658653_bin.35_CONCOCT_v1.1_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_937996775.1_SRR7658653_bin.35_CONCOCT_v1.1_MAG_genomic.fna/checkm_input GCA_937996775.1_SRR7658653_bin.35_CONCOCT_v1.1_MAG_genomic.fna/checkm_result
[2023-06-19 13:43:20,764] [INFO] Task succeeded: CheckM
[2023-06-19 13:43:20,765] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 94.44%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 13:43:20,786] [INFO] ===== Completeness check finished =====
[2023-06-19 13:43:20,786] [INFO] ===== Start GTDB Search =====
[2023-06-19 13:43:20,787] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_937996775.1_SRR7658653_bin.35_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta)
[2023-06-19 13:43:20,787] [INFO] Task started: Blastn
[2023-06-19 13:43:20,787] [INFO] Running command: blastn -query GCA_937996775.1_SRR7658653_bin.35_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgbe719378-a26c-4cff-ad86-13cc64469f58/dqc_reference/reference_markers_gtdb.fasta -out GCA_937996775.1_SRR7658653_bin.35_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 13:43:21,890] [INFO] Task succeeded: Blastn
[2023-06-19 13:43:21,894] [INFO] Selected 18 target genomes.
[2023-06-19 13:43:21,895] [INFO] Target genome list was writen to GCA_937996775.1_SRR7658653_bin.35_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 13:43:21,906] [INFO] Task started: fastANI
[2023-06-19 13:43:21,906] [INFO] Running command: fastANI --query /var/lib/cwl/stg2fb67c9f-d59c-4388-83dd-c7497ad09abf/GCA_937996775.1_SRR7658653_bin.35_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_937996775.1_SRR7658653_bin.35_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_937996775.1_SRR7658653_bin.35_CONCOCT_v1.1_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 13:43:31,659] [INFO] Task succeeded: fastANI
[2023-06-19 13:43:31,671] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 13:43:31,671] [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_900763885.1	s__UMGS1696 sp900763885	97.2427	716	980	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-272;g__UMGS1696	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_900554225.1	s__UMGS1696 sp900554225	88.966	588	980	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-272;g__UMGS1696	95.0	98.27	98.27	0.86	0.86	2	-
GCA_017540175.1	s__UMGS1696 sp902773525	77.3337	158	980	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-272;g__UMGS1696	95.0	98.81	98.75	0.96	0.96	3	-
GCA_015065385.1	s__UMGS1696 sp015065385	77.2278	146	980	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-272;g__UMGS1696	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902761695.1	s__UMGS1696 sp902761695	77.0708	109	980	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-272;g__UMGS1696	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017412675.1	s__UMGS1696 sp017412675	76.9267	144	980	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-272;g__UMGS1696	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015063745.1	s__UMGS1696 sp015063745	76.887	108	980	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-272;g__UMGS1696	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902783705.1	s__UMGS1696 sp902783705	76.855	105	980	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-272;g__UMGS1696	95.0	97.08	97.08	0.83	0.83	2	-
GCA_902782445.1	s__UMGS1696 sp902782445	76.8549	152	980	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-272;g__UMGS1696	95.0	97.30	97.10	0.87	0.82	3	-
GCA_017415325.1	s__UMGS1696 sp017415325	76.8162	115	980	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-272;g__UMGS1696	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017550315.1	s__UMGS1696 sp017550315	76.8052	151	980	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-272;g__UMGS1696	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015065295.1	s__UMGS1696 sp015065295	76.8039	114	980	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-272;g__UMGS1696	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017398585.1	s__UMGS1696 sp017398585	76.75	124	980	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-272;g__UMGS1696	95.0	99.10	99.10	0.90	0.90	2	-
GCA_017560565.1	s__UMGS1696 sp017560565	76.5918	93	980	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-272;g__UMGS1696	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017540285.1	s__UMGS1696 sp017540285	76.5639	115	980	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-272;g__UMGS1696	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-19 13:43:31,673] [INFO] GTDB search result was written to GCA_937996775.1_SRR7658653_bin.35_CONCOCT_v1.1_MAG_genomic.fna/result_gtdb.tsv
[2023-06-19 13:43:31,674] [INFO] ===== GTDB Search completed =====
[2023-06-19 13:43:31,677] [INFO] DFAST_QC result json was written to GCA_937996775.1_SRR7658653_bin.35_CONCOCT_v1.1_MAG_genomic.fna/dqc_result.json
[2023-06-19 13:43:31,677] [INFO] DFAST_QC completed!
[2023-06-19 13:43:31,677] [INFO] Total running time: 0h1m10s