[2023-03-15 22:23:01,942] [INFO] DFAST_QC pipeline started.
[2023-03-15 22:23:01,947] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 22:23:01,947] [INFO] DQC Reference Directory: /var/lib/cwl/stgccdb5818-dbe6-4f9d-b8bc-6f8bacb2f8e2/dqc_reference
[2023-03-15 22:23:03,675] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 22:23:03,675] [INFO] Task started: Prodigal
[2023-03-15 22:23:03,675] [INFO] Running command: cat /var/lib/cwl/stg3869ab6e-0176-478f-98d6-49a12146115f/OceanDNA-b22882.fa | prodigal -d OceanDNA-b22882/cds.fna -a OceanDNA-b22882/protein.faa -g 11 -q > /dev/null
[2023-03-15 22:23:46,035] [INFO] Task succeeded: Prodigal
[2023-03-15 22:23:46,035] [INFO] Task started: HMMsearch
[2023-03-15 22:23:46,035] [INFO] Running command: hmmsearch --tblout OceanDNA-b22882/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgccdb5818-dbe6-4f9d-b8bc-6f8bacb2f8e2/dqc_reference/reference_markers.hmm OceanDNA-b22882/protein.faa > /dev/null
[2023-03-15 22:23:46,340] [INFO] Task succeeded: HMMsearch
[2023-03-15 22:23:46,341] [INFO] Found 6/6 markers.
[2023-03-15 22:23:46,381] [INFO] Query marker FASTA was written to OceanDNA-b22882/markers.fasta
[2023-03-15 22:23:46,383] [INFO] Task started: Blastn
[2023-03-15 22:23:46,383] [INFO] Running command: blastn -query OceanDNA-b22882/markers.fasta -db /var/lib/cwl/stgccdb5818-dbe6-4f9d-b8bc-6f8bacb2f8e2/dqc_reference/reference_markers.fasta -out OceanDNA-b22882/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 22:23:46,992] [INFO] Task succeeded: Blastn
[2023-03-15 22:23:46,993] [INFO] Selected 23 target genomes.
[2023-03-15 22:23:46,993] [INFO] Target genome list was writen to OceanDNA-b22882/target_genomes.txt
[2023-03-15 22:23:47,008] [INFO] Task started: fastANI
[2023-03-15 22:23:47,009] [INFO] Running command: fastANI --query /var/lib/cwl/stg3869ab6e-0176-478f-98d6-49a12146115f/OceanDNA-b22882.fa --refList OceanDNA-b22882/target_genomes.txt --output OceanDNA-b22882/fastani_result.tsv --threads 1
[2023-03-15 22:24:08,974] [INFO] Task succeeded: fastANI
[2023-03-15 22:24:08,974] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgccdb5818-dbe6-4f9d-b8bc-6f8bacb2f8e2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 22:24:08,974] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgccdb5818-dbe6-4f9d-b8bc-6f8bacb2f8e2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 22:24:08,978] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 22:24:08,978] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 22:24:08,978] [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
Fuerstiella marisgermanici	strain=NH11	GCA_001983935.1	1891926	1891926	type	True	76.345	299	2290	95	below_threshold
Maioricimonas rarisocia	strain=Mal4	GCA_007747795.1	2528026	2528026	type	True	75.1338	55	2290	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 22:24:08,978] [INFO] DFAST Taxonomy check result was written to OceanDNA-b22882/tc_result.tsv
[2023-03-15 22:24:08,978] [INFO] ===== Taxonomy check completed =====
[2023-03-15 22:24:08,979] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 22:24:08,979] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgccdb5818-dbe6-4f9d-b8bc-6f8bacb2f8e2/dqc_reference/checkm_data
[2023-03-15 22:24:08,979] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 22:24:08,988] [INFO] Task started: CheckM
[2023-03-15 22:24:08,988] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b22882/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b22882/checkm_input OceanDNA-b22882/checkm_result
[2023-03-15 22:25:52,021] [INFO] Task succeeded: CheckM
[2023-03-15 22:25:52,021] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.52%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 22:25:52,026] [INFO] ===== Completeness check finished =====
[2023-03-15 22:25:52,026] [INFO] ===== Start GTDB Search =====
[2023-03-15 22:25:52,026] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b22882/markers.fasta)
[2023-03-15 22:25:52,026] [INFO] Task started: Blastn
[2023-03-15 22:25:52,026] [INFO] Running command: blastn -query OceanDNA-b22882/markers.fasta -db /var/lib/cwl/stgccdb5818-dbe6-4f9d-b8bc-6f8bacb2f8e2/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b22882/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 22:25:52,732] [INFO] Task succeeded: Blastn
[2023-03-15 22:25:52,733] [INFO] Selected 24 target genomes.
[2023-03-15 22:25:52,733] [INFO] Target genome list was writen to OceanDNA-b22882/target_genomes_gtdb.txt
[2023-03-15 22:25:52,836] [INFO] Task started: fastANI
[2023-03-15 22:25:52,836] [INFO] Running command: fastANI --query /var/lib/cwl/stg3869ab6e-0176-478f-98d6-49a12146115f/OceanDNA-b22882.fa --refList OceanDNA-b22882/target_genomes_gtdb.txt --output OceanDNA-b22882/fastani_result_gtdb.tsv --threads 1
[2023-03-15 22:26:17,200] [INFO] Task succeeded: fastANI
[2023-03-15 22:26:17,206] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 22:26:17,206] [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_014238335.1	s__Fuerstia sp014238335	76.5527	248	2290	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Fuerstia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001983935.1	s__Fuerstia marisgermanicae	76.3474	298	2290	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Fuerstia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016795105.1	s__F1-80-MAGs062 sp016795105	75.842	53	2290	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__F1-80-MAGs062	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016795145.1	s__SXXK01 sp016795145	75.4365	84	2290	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__SXXK01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003670925.1	s__SXXK01 sp003670925	75.3939	70	2290	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__SXXK01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903924405.1	s__SXXK01 sp903924405	75.2934	52	2290	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__SXXK01	95.0	99.71	99.71	0.88	0.88	2	-
GCA_016124895.1	s__JABMPE01 sp016124895	75.2371	66	2290	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__JABMPE01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007747795.1	s__Maioricimonas rarisocia	75.149	53	2290	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Maioricimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017795105.1	s__Rubinisphaera sp017795105	74.929	51	2290	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Rubinisphaera	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 22:26:17,206] [INFO] GTDB search result was written to OceanDNA-b22882/result_gtdb.tsv
[2023-03-15 22:26:17,206] [INFO] ===== GTDB Search completed =====
[2023-03-15 22:26:17,207] [INFO] DFAST_QC result json was written to OceanDNA-b22882/dqc_result.json
[2023-03-15 22:26:17,207] [INFO] DFAST_QC completed!
[2023-03-15 22:26:17,207] [INFO] Total running time: 0h3m15s