[2023-06-12 23:45:45,238] [INFO] DFAST_QC pipeline started.
[2023-06-12 23:45:45,246] [INFO] DFAST_QC version: 0.5.7
[2023-06-12 23:45:45,247] [INFO] DQC Reference Directory: /var/lib/cwl/stgb0502930-083f-479f-b908-8dd64690d034/dqc_reference
[2023-06-12 23:45:47,568] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-12 23:45:47,569] [INFO] Task started: Prodigal
[2023-06-12 23:45:47,570] [INFO] Running command: gunzip -c /var/lib/cwl/stg9965f06a-43f7-47e8-ac4f-422894ab043b/GCA_947073375.1_SRR12464011_bin.16_metawrap_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_947073375.1_SRR12464011_bin.16_metawrap_v1.3_MAG_genomic.fna/cds.fna -a GCA_947073375.1_SRR12464011_bin.16_metawrap_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-12 23:45:54,228] [INFO] Task succeeded: Prodigal
[2023-06-12 23:45:54,229] [INFO] Task started: HMMsearch
[2023-06-12 23:45:54,229] [INFO] Running command: hmmsearch --tblout GCA_947073375.1_SRR12464011_bin.16_metawrap_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb0502930-083f-479f-b908-8dd64690d034/dqc_reference/reference_markers.hmm GCA_947073375.1_SRR12464011_bin.16_metawrap_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-12 23:45:54,491] [INFO] Task succeeded: HMMsearch
[2023-06-12 23:45:54,493] [INFO] Found 6/6 markers.
[2023-06-12 23:45:54,525] [INFO] Query marker FASTA was written to GCA_947073375.1_SRR12464011_bin.16_metawrap_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-12 23:45:54,525] [INFO] Task started: Blastn
[2023-06-12 23:45:54,525] [INFO] Running command: blastn -query GCA_947073375.1_SRR12464011_bin.16_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgb0502930-083f-479f-b908-8dd64690d034/dqc_reference/reference_markers.fasta -out GCA_947073375.1_SRR12464011_bin.16_metawrap_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-12 23:45:55,181] [INFO] Task succeeded: Blastn
[2023-06-12 23:45:55,187] [INFO] Selected 37 target genomes.
[2023-06-12 23:45:55,188] [INFO] Target genome list was writen to GCA_947073375.1_SRR12464011_bin.16_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-12 23:45:55,192] [INFO] Task started: fastANI
[2023-06-12 23:45:55,193] [INFO] Running command: fastANI --query /var/lib/cwl/stg9965f06a-43f7-47e8-ac4f-422894ab043b/GCA_947073375.1_SRR12464011_bin.16_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_947073375.1_SRR12464011_bin.16_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_947073375.1_SRR12464011_bin.16_metawrap_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-12 23:46:18,146] [INFO] Task succeeded: fastANI
[2023-06-12 23:46:18,147] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb0502930-083f-479f-b908-8dd64690d034/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-12 23:46:18,148] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb0502930-083f-479f-b908-8dd64690d034/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-12 23:46:18,150] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-12 23:46:18,150] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-12 23:46:18,150] [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
--------------------------------------------------------------------------------
[2023-06-12 23:46:18,152] [INFO] DFAST Taxonomy check result was written to GCA_947073375.1_SRR12464011_bin.16_metawrap_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-12 23:46:18,153] [INFO] ===== Taxonomy check completed =====
[2023-06-12 23:46:18,153] [INFO] ===== Start completeness check using CheckM =====
[2023-06-12 23:46:18,154] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb0502930-083f-479f-b908-8dd64690d034/dqc_reference/checkm_data
[2023-06-12 23:46:18,157] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-12 23:46:18,193] [INFO] Task started: CheckM
[2023-06-12 23:46:18,194] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_947073375.1_SRR12464011_bin.16_metawrap_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_947073375.1_SRR12464011_bin.16_metawrap_v1.3_MAG_genomic.fna/checkm_input GCA_947073375.1_SRR12464011_bin.16_metawrap_v1.3_MAG_genomic.fna/checkm_result
[2023-06-12 23:46:44,558] [INFO] Task succeeded: CheckM
[2023-06-12 23:46:44,559] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 81.63%
Contamintation: 0.46%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-12 23:46:44,590] [INFO] ===== Completeness check finished =====
[2023-06-12 23:46:44,590] [INFO] ===== Start GTDB Search =====
[2023-06-12 23:46:44,590] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_947073375.1_SRR12464011_bin.16_metawrap_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-12 23:46:44,591] [INFO] Task started: Blastn
[2023-06-12 23:46:44,591] [INFO] Running command: blastn -query GCA_947073375.1_SRR12464011_bin.16_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgb0502930-083f-479f-b908-8dd64690d034/dqc_reference/reference_markers_gtdb.fasta -out GCA_947073375.1_SRR12464011_bin.16_metawrap_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-12 23:46:45,673] [INFO] Task succeeded: Blastn
[2023-06-12 23:46:45,678] [INFO] Selected 14 target genomes.
[2023-06-12 23:46:45,679] [INFO] Target genome list was writen to GCA_947073375.1_SRR12464011_bin.16_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-12 23:46:45,692] [INFO] Task started: fastANI
[2023-06-12 23:46:45,692] [INFO] Running command: fastANI --query /var/lib/cwl/stg9965f06a-43f7-47e8-ac4f-422894ab043b/GCA_947073375.1_SRR12464011_bin.16_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_947073375.1_SRR12464011_bin.16_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_947073375.1_SRR12464011_bin.16_metawrap_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-12 23:46:54,101] [INFO] Task succeeded: fastANI
[2023-06-12 23:46:54,115] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-12 23:46:54,115] [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_009774245.1	s__COE1 sp009774245	99.2276	697	725	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__COE1	95.0	99.95	99.95	0.99	0.99	2	conclusive
GCA_009774375.1	s__COE1 sp009774375	82.1857	438	725	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__COE1	95.0	99.47	99.47	0.88	0.88	2	-
GCA_910585765.1	s__COE1 sp910585765	81.8308	408	725	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__COE1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002491195.1	s__COE1 sp002491195	81.317	426	725	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__COE1	95.0	99.88	99.88	0.86	0.86	2	-
GCA_910588755.1	s__COE1 sp910588755	81.2263	401	725	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__COE1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910588595.1	s__COE1 sp910588595	81.22	393	725	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__COE1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009774345.1	s__COE1 sp009774345	79.2777	304	725	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__COE1	95.0	99.29	99.29	0.85	0.85	2	-
GCA_000403215.2	s__COE1 sp000403215	79.2239	318	725	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__COE1	95.0	98.27	98.03	0.92	0.91	3	-
GCA_017622845.1	s__COE1 sp017622845	77.4878	155	725	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__COE1	95.0	98.75	98.75	0.86	0.86	2	-
--------------------------------------------------------------------------------
[2023-06-12 23:46:54,117] [INFO] GTDB search result was written to GCA_947073375.1_SRR12464011_bin.16_metawrap_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-12 23:46:54,117] [INFO] ===== GTDB Search completed =====
[2023-06-12 23:46:54,120] [INFO] DFAST_QC result json was written to GCA_947073375.1_SRR12464011_bin.16_metawrap_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-12 23:46:54,121] [INFO] DFAST_QC completed!
[2023-06-12 23:46:54,121] [INFO] Total running time: 0h1m9s