[2023-06-13 20:44:21,407] [INFO] DFAST_QC pipeline started.
[2023-06-13 20:44:21,410] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 20:44:21,410] [INFO] DQC Reference Directory: /var/lib/cwl/stg8f73f4df-7168-4ff2-bba8-5d4dc00ba059/dqc_reference
[2023-06-13 20:44:22,590] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 20:44:22,591] [INFO] Task started: Prodigal
[2023-06-13 20:44:22,591] [INFO] Running command: gunzip -c /var/lib/cwl/stgfb176a5e-ecb6-465e-ba8a-b3b7545f1dd4/GCA_947365035.1_SRR14836540_bin.7_metawrap_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_947365035.1_SRR14836540_bin.7_metawrap_v1.3_MAG_genomic.fna/cds.fna -a GCA_947365035.1_SRR14836540_bin.7_metawrap_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 20:44:25,171] [INFO] Task succeeded: Prodigal
[2023-06-13 20:44:25,171] [INFO] Task started: HMMsearch
[2023-06-13 20:44:25,171] [INFO] Running command: hmmsearch --tblout GCA_947365035.1_SRR14836540_bin.7_metawrap_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8f73f4df-7168-4ff2-bba8-5d4dc00ba059/dqc_reference/reference_markers.hmm GCA_947365035.1_SRR14836540_bin.7_metawrap_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-13 20:44:25,340] [INFO] Task succeeded: HMMsearch
[2023-06-13 20:44:25,341] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgfb176a5e-ecb6-465e-ba8a-b3b7545f1dd4/GCA_947365035.1_SRR14836540_bin.7_metawrap_v1.3_MAG_genomic.fna.gz]
[2023-06-13 20:44:25,359] [INFO] Query marker FASTA was written to GCA_947365035.1_SRR14836540_bin.7_metawrap_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-13 20:44:25,359] [INFO] Task started: Blastn
[2023-06-13 20:44:25,359] [INFO] Running command: blastn -query GCA_947365035.1_SRR14836540_bin.7_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg8f73f4df-7168-4ff2-bba8-5d4dc00ba059/dqc_reference/reference_markers.fasta -out GCA_947365035.1_SRR14836540_bin.7_metawrap_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 20:44:25,917] [INFO] Task succeeded: Blastn
[2023-06-13 20:44:25,921] [INFO] Selected 23 target genomes.
[2023-06-13 20:44:25,921] [INFO] Target genome list was writen to GCA_947365035.1_SRR14836540_bin.7_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-13 20:44:25,923] [INFO] Task started: fastANI
[2023-06-13 20:44:25,923] [INFO] Running command: fastANI --query /var/lib/cwl/stgfb176a5e-ecb6-465e-ba8a-b3b7545f1dd4/GCA_947365035.1_SRR14836540_bin.7_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_947365035.1_SRR14836540_bin.7_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_947365035.1_SRR14836540_bin.7_metawrap_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 20:44:36,157] [INFO] Task succeeded: fastANI
[2023-06-13 20:44:36,158] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8f73f4df-7168-4ff2-bba8-5d4dc00ba059/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 20:44:36,158] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8f73f4df-7168-4ff2-bba8-5d4dc00ba059/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 20:44:36,160] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 20:44:36,160] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-13 20:44:36,160] [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
--------------------------------------------------------------------------------
[2023-06-13 20:44:36,162] [INFO] DFAST Taxonomy check result was written to GCA_947365035.1_SRR14836540_bin.7_metawrap_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-13 20:44:36,163] [INFO] ===== Taxonomy check completed =====
[2023-06-13 20:44:36,163] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 20:44:36,163] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8f73f4df-7168-4ff2-bba8-5d4dc00ba059/dqc_reference/checkm_data
[2023-06-13 20:44:36,166] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 20:44:36,188] [INFO] Task started: CheckM
[2023-06-13 20:44:36,188] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_947365035.1_SRR14836540_bin.7_metawrap_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_947365035.1_SRR14836540_bin.7_metawrap_v1.3_MAG_genomic.fna/checkm_input GCA_947365035.1_SRR14836540_bin.7_metawrap_v1.3_MAG_genomic.fna/checkm_result
[2023-06-13 20:44:51,212] [INFO] Task succeeded: CheckM
[2023-06-13 20:44:51,213] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 20:44:51,232] [INFO] ===== Completeness check finished =====
[2023-06-13 20:44:51,232] [INFO] ===== Start GTDB Search =====
[2023-06-13 20:44:51,232] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_947365035.1_SRR14836540_bin.7_metawrap_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-13 20:44:51,233] [INFO] Task started: Blastn
[2023-06-13 20:44:51,233] [INFO] Running command: blastn -query GCA_947365035.1_SRR14836540_bin.7_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg8f73f4df-7168-4ff2-bba8-5d4dc00ba059/dqc_reference/reference_markers_gtdb.fasta -out GCA_947365035.1_SRR14836540_bin.7_metawrap_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 20:44:52,006] [INFO] Task succeeded: Blastn
[2023-06-13 20:44:52,012] [INFO] Selected 15 target genomes.
[2023-06-13 20:44:52,012] [INFO] Target genome list was writen to GCA_947365035.1_SRR14836540_bin.7_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 20:44:52,015] [INFO] Task started: fastANI
[2023-06-13 20:44:52,015] [INFO] Running command: fastANI --query /var/lib/cwl/stgfb176a5e-ecb6-465e-ba8a-b3b7545f1dd4/GCA_947365035.1_SRR14836540_bin.7_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_947365035.1_SRR14836540_bin.7_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_947365035.1_SRR14836540_bin.7_metawrap_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 20:44:57,493] [INFO] Task succeeded: fastANI
[2023-06-13 20:44:57,498] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 20:44:57,499] [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_910577745.1	s__Pelethenecus sp910577745	99.1214	433	485	d__Bacteria;p__Firmicutes;c__Bacilli;o__Acholeplasmatales;f__Anaeroplasmataceae;g__Pelethenecus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_910584005.1	s__Pelethenecus sp910584005	78.6529	155	485	d__Bacteria;p__Firmicutes;c__Bacilli;o__Acholeplasmatales;f__Anaeroplasmataceae;g__Pelethenecus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900540705.1	s__Pelethenecus sp900540705	78.4135	157	485	d__Bacteria;p__Firmicutes;c__Bacilli;o__Acholeplasmatales;f__Anaeroplasmataceae;g__Pelethenecus	95.0	98.96	96.92	0.92	0.86	4	-
GCA_910579215.1	s__Pelethenecus sp910579215	78.2393	181	485	d__Bacteria;p__Firmicutes;c__Bacilli;o__Acholeplasmatales;f__Anaeroplasmataceae;g__Pelethenecus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 20:44:57,501] [INFO] GTDB search result was written to GCA_947365035.1_SRR14836540_bin.7_metawrap_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-13 20:44:57,502] [INFO] ===== GTDB Search completed =====
[2023-06-13 20:44:57,504] [INFO] DFAST_QC result json was written to GCA_947365035.1_SRR14836540_bin.7_metawrap_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-13 20:44:57,505] [INFO] DFAST_QC completed!
[2023-06-13 20:44:57,505] [INFO] Total running time: 0h0m36s