[2023-06-08 04:16:55,368] [INFO] DFAST_QC pipeline started.
[2023-06-08 04:16:55,376] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 04:16:55,376] [INFO] DQC Reference Directory: /var/lib/cwl/stg3e6a5737-8ae4-4479-8602-f1b0df439833/dqc_reference
[2023-06-08 04:16:56,890] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 04:16:56,891] [INFO] Task started: Prodigal
[2023-06-08 04:16:56,892] [INFO] Running command: gunzip -c /var/lib/cwl/stgdc5f7538-f25d-4069-bb00-2e6a3231d6f6/GCA_902520435.1_AG-894-K16_genomic.fna.gz | prodigal -d GCA_902520435.1_AG-894-K16_genomic.fna/cds.fna -a GCA_902520435.1_AG-894-K16_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 04:16:58,951] [INFO] Task succeeded: Prodigal
[2023-06-08 04:16:58,952] [INFO] Task started: HMMsearch
[2023-06-08 04:16:58,952] [INFO] Running command: hmmsearch --tblout GCA_902520435.1_AG-894-K16_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3e6a5737-8ae4-4479-8602-f1b0df439833/dqc_reference/reference_markers.hmm GCA_902520435.1_AG-894-K16_genomic.fna/protein.faa > /dev/null
[2023-06-08 04:16:59,162] [INFO] Task succeeded: HMMsearch
[2023-06-08 04:16:59,165] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgdc5f7538-f25d-4069-bb00-2e6a3231d6f6/GCA_902520435.1_AG-894-K16_genomic.fna.gz]
[2023-06-08 04:16:59,184] [INFO] Query marker FASTA was written to GCA_902520435.1_AG-894-K16_genomic.fna/markers.fasta
[2023-06-08 04:16:59,185] [INFO] Task started: Blastn
[2023-06-08 04:16:59,185] [INFO] Running command: blastn -query GCA_902520435.1_AG-894-K16_genomic.fna/markers.fasta -db /var/lib/cwl/stg3e6a5737-8ae4-4479-8602-f1b0df439833/dqc_reference/reference_markers.fasta -out GCA_902520435.1_AG-894-K16_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 04:16:59,816] [INFO] Task succeeded: Blastn
[2023-06-08 04:16:59,824] [INFO] Selected 17 target genomes.
[2023-06-08 04:16:59,825] [INFO] Target genome list was writen to GCA_902520435.1_AG-894-K16_genomic.fna/target_genomes.txt
[2023-06-08 04:16:59,827] [INFO] Task started: fastANI
[2023-06-08 04:16:59,827] [INFO] Running command: fastANI --query /var/lib/cwl/stgdc5f7538-f25d-4069-bb00-2e6a3231d6f6/GCA_902520435.1_AG-894-K16_genomic.fna.gz --refList GCA_902520435.1_AG-894-K16_genomic.fna/target_genomes.txt --output GCA_902520435.1_AG-894-K16_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 04:17:09,006] [INFO] Task succeeded: fastANI
[2023-06-08 04:17:09,007] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3e6a5737-8ae4-4479-8602-f1b0df439833/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 04:17:09,007] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3e6a5737-8ae4-4479-8602-f1b0df439833/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 04:17:09,009] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 04:17:09,009] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-08 04:17:09,009] [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 04:17:09,011] [INFO] DFAST Taxonomy check result was written to GCA_902520435.1_AG-894-K16_genomic.fna/tc_result.tsv
[2023-06-08 04:17:09,012] [INFO] ===== Taxonomy check completed =====
[2023-06-08 04:17:09,012] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 04:17:09,012] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3e6a5737-8ae4-4479-8602-f1b0df439833/dqc_reference/checkm_data
[2023-06-08 04:17:09,015] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 04:17:09,030] [INFO] Task started: CheckM
[2023-06-08 04:17:09,031] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902520435.1_AG-894-K16_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902520435.1_AG-894-K16_genomic.fna/checkm_input GCA_902520435.1_AG-894-K16_genomic.fna/checkm_result
[2023-06-08 04:17:24,531] [INFO] Task succeeded: CheckM
[2023-06-08 04:17:24,533] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 41.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 04:17:24,553] [INFO] ===== Completeness check finished =====
[2023-06-08 04:17:24,553] [INFO] ===== Start GTDB Search =====
[2023-06-08 04:17:24,554] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902520435.1_AG-894-K16_genomic.fna/markers.fasta)
[2023-06-08 04:17:24,554] [INFO] Task started: Blastn
[2023-06-08 04:17:24,555] [INFO] Running command: blastn -query GCA_902520435.1_AG-894-K16_genomic.fna/markers.fasta -db /var/lib/cwl/stg3e6a5737-8ae4-4479-8602-f1b0df439833/dqc_reference/reference_markers_gtdb.fasta -out GCA_902520435.1_AG-894-K16_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 04:17:25,353] [INFO] Task succeeded: Blastn
[2023-06-08 04:17:25,358] [INFO] Selected 8 target genomes.
[2023-06-08 04:17:25,358] [INFO] Target genome list was writen to GCA_902520435.1_AG-894-K16_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 04:17:25,360] [INFO] Task started: fastANI
[2023-06-08 04:17:25,360] [INFO] Running command: fastANI --query /var/lib/cwl/stgdc5f7538-f25d-4069-bb00-2e6a3231d6f6/GCA_902520435.1_AG-894-K16_genomic.fna.gz --refList GCA_902520435.1_AG-894-K16_genomic.fna/target_genomes_gtdb.txt --output GCA_902520435.1_AG-894-K16_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 04:17:27,322] [INFO] Task succeeded: fastANI
[2023-06-08 04:17:27,330] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 04:17:27,330] [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	95.0155	317	361	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	94.6673	282	361	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_902574355.1	s__GCA-2707915 sp902574355	92.218	298	361	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_902605935.1	s__GCA-2707915 sp902605935	92.0381	145	361	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	91.9746	265	361	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	91.2816	265	361	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	89.3864	263	361	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 04:17:27,332] [INFO] GTDB search result was written to GCA_902520435.1_AG-894-K16_genomic.fna/result_gtdb.tsv
[2023-06-08 04:17:27,333] [INFO] ===== GTDB Search completed =====
[2023-06-08 04:17:27,335] [INFO] DFAST_QC result json was written to GCA_902520435.1_AG-894-K16_genomic.fna/dqc_result.json
[2023-06-08 04:17:27,336] [INFO] DFAST_QC completed!
[2023-06-08 04:17:27,336] [INFO] Total running time: 0h0m32s