[2023-06-08 00:54:30,259] [INFO] DFAST_QC pipeline started.
[2023-06-08 00:54:30,267] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 00:54:30,268] [INFO] DQC Reference Directory: /var/lib/cwl/stg0f203184-bb82-4de3-89ca-c7cf8ebb125a/dqc_reference
[2023-06-08 00:54:31,613] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 00:54:31,614] [INFO] Task started: Prodigal
[2023-06-08 00:54:31,614] [INFO] Running command: gunzip -c /var/lib/cwl/stge46a68b5-1810-41f9-978c-e8d1ceaa250e/GCA_902623465.1_AG-893-N17_genomic.fna.gz | prodigal -d GCA_902623465.1_AG-893-N17_genomic.fna/cds.fna -a GCA_902623465.1_AG-893-N17_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 00:54:33,634] [INFO] Task succeeded: Prodigal
[2023-06-08 00:54:33,634] [INFO] Task started: HMMsearch
[2023-06-08 00:54:33,634] [INFO] Running command: hmmsearch --tblout GCA_902623465.1_AG-893-N17_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0f203184-bb82-4de3-89ca-c7cf8ebb125a/dqc_reference/reference_markers.hmm GCA_902623465.1_AG-893-N17_genomic.fna/protein.faa > /dev/null
[2023-06-08 00:54:33,856] [INFO] Task succeeded: HMMsearch
[2023-06-08 00:54:33,857] [WARNING] Found 4/6 markers. [/var/lib/cwl/stge46a68b5-1810-41f9-978c-e8d1ceaa250e/GCA_902623465.1_AG-893-N17_genomic.fna.gz]
[2023-06-08 00:54:33,879] [INFO] Query marker FASTA was written to GCA_902623465.1_AG-893-N17_genomic.fna/markers.fasta
[2023-06-08 00:54:33,879] [INFO] Task started: Blastn
[2023-06-08 00:54:33,879] [INFO] Running command: blastn -query GCA_902623465.1_AG-893-N17_genomic.fna/markers.fasta -db /var/lib/cwl/stg0f203184-bb82-4de3-89ca-c7cf8ebb125a/dqc_reference/reference_markers.fasta -out GCA_902623465.1_AG-893-N17_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 00:54:34,489] [INFO] Task succeeded: Blastn
[2023-06-08 00:54:34,493] [INFO] Selected 21 target genomes.
[2023-06-08 00:54:34,493] [INFO] Target genome list was writen to GCA_902623465.1_AG-893-N17_genomic.fna/target_genomes.txt
[2023-06-08 00:54:34,497] [INFO] Task started: fastANI
[2023-06-08 00:54:34,497] [INFO] Running command: fastANI --query /var/lib/cwl/stge46a68b5-1810-41f9-978c-e8d1ceaa250e/GCA_902623465.1_AG-893-N17_genomic.fna.gz --refList GCA_902623465.1_AG-893-N17_genomic.fna/target_genomes.txt --output GCA_902623465.1_AG-893-N17_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 00:54:45,219] [INFO] Task succeeded: fastANI
[2023-06-08 00:54:45,220] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0f203184-bb82-4de3-89ca-c7cf8ebb125a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 00:54:45,220] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0f203184-bb82-4de3-89ca-c7cf8ebb125a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 00:54:45,222] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 00:54:45,222] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-08 00:54:45,222] [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 00:54:45,225] [INFO] DFAST Taxonomy check result was written to GCA_902623465.1_AG-893-N17_genomic.fna/tc_result.tsv
[2023-06-08 00:54:45,227] [INFO] ===== Taxonomy check completed =====
[2023-06-08 00:54:45,227] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 00:54:45,227] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0f203184-bb82-4de3-89ca-c7cf8ebb125a/dqc_reference/checkm_data
[2023-06-08 00:54:45,230] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 00:54:45,250] [INFO] Task started: CheckM
[2023-06-08 00:54:45,250] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902623465.1_AG-893-N17_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902623465.1_AG-893-N17_genomic.fna/checkm_input GCA_902623465.1_AG-893-N17_genomic.fna/checkm_result
[2023-06-08 00:55:00,808] [INFO] Task succeeded: CheckM
[2023-06-08 00:55:00,810] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 80.09%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 00:55:00,840] [INFO] ===== Completeness check finished =====
[2023-06-08 00:55:00,841] [INFO] ===== Start GTDB Search =====
[2023-06-08 00:55:00,842] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902623465.1_AG-893-N17_genomic.fna/markers.fasta)
[2023-06-08 00:55:00,842] [INFO] Task started: Blastn
[2023-06-08 00:55:00,842] [INFO] Running command: blastn -query GCA_902623465.1_AG-893-N17_genomic.fna/markers.fasta -db /var/lib/cwl/stg0f203184-bb82-4de3-89ca-c7cf8ebb125a/dqc_reference/reference_markers_gtdb.fasta -out GCA_902623465.1_AG-893-N17_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 00:55:01,695] [INFO] Task succeeded: Blastn
[2023-06-08 00:55:01,699] [INFO] Selected 8 target genomes.
[2023-06-08 00:55:01,699] [INFO] Target genome list was writen to GCA_902623465.1_AG-893-N17_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 00:55:01,702] [INFO] Task started: fastANI
[2023-06-08 00:55:01,702] [INFO] Running command: fastANI --query /var/lib/cwl/stge46a68b5-1810-41f9-978c-e8d1ceaa250e/GCA_902623465.1_AG-893-N17_genomic.fna.gz --refList GCA_902623465.1_AG-893-N17_genomic.fna/target_genomes_gtdb.txt --output GCA_902623465.1_AG-893-N17_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 00:55:04,017] [INFO] Task succeeded: fastANI
[2023-06-08 00:55:04,031] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 00:55:04,031] [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_902620785.1	s__GCA-2707915 sp902620785	95.0216	312	357	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__SAR86;g__GCA-2707915	95.0	95.48	95.02	0.87	0.85	6	conclusive
GCA_902618945.1	s__GCA-2707915 sp902618945	94.9453	276	357	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__SAR86;g__GCA-2707915	95.0	95.64	95.64	0.79	0.79	2	-
GCA_902605935.1	s__GCA-2707915 sp902605935	92.2237	154	357	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__SAR86;g__GCA-2707915	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902574355.1	s__GCA-2707915 sp902574355	91.9043	291	357	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__SAR86;g__GCA-2707915	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902542325.1	s__GCA-2707915 sp902542325	91.3348	259	357	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__SAR86;g__GCA-2707915	95.0	99.62	99.62	0.80	0.80	2	-
GCA_902604855.1	s__GCA-2707915 sp902604855	90.5899	248	357	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__SAR86;g__GCA-2707915	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902606175.1	s__GCA-2707915 sp902606175	89.2716	247	357	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__SAR86;g__GCA-2707915	95.0	95.24	95.17	0.72	0.71	3	-
--------------------------------------------------------------------------------
[2023-06-08 00:55:04,033] [INFO] GTDB search result was written to GCA_902623465.1_AG-893-N17_genomic.fna/result_gtdb.tsv
[2023-06-08 00:55:04,034] [INFO] ===== GTDB Search completed =====
[2023-06-08 00:55:04,037] [INFO] DFAST_QC result json was written to GCA_902623465.1_AG-893-N17_genomic.fna/dqc_result.json
[2023-06-08 00:55:04,037] [INFO] DFAST_QC completed!
[2023-06-08 00:55:04,037] [INFO] Total running time: 0h0m34s