[2023-06-13 02:32:30,431] [INFO] DFAST_QC pipeline started.
[2023-06-13 02:32:30,440] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 02:32:30,440] [INFO] DQC Reference Directory: /var/lib/cwl/stg2c3884e9-036a-43c2-9e5a-957ec39dcaf1/dqc_reference
[2023-06-13 02:32:32,660] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 02:32:32,661] [INFO] Task started: Prodigal
[2023-06-13 02:32:32,662] [INFO] Running command: gunzip -c /var/lib/cwl/stg4ad094db-8cdf-4b61-8a39-984e717f9c12/GCA_938040335.1_ERR321429_bin.36_CONCOCT_v1.1_MAG_genomic.fna.gz | prodigal -d GCA_938040335.1_ERR321429_bin.36_CONCOCT_v1.1_MAG_genomic.fna/cds.fna -a GCA_938040335.1_ERR321429_bin.36_CONCOCT_v1.1_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 02:32:34,999] [INFO] Task succeeded: Prodigal
[2023-06-13 02:32:35,000] [INFO] Task started: HMMsearch
[2023-06-13 02:32:35,000] [INFO] Running command: hmmsearch --tblout GCA_938040335.1_ERR321429_bin.36_CONCOCT_v1.1_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2c3884e9-036a-43c2-9e5a-957ec39dcaf1/dqc_reference/reference_markers.hmm GCA_938040335.1_ERR321429_bin.36_CONCOCT_v1.1_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-13 02:32:35,215] [INFO] Task succeeded: HMMsearch
[2023-06-13 02:32:35,216] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg4ad094db-8cdf-4b61-8a39-984e717f9c12/GCA_938040335.1_ERR321429_bin.36_CONCOCT_v1.1_MAG_genomic.fna.gz]
[2023-06-13 02:32:35,238] [INFO] Query marker FASTA was written to GCA_938040335.1_ERR321429_bin.36_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta
[2023-06-13 02:32:35,238] [INFO] Task started: Blastn
[2023-06-13 02:32:35,239] [INFO] Running command: blastn -query GCA_938040335.1_ERR321429_bin.36_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg2c3884e9-036a-43c2-9e5a-957ec39dcaf1/dqc_reference/reference_markers.fasta -out GCA_938040335.1_ERR321429_bin.36_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 02:32:36,874] [INFO] Task succeeded: Blastn
[2023-06-13 02:32:36,880] [INFO] Selected 21 target genomes.
[2023-06-13 02:32:36,880] [INFO] Target genome list was writen to GCA_938040335.1_ERR321429_bin.36_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt
[2023-06-13 02:32:36,885] [INFO] Task started: fastANI
[2023-06-13 02:32:36,885] [INFO] Running command: fastANI --query /var/lib/cwl/stg4ad094db-8cdf-4b61-8a39-984e717f9c12/GCA_938040335.1_ERR321429_bin.36_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_938040335.1_ERR321429_bin.36_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt --output GCA_938040335.1_ERR321429_bin.36_CONCOCT_v1.1_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 02:32:45,508] [INFO] Task succeeded: fastANI
[2023-06-13 02:32:45,509] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2c3884e9-036a-43c2-9e5a-957ec39dcaf1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 02:32:45,509] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2c3884e9-036a-43c2-9e5a-957ec39dcaf1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 02:32:45,511] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 02:32:45,511] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-13 02:32:45,512] [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 02:32:45,514] [INFO] DFAST Taxonomy check result was written to GCA_938040335.1_ERR321429_bin.36_CONCOCT_v1.1_MAG_genomic.fna/tc_result.tsv
[2023-06-13 02:32:45,515] [INFO] ===== Taxonomy check completed =====
[2023-06-13 02:32:45,515] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 02:32:45,515] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2c3884e9-036a-43c2-9e5a-957ec39dcaf1/dqc_reference/checkm_data
[2023-06-13 02:32:45,520] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 02:32:45,535] [INFO] Task started: CheckM
[2023-06-13 02:32:45,536] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_938040335.1_ERR321429_bin.36_CONCOCT_v1.1_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_938040335.1_ERR321429_bin.36_CONCOCT_v1.1_MAG_genomic.fna/checkm_input GCA_938040335.1_ERR321429_bin.36_CONCOCT_v1.1_MAG_genomic.fna/checkm_result
[2023-06-13 02:33:00,748] [INFO] Task succeeded: CheckM
[2023-06-13 02:33:00,751] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 65.16%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 02:33:00,770] [INFO] ===== Completeness check finished =====
[2023-06-13 02:33:00,770] [INFO] ===== Start GTDB Search =====
[2023-06-13 02:33:00,770] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_938040335.1_ERR321429_bin.36_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta)
[2023-06-13 02:33:00,771] [INFO] Task started: Blastn
[2023-06-13 02:33:00,771] [INFO] Running command: blastn -query GCA_938040335.1_ERR321429_bin.36_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg2c3884e9-036a-43c2-9e5a-957ec39dcaf1/dqc_reference/reference_markers_gtdb.fasta -out GCA_938040335.1_ERR321429_bin.36_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 02:33:01,570] [INFO] Task succeeded: Blastn
[2023-06-13 02:33:01,575] [INFO] Selected 20 target genomes.
[2023-06-13 02:33:01,576] [INFO] Target genome list was writen to GCA_938040335.1_ERR321429_bin.36_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 02:33:01,586] [INFO] Task started: fastANI
[2023-06-13 02:33:01,586] [INFO] Running command: fastANI --query /var/lib/cwl/stg4ad094db-8cdf-4b61-8a39-984e717f9c12/GCA_938040335.1_ERR321429_bin.36_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_938040335.1_ERR321429_bin.36_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_938040335.1_ERR321429_bin.36_CONCOCT_v1.1_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 02:33:06,389] [INFO] Task succeeded: fastANI
[2023-06-13 02:33:06,393] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 02:33:06,393] [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_900557585.1	s__UMGS2069 sp900557585	99.3938	177	236	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__UBA1242;g__UMGS2069	95.0	99.82	99.82	0.90	0.90	2	conclusive
GCA_900554955.1	s__UMGS2069 sp900554955	84.4708	138	236	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__UBA1242;g__UMGS2069	95.0	98.20	98.09	0.99	0.98	3	-
--------------------------------------------------------------------------------
[2023-06-13 02:33:06,395] [INFO] GTDB search result was written to GCA_938040335.1_ERR321429_bin.36_CONCOCT_v1.1_MAG_genomic.fna/result_gtdb.tsv
[2023-06-13 02:33:06,396] [INFO] ===== GTDB Search completed =====
[2023-06-13 02:33:06,398] [INFO] DFAST_QC result json was written to GCA_938040335.1_ERR321429_bin.36_CONCOCT_v1.1_MAG_genomic.fna/dqc_result.json
[2023-06-13 02:33:06,398] [INFO] DFAST_QC completed!
[2023-06-13 02:33:06,398] [INFO] Total running time: 0h0m36s