[2023-06-08 14:28:03,027] [INFO] DFAST_QC pipeline started.
[2023-06-08 14:28:03,036] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 14:28:03,037] [INFO] DQC Reference Directory: /var/lib/cwl/stge7605723-f3e2-4546-b4c3-0dc31ce203f4/dqc_reference
[2023-06-08 14:28:04,579] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 14:28:04,581] [INFO] Task started: Prodigal
[2023-06-08 14:28:04,581] [INFO] Running command: gunzip -c /var/lib/cwl/stg52559772-8f48-4826-bd23-64637a76379c/GCA_902526175.1_AG-896-A16_genomic.fna.gz | prodigal -d GCA_902526175.1_AG-896-A16_genomic.fna/cds.fna -a GCA_902526175.1_AG-896-A16_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 14:28:06,797] [INFO] Task succeeded: Prodigal
[2023-06-08 14:28:06,798] [INFO] Task started: HMMsearch
[2023-06-08 14:28:06,798] [INFO] Running command: hmmsearch --tblout GCA_902526175.1_AG-896-A16_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge7605723-f3e2-4546-b4c3-0dc31ce203f4/dqc_reference/reference_markers.hmm GCA_902526175.1_AG-896-A16_genomic.fna/protein.faa > /dev/null
[2023-06-08 14:28:07,040] [INFO] Task succeeded: HMMsearch
[2023-06-08 14:28:07,047] [INFO] Found 6/6 markers.
[2023-06-08 14:28:07,072] [INFO] Query marker FASTA was written to GCA_902526175.1_AG-896-A16_genomic.fna/markers.fasta
[2023-06-08 14:28:07,072] [INFO] Task started: Blastn
[2023-06-08 14:28:07,073] [INFO] Running command: blastn -query GCA_902526175.1_AG-896-A16_genomic.fna/markers.fasta -db /var/lib/cwl/stge7605723-f3e2-4546-b4c3-0dc31ce203f4/dqc_reference/reference_markers.fasta -out GCA_902526175.1_AG-896-A16_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 14:28:07,632] [INFO] Task succeeded: Blastn
[2023-06-08 14:28:07,637] [INFO] Selected 17 target genomes.
[2023-06-08 14:28:07,638] [INFO] Target genome list was writen to GCA_902526175.1_AG-896-A16_genomic.fna/target_genomes.txt
[2023-06-08 14:28:07,641] [INFO] Task started: fastANI
[2023-06-08 14:28:07,641] [INFO] Running command: fastANI --query /var/lib/cwl/stg52559772-8f48-4826-bd23-64637a76379c/GCA_902526175.1_AG-896-A16_genomic.fna.gz --refList GCA_902526175.1_AG-896-A16_genomic.fna/target_genomes.txt --output GCA_902526175.1_AG-896-A16_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 14:28:15,353] [INFO] Task succeeded: fastANI
[2023-06-08 14:28:15,354] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge7605723-f3e2-4546-b4c3-0dc31ce203f4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 14:28:15,354] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge7605723-f3e2-4546-b4c3-0dc31ce203f4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 14:28:15,356] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 14:28:15,356] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-08 14:28:15,357] [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
--------------------------------------------------------------------------------
[2023-06-08 14:28:15,359] [INFO] DFAST Taxonomy check result was written to GCA_902526175.1_AG-896-A16_genomic.fna/tc_result.tsv
[2023-06-08 14:28:15,360] [INFO] ===== Taxonomy check completed =====
[2023-06-08 14:28:15,360] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 14:28:15,360] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge7605723-f3e2-4546-b4c3-0dc31ce203f4/dqc_reference/checkm_data
[2023-06-08 14:28:15,364] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 14:28:15,386] [INFO] Task started: CheckM
[2023-06-08 14:28:15,387] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902526175.1_AG-896-A16_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902526175.1_AG-896-A16_genomic.fna/checkm_input GCA_902526175.1_AG-896-A16_genomic.fna/checkm_result
[2023-06-08 14:28:30,588] [INFO] Task succeeded: CheckM
[2023-06-08 14:28:30,589] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 14:28:30,614] [INFO] ===== Completeness check finished =====
[2023-06-08 14:28:30,614] [INFO] ===== Start GTDB Search =====
[2023-06-08 14:28:30,615] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902526175.1_AG-896-A16_genomic.fna/markers.fasta)
[2023-06-08 14:28:30,615] [INFO] Task started: Blastn
[2023-06-08 14:28:30,615] [INFO] Running command: blastn -query GCA_902526175.1_AG-896-A16_genomic.fna/markers.fasta -db /var/lib/cwl/stge7605723-f3e2-4546-b4c3-0dc31ce203f4/dqc_reference/reference_markers_gtdb.fasta -out GCA_902526175.1_AG-896-A16_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 14:28:31,436] [INFO] Task succeeded: Blastn
[2023-06-08 14:28:31,440] [INFO] Selected 18 target genomes.
