[2023-06-17 12:25:01,555] [INFO] DFAST_QC pipeline started.
[2023-06-17 12:25:01,558] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 12:25:01,558] [INFO] DQC Reference Directory: /var/lib/cwl/stga43c182b-7287-478a-a7f7-f97665ecc2ac/dqc_reference
[2023-06-17 12:25:02,865] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 12:25:02,866] [INFO] Task started: Prodigal
[2023-06-17 12:25:02,866] [INFO] Running command: gunzip -c /var/lib/cwl/stg5d08a45f-2d37-4c60-b4fd-9e06b14ab321/GCA_905211065.1_ERR414252-mag-bin.1_genomic.fna.gz | prodigal -d GCA_905211065.1_ERR414252-mag-bin.1_genomic.fna/cds.fna -a GCA_905211065.1_ERR414252-mag-bin.1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 12:25:04,622] [INFO] Task succeeded: Prodigal
[2023-06-17 12:25:04,623] [INFO] Task started: HMMsearch
[2023-06-17 12:25:04,623] [INFO] Running command: hmmsearch --tblout GCA_905211065.1_ERR414252-mag-bin.1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga43c182b-7287-478a-a7f7-f97665ecc2ac/dqc_reference/reference_markers.hmm GCA_905211065.1_ERR414252-mag-bin.1_genomic.fna/protein.faa > /dev/null
[2023-06-17 12:25:04,877] [INFO] Task succeeded: HMMsearch
[2023-06-17 12:25:04,878] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg5d08a45f-2d37-4c60-b4fd-9e06b14ab321/GCA_905211065.1_ERR414252-mag-bin.1_genomic.fna.gz]
[2023-06-17 12:25:04,913] [INFO] Query marker FASTA was written to GCA_905211065.1_ERR414252-mag-bin.1_genomic.fna/markers.fasta
[2023-06-17 12:25:04,913] [INFO] Task started: Blastn
[2023-06-17 12:25:04,914] [INFO] Running command: blastn -query GCA_905211065.1_ERR414252-mag-bin.1_genomic.fna/markers.fasta -db /var/lib/cwl/stga43c182b-7287-478a-a7f7-f97665ecc2ac/dqc_reference/reference_markers.fasta -out GCA_905211065.1_ERR414252-mag-bin.1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 12:25:05,703] [INFO] Task succeeded: Blastn
[2023-06-17 12:25:05,708] [INFO] Selected 23 target genomes.
[2023-06-17 12:25:05,709] [INFO] Target genome list was writen to GCA_905211065.1_ERR414252-mag-bin.1_genomic.fna/target_genomes.txt
[2023-06-17 12:25:05,721] [INFO] Task started: fastANI
[2023-06-17 12:25:05,722] [INFO] Running command: fastANI --query /var/lib/cwl/stg5d08a45f-2d37-4c60-b4fd-9e06b14ab321/GCA_905211065.1_ERR414252-mag-bin.1_genomic.fna.gz --refList GCA_905211065.1_ERR414252-mag-bin.1_genomic.fna/target_genomes.txt --output GCA_905211065.1_ERR414252-mag-bin.1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 12:25:15,056] [INFO] Task succeeded: fastANI
[2023-06-17 12:25:15,057] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga43c182b-7287-478a-a7f7-f97665ecc2ac/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 12:25:15,057] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga43c182b-7287-478a-a7f7-f97665ecc2ac/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 12:25:15,059] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 12:25:15,059] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-17 12:25:15,060] [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
--------------------------------------------------------------------------------
[2023-06-17 12:25:15,062] [INFO] DFAST Taxonomy check result was written to GCA_905211065.1_ERR414252-mag-bin.1_genomic.fna/tc_result.tsv
[2023-06-17 12:25:15,062] [INFO] ===== Taxonomy check completed =====
[2023-06-17 12:25:15,062] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 12:25:15,063] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga43c182b-7287-478a-a7f7-f97665ecc2ac/dqc_reference/checkm_data
[2023-06-17 12:25:15,066] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 12:25:15,103] [INFO] Task started: CheckM
[2023-06-17 12:25:15,103] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_905211065.1_ERR414252-mag-bin.1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_905211065.1_ERR414252-mag-bin.1_genomic.fna/checkm_input GCA_905211065.1_ERR414252-mag-bin.1_genomic.fna/checkm_result
[2023-06-17 12:25:29,171] [INFO] Task succeeded: CheckM
[2023-06-17 12:25:29,172] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-17 12:25:29,192] [INFO] ===== Completeness check finished =====
[2023-06-17 12:25:29,193] [INFO] ===== Start GTDB Search =====
[2023-06-17 12:25:29,193] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_905211065.1_ERR414252-mag-bin.1_genomic.fna/markers.fasta)
[2023-06-17 12:25:29,194] [INFO] Task started: Blastn
[2023-06-17 12:25:29,194] [INFO] Running command: blastn -query GCA_905211065.1_ERR414252-mag-bin.1_genomic.fna/markers.fasta -db /var/lib/cwl/stga43c182b-7287-478a-a7f7-f97665ecc2ac/dqc_reference/reference_markers_gtdb.fasta -out GCA_905211065.1_ERR414252-mag-bin.1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 12:25:30,040] [INFO] Task succeeded: Blastn
[2023-06-17 12:25:30,045] [INFO] Selected 8 target genomes.
[2023-06-17 12:25:30,045] [INFO] Target genome list was writen to GCA_905211065.1_ERR414252-mag-bin.1_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 12:25:30,054] [INFO] Task started: fastANI
[2023-06-17 12:25:30,054] [INFO] Running command: fastANI --query /var/lib/cwl/stg5d08a45f-2d37-4c60-b4fd-9e06b14ab321/GCA_905211065.1_ERR414252-mag-bin.1_genomic.fna.gz --refList GCA_905211065.1_ERR414252-mag-bin.1_genomic.fna/target_genomes_gtdb.txt --output GCA_905211065.1_ERR414252-mag-bin.1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 12:25:32,364] [INFO] Task succeeded: fastANI
[2023-06-17 12:25:32,377] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-17 12:25:32,377] [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_900549285.1	s__Caccenecus sp900549285	100.0	381	383	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__Caccenecus	95.0	99.98	99.96	0.98	0.96	3	conclusive
GCA_000438195.1	s__Caccenecus sp000438195	86.0108	310	383	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__Caccenecus	95.0	99.99	99.99	0.98	0.98	3	-
GCA_900758895.1	s__Caccenecus sp900758895	80.9038	195	383	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__Caccenecus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017888105.1	s__Caccenecus sp017888105	80.7646	214	383	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__Caccenecus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018716965.1	s__Caccenecus avistercoris	80.3361	206	383	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__Caccenecus	95.0	99.97	99.97	0.89	0.89	2	-
GCA_015059425.1	s__Caccenecus sp015059425	78.6968	145	383	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__Caccenecus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910585045.1	s__Caccenecus sp910585045	78.1425	156	383	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__Caccenecus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-17 12:25:32,379] [INFO] GTDB search result was written to GCA_905211065.1_ERR414252-mag-bin.1_genomic.fna/result_gtdb.tsv
[2023-06-17 12:25:32,380] [INFO] ===== GTDB Search completed =====
[2023-06-17 12:25:32,382] [INFO] DFAST_QC result json was written to GCA_905211065.1_ERR414252-mag-bin.1_genomic.fna/dqc_result.json
[2023-06-17 12:25:32,382] [INFO] DFAST_QC completed!
[2023-06-17 12:25:32,382] [INFO] Total running time: 0h0m31s