[2023-06-19 02:25:11,293] [INFO] DFAST_QC pipeline started.
[2023-06-19 02:25:11,295] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 02:25:11,295] [INFO] DQC Reference Directory: /var/lib/cwl/stg4049843e-7250-49be-aa6c-27219f470ad8/dqc_reference
[2023-06-19 02:25:12,505] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 02:25:12,505] [INFO] Task started: Prodigal
[2023-06-19 02:25:12,506] [INFO] Running command: gunzip -c /var/lib/cwl/stg7a63bcc5-6ecf-424f-9346-9bc25de0e6ed/GCA_018607985.1_ASM1860798v1_genomic.fna.gz | prodigal -d GCA_018607985.1_ASM1860798v1_genomic.fna/cds.fna -a GCA_018607985.1_ASM1860798v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 02:25:16,971] [INFO] Task succeeded: Prodigal
[2023-06-19 02:25:16,971] [INFO] Task started: HMMsearch
[2023-06-19 02:25:16,972] [INFO] Running command: hmmsearch --tblout GCA_018607985.1_ASM1860798v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4049843e-7250-49be-aa6c-27219f470ad8/dqc_reference/reference_markers.hmm GCA_018607985.1_ASM1860798v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 02:25:17,207] [INFO] Task succeeded: HMMsearch
[2023-06-19 02:25:17,209] [INFO] Found 6/6 markers.
[2023-06-19 02:25:17,231] [INFO] Query marker FASTA was written to GCA_018607985.1_ASM1860798v1_genomic.fna/markers.fasta
[2023-06-19 02:25:17,232] [INFO] Task started: Blastn
[2023-06-19 02:25:17,232] [INFO] Running command: blastn -query GCA_018607985.1_ASM1860798v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4049843e-7250-49be-aa6c-27219f470ad8/dqc_reference/reference_markers.fasta -out GCA_018607985.1_ASM1860798v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 02:25:17,877] [INFO] Task succeeded: Blastn
[2023-06-19 02:25:17,899] [INFO] Selected 27 target genomes.
[2023-06-19 02:25:17,900] [INFO] Target genome list was writen to GCA_018607985.1_ASM1860798v1_genomic.fna/target_genomes.txt
[2023-06-19 02:25:17,902] [INFO] Task started: fastANI
[2023-06-19 02:25:17,902] [INFO] Running command: fastANI --query /var/lib/cwl/stg7a63bcc5-6ecf-424f-9346-9bc25de0e6ed/GCA_018607985.1_ASM1860798v1_genomic.fna.gz --refList GCA_018607985.1_ASM1860798v1_genomic.fna/target_genomes.txt --output GCA_018607985.1_ASM1860798v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 02:25:31,866] [INFO] Task succeeded: fastANI
[2023-06-19 02:25:31,866] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4049843e-7250-49be-aa6c-27219f470ad8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 02:25:31,867] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4049843e-7250-49be-aa6c-27219f470ad8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 02:25:31,870] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 02:25:31,870] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-19 02:25:31,870] [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
--------------------------------------------------------------------------------
[2023-06-19 02:25:31,876] [INFO] DFAST Taxonomy check result was written to GCA_018607985.1_ASM1860798v1_genomic.fna/tc_result.tsv
[2023-06-19 02:25:31,877] [INFO] ===== Taxonomy check completed =====
[2023-06-19 02:25:31,877] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 02:25:31,878] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4049843e-7250-49be-aa6c-27219f470ad8/dqc_reference/checkm_data
[2023-06-19 02:25:31,882] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 02:25:31,908] [INFO] Task started: CheckM
[2023-06-19 02:25:31,908] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018607985.1_ASM1860798v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018607985.1_ASM1860798v1_genomic.fna/checkm_input GCA_018607985.1_ASM1860798v1_genomic.fna/checkm_result
[2023-06-19 02:25:52,470] [INFO] Task succeeded: CheckM
[2023-06-19 02:25:52,472] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 86.36%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-19 02:25:52,492] [INFO] ===== Completeness check finished =====
[2023-06-19 02:25:52,493] [INFO] ===== Start GTDB Search =====
[2023-06-19 02:25:52,493] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018607985.1_ASM1860798v1_genomic.fna/markers.fasta)
[2023-06-19 02:25:52,493] [INFO] Task started: Blastn
[2023-06-19 02:25:52,494] [INFO] Running command: blastn -query GCA_018607985.1_ASM1860798v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4049843e-7250-49be-aa6c-27219f470ad8/dqc_reference/reference_markers_gtdb.fasta -out GCA_018607985.1_ASM1860798v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 02:25:53,471] [INFO] Task succeeded: Blastn
[2023-06-19 02:25:53,476] [INFO] Selected 22 target genomes.
[2023-06-19 02:25:53,476] [INFO] Target genome list was writen to GCA_018607985.1_ASM1860798v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 02:25:53,488] [INFO] Task started: fastANI
[2023-06-19 02:25:53,488] [INFO] Running command: fastANI --query /var/lib/cwl/stg7a63bcc5-6ecf-424f-9346-9bc25de0e6ed/GCA_018607985.1_ASM1860798v1_genomic.fna.gz --refList GCA_018607985.1_ASM1860798v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018607985.1_ASM1860798v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 02:26:03,411] [INFO] Task succeeded: fastANI
[2023-06-19 02:26:03,421] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 02:26:03,421] [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_017856985.1	s__Planktomarina sp017856985	99.4057	554	609	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Planktomarina	95.0	99.41	99.40	0.91	0.87	5	conclusive
GCA_905182325.1	s__Planktomarina sp905182325	81.4292	397	609	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Planktomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905182195.1	s__Planktomarina sp905182195	78.8387	101	609	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Planktomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002698165.1	s__Planktomarina sp002698165	78.0039	159	609	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Planktomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905182425.1	s__Planktomarina sp905182425	77.3266	65	609	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Planktomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000981705.1	s__Planktomarina sp000981705	76.7811	88	609	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Planktomarina	95.0	98.80	98.80	0.86	0.86	2	-
--------------------------------------------------------------------------------
[2023-06-19 02:26:03,423] [INFO] GTDB search result was written to GCA_018607985.1_ASM1860798v1_genomic.fna/result_gtdb.tsv
[2023-06-19 02:26:03,423] [INFO] ===== GTDB Search completed =====
[2023-06-19 02:26:03,426] [INFO] DFAST_QC result json was written to GCA_018607985.1_ASM1860798v1_genomic.fna/dqc_result.json
[2023-06-19 02:26:03,426] [INFO] DFAST_QC completed!
[2023-06-19 02:26:03,426] [INFO] Total running time: 0h0m52s