[2023-06-08 14:28:31,440] [INFO] Target genome list was writen to GCA_902526175.1_AG-896-A16_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 14:28:31,468] [INFO] Task started: fastANI
[2023-06-08 14:28:31,468] [INFO] Running command: fastANI --query /var/lib/cwl/stg52559772-8f48-4826-bd23-64637a76379c/GCA_902526175.1_AG-896-A16_genomic.fna.gz --refList GCA_902526175.1_AG-896-A16_genomic.fna/target_genomes_gtdb.txt --output GCA_902526175.1_AG-896-A16_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 14:28:35,589] [INFO] Task succeeded: fastANI
[2023-06-08 14:28:35,602] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 14:28:35,602] [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_902526175.1	s__CACBWF01 sp902526175	100.0	427	427	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__TMED127;f__TMED127;g__CACBWF01	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_902542925.1	s__CACBWF01 sp902542925	91.5013	205	427	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__TMED127;f__TMED127;g__CACBWF01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902618535.1	s__GCA-002690875 sp902618535	77.1022	56	427	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__TMED127;f__TMED127;g__GCA-002690875	95.0	97.44	97.44	0.66	0.66	2	-
GCA_902522465.1	s__GCA-2691245 sp902522465	77.0951	55	427	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__TMED127;f__TMED127;g__GCA-2691245	95.0	99.84	99.84	0.89	0.89	2	-
GCA_002691145.1	s__GCA-2691145 sp002691145	77.0837	75	427	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__TMED127;f__TMED127;g__GCA-2691145	95.0	99.68	99.51	0.96	0.92	4	-
GCA_902547955.1	s__MED-G10 sp902547955	76.6582	64	427	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__TMED127;f__TMED127;g__MED-G10	95.0	97.61	97.06	0.82	0.80	5	-
GCA_902537615.1	s__GCA-002690875 sp902537615	76.6309	56	427	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__TMED127;f__TMED127;g__GCA-002690875	95.0	96.75	96.75	0.77	0.77	2	-
GCA_002167215.1	s__GCA-2691245 sp002167215	75.503	62	427	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__TMED127;f__TMED127;g__GCA-2691245	95.0	97.98	96.11	0.71	0.71	3	-
--------------------------------------------------------------------------------
[2023-06-08 14:28:35,605] [INFO] GTDB search result was written to GCA_902526175.1_AG-896-A16_genomic.fna/result_gtdb.tsv
[2023-06-08 14:28:35,605] [INFO] ===== GTDB Search completed =====
[2023-06-08 14:28:35,608] [INFO] DFAST_QC result json was written to GCA_902526175.1_AG-896-A16_genomic.fna/dqc_result.json
[2023-06-08 14:28:35,608] [INFO] DFAST_QC completed!
[2023-06-08 14:28:35,608] [INFO] Total running time: 0h0m33s