[2023-06-17 12:34:55,993] [INFO] DFAST_QC pipeline started.
[2023-06-17 12:34:55,995] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 12:34:55,996] [INFO] DQC Reference Directory: /var/lib/cwl/stg5f273e41-fcaa-4226-90f6-4fd5174c1bed/dqc_reference
[2023-06-17 12:34:57,296] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 12:34:57,297] [INFO] Task started: Prodigal
[2023-06-17 12:34:57,297] [INFO] Running command: gunzip -c /var/lib/cwl/stga09c612d-cf1f-4617-8014-16d72aad2231/GCA_905202255.1_ERR1190865-mag-bin.22_genomic.fna.gz | prodigal -d GCA_905202255.1_ERR1190865-mag-bin.22_genomic.fna/cds.fna -a GCA_905202255.1_ERR1190865-mag-bin.22_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 12:35:02,128] [INFO] Task succeeded: Prodigal
[2023-06-17 12:35:02,129] [INFO] Task started: HMMsearch
[2023-06-17 12:35:02,129] [INFO] Running command: hmmsearch --tblout GCA_905202255.1_ERR1190865-mag-bin.22_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5f273e41-fcaa-4226-90f6-4fd5174c1bed/dqc_reference/reference_markers.hmm GCA_905202255.1_ERR1190865-mag-bin.22_genomic.fna/protein.faa > /dev/null
[2023-06-17 12:35:02,407] [INFO] Task succeeded: HMMsearch
[2023-06-17 12:35:02,408] [INFO] Found 6/6 markers.
[2023-06-17 12:35:02,430] [INFO] Query marker FASTA was written to GCA_905202255.1_ERR1190865-mag-bin.22_genomic.fna/markers.fasta
[2023-06-17 12:35:02,430] [INFO] Task started: Blastn
[2023-06-17 12:35:02,431] [INFO] Running command: blastn -query GCA_905202255.1_ERR1190865-mag-bin.22_genomic.fna/markers.fasta -db /var/lib/cwl/stg5f273e41-fcaa-4226-90f6-4fd5174c1bed/dqc_reference/reference_markers.fasta -out GCA_905202255.1_ERR1190865-mag-bin.22_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 12:35:03,159] [INFO] Task succeeded: Blastn
[2023-06-17 12:35:03,163] [INFO] Selected 18 target genomes.
[2023-06-17 12:35:03,163] [INFO] Target genome list was writen to GCA_905202255.1_ERR1190865-mag-bin.22_genomic.fna/target_genomes.txt
[2023-06-17 12:35:03,168] [INFO] Task started: fastANI
[2023-06-17 12:35:03,168] [INFO] Running command: fastANI --query /var/lib/cwl/stga09c612d-cf1f-4617-8014-16d72aad2231/GCA_905202255.1_ERR1190865-mag-bin.22_genomic.fna.gz --refList GCA_905202255.1_ERR1190865-mag-bin.22_genomic.fna/target_genomes.txt --output GCA_905202255.1_ERR1190865-mag-bin.22_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 12:35:15,614] [INFO] Task succeeded: fastANI
[2023-06-17 12:35:15,614] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5f273e41-fcaa-4226-90f6-4fd5174c1bed/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 12:35:15,615] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5f273e41-fcaa-4226-90f6-4fd5174c1bed/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 12:35:15,617] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 12:35:15,617] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-17 12:35:15,618] [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 12:35:15,620] [INFO] DFAST Taxonomy check result was written to GCA_905202255.1_ERR1190865-mag-bin.22_genomic.fna/tc_result.tsv
[2023-06-17 12:35:15,620] [INFO] ===== Taxonomy check completed =====
[2023-06-17 12:35:15,621] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 12:35:15,621] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5f273e41-fcaa-4226-90f6-4fd5174c1bed/dqc_reference/checkm_data
[2023-06-17 12:35:15,624] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 12:35:15,664] [INFO] Task started: CheckM
[2023-06-17 12:35:15,665] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_905202255.1_ERR1190865-mag-bin.22_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_905202255.1_ERR1190865-mag-bin.22_genomic.fna/checkm_input GCA_905202255.1_ERR1190865-mag-bin.22_genomic.fna/checkm_result
[2023-06-17 12:35:37,626] [INFO] Task succeeded: CheckM
[2023-06-17 12:35:37,628] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 86.74%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-17 12:35:37,651] [INFO] ===== Completeness check finished =====
[2023-06-17 12:35:37,651] [INFO] ===== Start GTDB Search =====
[2023-06-17 12:35:37,652] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_905202255.1_ERR1190865-mag-bin.22_genomic.fna/markers.fasta)
[2023-06-17 12:35:37,652] [INFO] Task started: Blastn
[2023-06-17 12:35:37,652] [INFO] Running command: blastn -query GCA_905202255.1_ERR1190865-mag-bin.22_genomic.fna/markers.fasta -db /var/lib/cwl/stg5f273e41-fcaa-4226-90f6-4fd5174c1bed/dqc_reference/reference_markers_gtdb.fasta -out GCA_905202255.1_ERR1190865-mag-bin.22_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 12:35:38,754] [INFO] Task succeeded: Blastn
[2023-06-17 12:35:38,761] [INFO] Selected 15 target genomes.
[2023-06-17 12:35:38,761] [INFO] Target genome list was writen to GCA_905202255.1_ERR1190865-mag-bin.22_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 12:35:38,774] [INFO] Task started: fastANI
[2023-06-17 12:35:38,775] [INFO] Running command: fastANI --query /var/lib/cwl/stga09c612d-cf1f-4617-8014-16d72aad2231/GCA_905202255.1_ERR1190865-mag-bin.22_genomic.fna.gz --refList GCA_905202255.1_ERR1190865-mag-bin.22_genomic.fna/target_genomes_gtdb.txt --output GCA_905202255.1_ERR1190865-mag-bin.22_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 12:35:44,571] [INFO] Task succeeded: fastANI
[2023-06-17 12:35:44,579] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-17 12:35:44,580] [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_905202255.1	s__CAG-724 sp905202255	99.9999	596	601	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-272;g__CAG-724	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_003524145.1	s__CAG-724 sp003524145	94.8622	455	601	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-272;g__CAG-724	95.0	98.59	98.21	0.88	0.83	6	-
GCA_900551005.1	s__CAG-724 sp900551005	81.9345	349	601	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-272;g__CAG-724	95.0	99.35	98.70	0.93	0.88	3	-
GCA_018383975.1	s__CAG-841 sp018383975	77.8647	82	601	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-272;g__CAG-841	95.0	98.92	98.92	0.89	0.89	2	-
--------------------------------------------------------------------------------
[2023-06-17 12:35:44,582] [INFO] GTDB search result was written to GCA_905202255.1_ERR1190865-mag-bin.22_genomic.fna/result_gtdb.tsv
[2023-06-17 12:35:44,582] [INFO] ===== GTDB Search completed =====
[2023-06-17 12:35:44,585] [INFO] DFAST_QC result json was written to GCA_905202255.1_ERR1190865-mag-bin.22_genomic.fna/dqc_result.json
[2023-06-17 12:35:44,585] [INFO] DFAST_QC completed!
[2023-06-17 12:35:44,585] [INFO] Total running time: 0h0m49s