[2023-03-18 21:15:29,378] [INFO] DFAST_QC pipeline started.
[2023-03-18 21:15:29,379] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 21:15:29,379] [INFO] DQC Reference Directory: /var/lib/cwl/stg539cc6f6-5041-4dd1-a776-a89c14e8fda3/dqc_reference
[2023-03-18 21:15:31,042] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 21:15:31,044] [INFO] Task started: Prodigal
[2023-03-18 21:15:31,044] [INFO] Running command: cat /var/lib/cwl/stga3df620f-09c8-439d-a8f5-640c11aee1eb/OceanDNA-b425.fa | prodigal -d OceanDNA-b425/cds.fna -a OceanDNA-b425/protein.faa -g 11 -q > /dev/null
[2023-03-18 21:15:43,578] [INFO] Task succeeded: Prodigal
[2023-03-18 21:15:43,579] [INFO] Task started: HMMsearch
[2023-03-18 21:15:43,579] [INFO] Running command: hmmsearch --tblout OceanDNA-b425/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg539cc6f6-5041-4dd1-a776-a89c14e8fda3/dqc_reference/reference_markers.hmm OceanDNA-b425/protein.faa > /dev/null
[2023-03-18 21:15:43,757] [INFO] Task succeeded: HMMsearch
[2023-03-18 21:15:43,757] [INFO] Found 6/6 markers.
[2023-03-18 21:15:43,783] [INFO] Query marker FASTA was written to OceanDNA-b425/markers.fasta
[2023-03-18 21:15:43,785] [INFO] Task started: Blastn
[2023-03-18 21:15:43,785] [INFO] Running command: blastn -query OceanDNA-b425/markers.fasta -db /var/lib/cwl/stg539cc6f6-5041-4dd1-a776-a89c14e8fda3/dqc_reference/reference_markers.fasta -out OceanDNA-b425/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 21:15:44,308] [INFO] Task succeeded: Blastn
[2023-03-18 21:15:44,311] [INFO] Selected 20 target genomes.
[2023-03-18 21:15:44,311] [INFO] Target genome list was writen to OceanDNA-b425/target_genomes.txt
[2023-03-18 21:15:44,325] [INFO] Task started: fastANI
[2023-03-18 21:15:44,325] [INFO] Running command: fastANI --query /var/lib/cwl/stga3df620f-09c8-439d-a8f5-640c11aee1eb/OceanDNA-b425.fa --refList OceanDNA-b425/target_genomes.txt --output OceanDNA-b425/fastani_result.tsv --threads 1
[2023-03-18 21:15:57,946] [INFO] Task succeeded: fastANI
[2023-03-18 21:15:57,946] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg539cc6f6-5041-4dd1-a776-a89c14e8fda3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 21:15:57,946] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg539cc6f6-5041-4dd1-a776-a89c14e8fda3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 21:15:57,947] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 21:15:57,947] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 21:15:57,947] [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
--------------------------------------------------------------------------------
[2023-03-18 21:15:57,948] [INFO] DFAST Taxonomy check result was written to OceanDNA-b425/tc_result.tsv
[2023-03-18 21:15:57,948] [INFO] ===== Taxonomy check completed =====
[2023-03-18 21:15:57,948] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 21:15:57,948] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg539cc6f6-5041-4dd1-a776-a89c14e8fda3/dqc_reference/checkm_data
[2023-03-18 21:15:57,951] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 21:15:57,955] [INFO] Task started: CheckM
[2023-03-18 21:15:57,955] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b425/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b425/checkm_input OceanDNA-b425/checkm_result
[2023-03-18 21:16:33,818] [INFO] Task succeeded: CheckM
[2023-03-18 21:16:33,818] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-18 21:16:33,830] [INFO] ===== Completeness check finished =====
[2023-03-18 21:16:33,830] [INFO] ===== Start GTDB Search =====
[2023-03-18 21:16:33,830] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b425/markers.fasta)
[2023-03-18 21:16:33,831] [INFO] Task started: Blastn
[2023-03-18 21:16:33,831] [INFO] Running command: blastn -query OceanDNA-b425/markers.fasta -db /var/lib/cwl/stg539cc6f6-5041-4dd1-a776-a89c14e8fda3/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b425/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 21:16:34,552] [INFO] Task succeeded: Blastn
[2023-03-18 21:16:34,556] [INFO] Selected 11 target genomes.
[2023-03-18 21:16:34,556] [INFO] Target genome list was writen to OceanDNA-b425/target_genomes_gtdb.txt
[2023-03-18 21:16:34,576] [INFO] Task started: fastANI
[2023-03-18 21:16:34,576] [INFO] Running command: fastANI --query /var/lib/cwl/stga3df620f-09c8-439d-a8f5-640c11aee1eb/OceanDNA-b425.fa --refList OceanDNA-b425/target_genomes_gtdb.txt --output OceanDNA-b425/fastani_result_gtdb.tsv --threads 1
[2023-03-18 21:16:38,872] [INFO] Task succeeded: fastANI
[2023-03-18 21:16:38,877] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 21:16:38,878] [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_009694465.1	s__Casp-actino8 sp009694465	94.1146	365	636	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Casp-actino8	95.0	95.85	95.85	0.64	0.64	2	-
GCA_014190215.1	s__Casp-actino8 sp014190215	92.9414	488	636	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Casp-actino8	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009705435.1	s__Casp-actino8 sp009705435	92.4234	422	636	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Casp-actino8	95.0	98.36	98.35	0.80	0.80	3	-
GCA_005801025.1	s__Casp-actino8 sp005801025	90.9478	348	636	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Casp-actino8	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903872155.1	s__Casp-actino8 sp903872155	78.3217	198	636	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Casp-actino8	95.0	98.87	96.83	0.92	0.86	4	-
GCA_001510335.1	s__Casp-actino8 sp001510335	77.9005	120	636	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Casp-actino8	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009700145.1	s__Casp-actino8 sp009700145	77.7331	126	636	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Casp-actino8	95.0	99.51	99.42	0.81	0.73	6	-
--------------------------------------------------------------------------------
[2023-03-18 21:16:38,879] [INFO] GTDB search result was written to OceanDNA-b425/result_gtdb.tsv
[2023-03-18 21:16:38,881] [INFO] ===== GTDB Search completed =====
[2023-03-18 21:16:38,883] [INFO] DFAST_QC result json was written to OceanDNA-b425/dqc_result.json
[2023-03-18 21:16:38,884] [INFO] DFAST_QC completed!
[2023-03-18 21:16:38,884] [INFO] Total running time: 0h1m10s