[2023-03-18 07:29:29,823] [INFO] DFAST_QC pipeline started.
[2023-03-18 07:29:29,824] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 07:29:29,824] [INFO] DQC Reference Directory: /var/lib/cwl/stg8b27eb75-257a-479a-815f-7f0408136671/dqc_reference
[2023-03-18 07:29:30,929] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 07:29:30,929] [INFO] Task started: Prodigal
[2023-03-18 07:29:30,929] [INFO] Running command: cat /var/lib/cwl/stg723f5b07-849d-45c9-b25f-c61659caa0ec/OceanDNA-b22089.fa | prodigal -d OceanDNA-b22089/cds.fna -a OceanDNA-b22089/protein.faa -g 11 -q > /dev/null
[2023-03-18 07:29:43,717] [INFO] Task succeeded: Prodigal
[2023-03-18 07:29:43,718] [INFO] Task started: HMMsearch
[2023-03-18 07:29:43,718] [INFO] Running command: hmmsearch --tblout OceanDNA-b22089/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8b27eb75-257a-479a-815f-7f0408136671/dqc_reference/reference_markers.hmm OceanDNA-b22089/protein.faa > /dev/null
[2023-03-18 07:29:43,838] [INFO] Task succeeded: HMMsearch
[2023-03-18 07:29:43,839] [WARNING] Found 1/6 markers. [/var/lib/cwl/stg723f5b07-849d-45c9-b25f-c61659caa0ec/OceanDNA-b22089.fa]
[2023-03-18 07:29:43,853] [INFO] Query marker FASTA was written to OceanDNA-b22089/markers.fasta
[2023-03-18 07:29:43,853] [INFO] Task started: Blastn
[2023-03-18 07:29:43,853] [INFO] Running command: blastn -query OceanDNA-b22089/markers.fasta -db /var/lib/cwl/stg8b27eb75-257a-479a-815f-7f0408136671/dqc_reference/reference_markers.fasta -out OceanDNA-b22089/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 07:29:44,260] [INFO] Task succeeded: Blastn
[2023-03-18 07:29:44,261] [INFO] Selected 5 target genomes.
[2023-03-18 07:29:44,261] [INFO] Target genome list was writen to OceanDNA-b22089/target_genomes.txt
[2023-03-18 07:29:44,263] [INFO] Task started: fastANI
[2023-03-18 07:29:44,263] [INFO] Running command: fastANI --query /var/lib/cwl/stg723f5b07-849d-45c9-b25f-c61659caa0ec/OceanDNA-b22089.fa --refList OceanDNA-b22089/target_genomes.txt --output OceanDNA-b22089/fastani_result.tsv --threads 1
[2023-03-18 07:29:47,121] [INFO] Task succeeded: fastANI
[2023-03-18 07:29:47,121] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8b27eb75-257a-479a-815f-7f0408136671/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 07:29:47,121] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8b27eb75-257a-479a-815f-7f0408136671/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 07:29:47,125] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 07:29:47,125] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 07:29:47,125] [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
Algisphaera agarilytica	strain=DSM 103725	GCA_014207595.1	1385975	1385975	type	True	76.8379	95	338	95	below_threshold
Phycisphaera mikurensis	strain=NBRC 102666	GCA_000284115.1	547188	547188	type	True	76.8103	155	338	95	below_threshold
Phycisphaera mikurensis	strain=DSM 103959	GCA_014207395.1	547188	547188	type	True	76.7926	155	338	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 07:29:47,125] [INFO] DFAST Taxonomy check result was written to OceanDNA-b22089/tc_result.tsv
[2023-03-18 07:29:47,126] [INFO] ===== Taxonomy check completed =====
[2023-03-18 07:29:47,126] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 07:29:47,126] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8b27eb75-257a-479a-815f-7f0408136671/dqc_reference/checkm_data
[2023-03-18 07:29:47,126] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 07:29:47,130] [INFO] Task started: CheckM
[2023-03-18 07:29:47,130] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b22089/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b22089/checkm_input OceanDNA-b22089/checkm_result
[2023-03-18 07:30:22,123] [INFO] Task succeeded: CheckM
[2023-03-18 07:30:22,123] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 68.13%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-18 07:30:22,125] [INFO] ===== Completeness check finished =====
[2023-03-18 07:30:22,125] [INFO] ===== Start GTDB Search =====
[2023-03-18 07:30:22,126] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b22089/markers.fasta)
[2023-03-18 07:30:22,126] [INFO] Task started: Blastn
[2023-03-18 07:30:22,126] [INFO] Running command: blastn -query OceanDNA-b22089/markers.fasta -db /var/lib/cwl/stg8b27eb75-257a-479a-815f-7f0408136671/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b22089/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 07:30:22,485] [INFO] Task succeeded: Blastn
[2023-03-18 07:30:22,486] [INFO] Selected 5 target genomes.
[2023-03-18 07:30:22,486] [INFO] Target genome list was writen to OceanDNA-b22089/target_genomes_gtdb.txt
[2023-03-18 07:30:22,536] [INFO] Task started: fastANI
[2023-03-18 07:30:22,537] [INFO] Running command: fastANI --query /var/lib/cwl/stg723f5b07-849d-45c9-b25f-c61659caa0ec/OceanDNA-b22089.fa --refList OceanDNA-b22089/target_genomes_gtdb.txt --output OceanDNA-b22089/fastani_result_gtdb.tsv --threads 1
[2023-03-18 07:30:25,837] [INFO] Task succeeded: fastANI
[2023-03-18 07:30:25,841] [INFO] Found 4 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 07:30:25,841] [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
GCF_014207595.1	s__Algisphaera agarilytica	76.8606	94	338	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__Phycisphaeraceae;g__Algisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000284115.1	s__Phycisphaera mikurensis	76.7655	158	338	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__Phycisphaeraceae;g__Phycisphaera	95.0	99.99	99.99	1.00	1.00	2	-
GCA_016125215.1	s__RI-382 sp016125215	76.0159	50	338	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__Phycisphaeraceae;g__RI-382	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002686995.1	s__GCA-2686995 sp002686995	75.0984	56	338	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__Phycisphaeraceae;g__GCA-2686995	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 07:30:25,841] [INFO] GTDB search result was written to OceanDNA-b22089/result_gtdb.tsv
[2023-03-18 07:30:25,841] [INFO] ===== GTDB Search completed =====
[2023-03-18 07:30:25,842] [INFO] DFAST_QC result json was written to OceanDNA-b22089/dqc_result.json
[2023-03-18 07:30:25,842] [INFO] DFAST_QC completed!
[2023-03-18 07:30:25,842] [INFO] Total running time: 0h0m56s