[2023-06-08 05:33:51,878] [INFO] DFAST_QC pipeline started.
[2023-06-08 05:33:51,881] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 05:33:51,881] [INFO] DQC Reference Directory: /var/lib/cwl/stg6dd9307f-1742-405e-bcb5-4352b04e4ca4/dqc_reference
[2023-06-08 05:33:53,258] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 05:33:53,259] [INFO] Task started: Prodigal
[2023-06-08 05:33:53,260] [INFO] Running command: gunzip -c /var/lib/cwl/stg17f2c453-b27d-4e80-9e67-3a2349cbd7e6/GCA_902526415.1_AG-337-J19_genomic.fna.gz | prodigal -d GCA_902526415.1_AG-337-J19_genomic.fna/cds.fna -a GCA_902526415.1_AG-337-J19_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 05:33:54,745] [INFO] Task succeeded: Prodigal
[2023-06-08 05:33:54,746] [INFO] Task started: HMMsearch
[2023-06-08 05:33:54,746] [INFO] Running command: hmmsearch --tblout GCA_902526415.1_AG-337-J19_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6dd9307f-1742-405e-bcb5-4352b04e4ca4/dqc_reference/reference_markers.hmm GCA_902526415.1_AG-337-J19_genomic.fna/protein.faa > /dev/null
[2023-06-08 05:33:54,995] [INFO] Task succeeded: HMMsearch
[2023-06-08 05:33:54,997] [INFO] Found 6/6 markers.
[2023-06-08 05:33:55,015] [INFO] Query marker FASTA was written to GCA_902526415.1_AG-337-J19_genomic.fna/markers.fasta
[2023-06-08 05:33:55,015] [INFO] Task started: Blastn
[2023-06-08 05:33:55,016] [INFO] Running command: blastn -query GCA_902526415.1_AG-337-J19_genomic.fna/markers.fasta -db /var/lib/cwl/stg6dd9307f-1742-405e-bcb5-4352b04e4ca4/dqc_reference/reference_markers.fasta -out GCA_902526415.1_AG-337-J19_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 05:33:55,627] [INFO] Task succeeded: Blastn
[2023-06-08 05:33:55,632] [INFO] Selected 15 target genomes.
[2023-06-08 05:33:55,633] [INFO] Target genome list was writen to GCA_902526415.1_AG-337-J19_genomic.fna/target_genomes.txt
[2023-06-08 05:33:55,635] [INFO] Task started: fastANI
[2023-06-08 05:33:55,636] [INFO] Running command: fastANI --query /var/lib/cwl/stg17f2c453-b27d-4e80-9e67-3a2349cbd7e6/GCA_902526415.1_AG-337-J19_genomic.fna.gz --refList GCA_902526415.1_AG-337-J19_genomic.fna/target_genomes.txt --output GCA_902526415.1_AG-337-J19_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 05:34:02,053] [INFO] Task succeeded: fastANI
[2023-06-08 05:34:02,054] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6dd9307f-1742-405e-bcb5-4352b04e4ca4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 05:34:02,054] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6dd9307f-1742-405e-bcb5-4352b04e4ca4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 05:34:02,056] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 05:34:02,056] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-08 05:34:02,057] [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 05:34:02,059] [INFO] DFAST Taxonomy check result was written to GCA_902526415.1_AG-337-J19_genomic.fna/tc_result.tsv
[2023-06-08 05:34:02,059] [INFO] ===== Taxonomy check completed =====
[2023-06-08 05:34:02,060] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 05:34:02,060] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6dd9307f-1742-405e-bcb5-4352b04e4ca4/dqc_reference/checkm_data
[2023-06-08 05:34:02,065] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 05:34:02,079] [INFO] Task started: CheckM
[2023-06-08 05:34:02,079] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902526415.1_AG-337-J19_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902526415.1_AG-337-J19_genomic.fna/checkm_input GCA_902526415.1_AG-337-J19_genomic.fna/checkm_result
[2023-06-08 05:34:15,716] [INFO] Task succeeded: CheckM
[2023-06-08 05:34:15,717] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 05:34:15,731] [INFO] ===== Completeness check finished =====
[2023-06-08 05:34:15,732] [INFO] ===== Start GTDB Search =====
[2023-06-08 05:34:15,732] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902526415.1_AG-337-J19_genomic.fna/markers.fasta)
[2023-06-08 05:34:15,732] [INFO] Task started: Blastn
[2023-06-08 05:34:15,732] [INFO] Running command: blastn -query GCA_902526415.1_AG-337-J19_genomic.fna/markers.fasta -db /var/lib/cwl/stg6dd9307f-1742-405e-bcb5-4352b04e4ca4/dqc_reference/reference_markers_gtdb.fasta -out GCA_902526415.1_AG-337-J19_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 05:34:16,716] [INFO] Task succeeded: Blastn
[2023-06-08 05:34:16,721] [INFO] Selected 17 target genomes.
[2023-06-08 05:34:16,721] [INFO] Target genome list was writen to GCA_902526415.1_AG-337-J19_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 05:34:16,727] [INFO] Task started: fastANI
[2023-06-08 05:34:16,727] [INFO] Running command: fastANI --query /var/lib/cwl/stg17f2c453-b27d-4e80-9e67-3a2349cbd7e6/GCA_902526415.1_AG-337-J19_genomic.fna.gz --refList GCA_902526415.1_AG-337-J19_genomic.fna/target_genomes_gtdb.txt --output GCA_902526415.1_AG-337-J19_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 05:34:20,179] [INFO] Task succeeded: fastANI
[2023-06-08 05:34:20,194] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 05:34:20,195] [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_003282105.1	s__AG-339-G14 sp003282105	95.2949	188	264	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__AG-339-G14;g__AG-339-G14	95.0	95.52	95.11	0.79	0.67	11	conclusive
GCA_902613455.1	s__AG-339-G14 sp902613455	93.5968	243	264	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__AG-339-G14;g__AG-339-G14	95.0	97.22	96.70	0.93	0.90	20	-
GCA_004213955.1	s__AG-339-G14 sp004213955	79.1384	118	264	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__AG-339-G14;g__AG-339-G14	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902616715.1	s__AG-339-G14 sp902616715	79.129	131	264	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__AG-339-G14;g__AG-339-G14	95.0	98.52	98.27	0.93	0.90	8	-
GCA_902527995.1	s__AG-339-G14 sp902527995	78.9539	78	264	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__AG-339-G14;g__AG-339-G14	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902562135.1	s__AG-339-G14 sp902562135	78.4172	100	264	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__AG-339-G14;g__AG-339-G14	95.0	97.66	97.66	0.82	0.82	2	-
GCA_902536295.1	s__AG-339-G14 sp902536295	78.4022	109	264	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__AG-339-G14;g__AG-339-G14	95.0	97.79	97.73	0.85	0.77	3	-
--------------------------------------------------------------------------------
[2023-06-08 05:34:20,197] [INFO] GTDB search result was written to GCA_902526415.1_AG-337-J19_genomic.fna/result_gtdb.tsv
[2023-06-08 05:34:20,198] [INFO] ===== GTDB Search completed =====
[2023-06-08 05:34:20,201] [INFO] DFAST_QC result json was written to GCA_902526415.1_AG-337-J19_genomic.fna/dqc_result.json
[2023-06-08 05:34:20,202] [INFO] DFAST_QC completed!
[2023-06-08 05:34:20,202] [INFO] Total running time: 0h0m28s