[2023-03-14 12:59:46,652] [INFO] DFAST_QC pipeline started.
[2023-03-14 12:59:46,652] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 12:59:46,652] [INFO] DQC Reference Directory: /var/lib/cwl/stgde0a7992-44d3-4187-9929-101c61ff4852/dqc_reference
[2023-03-14 12:59:48,647] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 12:59:48,652] [INFO] Task started: Prodigal
[2023-03-14 12:59:48,652] [INFO] Running command: cat /var/lib/cwl/stg35272119-30ac-4571-8cc5-cf53c90d794c/OceanDNA-b22054.fa | prodigal -d OceanDNA-b22054/cds.fna -a OceanDNA-b22054/protein.faa -g 11 -q > /dev/null
[2023-03-14 12:59:58,216] [INFO] Task succeeded: Prodigal
[2023-03-14 12:59:58,216] [INFO] Task started: HMMsearch
[2023-03-14 12:59:58,216] [INFO] Running command: hmmsearch --tblout OceanDNA-b22054/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgde0a7992-44d3-4187-9929-101c61ff4852/dqc_reference/reference_markers.hmm OceanDNA-b22054/protein.faa > /dev/null
[2023-03-14 12:59:58,393] [INFO] Task succeeded: HMMsearch
[2023-03-14 12:59:58,394] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg35272119-30ac-4571-8cc5-cf53c90d794c/OceanDNA-b22054.fa]
[2023-03-14 12:59:58,409] [INFO] Query marker FASTA was written to OceanDNA-b22054/markers.fasta
[2023-03-14 12:59:58,411] [INFO] Task started: Blastn
[2023-03-14 12:59:58,411] [INFO] Running command: blastn -query OceanDNA-b22054/markers.fasta -db /var/lib/cwl/stgde0a7992-44d3-4187-9929-101c61ff4852/dqc_reference/reference_markers.fasta -out OceanDNA-b22054/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 12:59:58,935] [INFO] Task succeeded: Blastn
[2023-03-14 12:59:58,936] [INFO] Selected 7 target genomes.
[2023-03-14 12:59:58,936] [INFO] Target genome list was writen to OceanDNA-b22054/target_genomes.txt
[2023-03-14 12:59:58,942] [INFO] Task started: fastANI
[2023-03-14 12:59:58,943] [INFO] Running command: fastANI --query /var/lib/cwl/stg35272119-30ac-4571-8cc5-cf53c90d794c/OceanDNA-b22054.fa --refList OceanDNA-b22054/target_genomes.txt --output OceanDNA-b22054/fastani_result.tsv --threads 1
[2023-03-14 13:00:02,678] [INFO] Task succeeded: fastANI
[2023-03-14 13:00:02,679] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgde0a7992-44d3-4187-9929-101c61ff4852/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 13:00:02,679] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgde0a7992-44d3-4187-9929-101c61ff4852/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 13:00:02,679] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 13:00:02,679] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-14 13:00:02,679] [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
--------------------------------------------------------------------------------
[2023-03-14 13:00:02,679] [INFO] DFAST Taxonomy check result was written to OceanDNA-b22054/tc_result.tsv
[2023-03-14 13:00:02,679] [INFO] ===== Taxonomy check completed =====
[2023-03-14 13:00:02,680] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 13:00:02,680] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgde0a7992-44d3-4187-9929-101c61ff4852/dqc_reference/checkm_data
[2023-03-14 13:00:02,683] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 13:00:02,757] [INFO] Task started: CheckM
[2023-03-14 13:00:02,757] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b22054/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b22054/checkm_input OceanDNA-b22054/checkm_result
[2023-03-14 13:00:24,368] [INFO] Task succeeded: CheckM
[2023-03-14 13:00:24,368] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 77.48%
Contamintation: 5.15%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-14 13:00:24,370] [INFO] ===== Completeness check finished =====
[2023-03-14 13:00:24,370] [INFO] ===== Start GTDB Search =====
[2023-03-14 13:00:24,370] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b22054/markers.fasta)
[2023-03-14 13:00:24,371] [INFO] Task started: Blastn
[2023-03-14 13:00:24,372] [INFO] Running command: blastn -query OceanDNA-b22054/markers.fasta -db /var/lib/cwl/stgde0a7992-44d3-4187-9929-101c61ff4852/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b22054/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 13:00:25,062] [INFO] Task succeeded: Blastn
[2023-03-14 13:00:25,063] [INFO] Selected 13 target genomes.
[2023-03-14 13:00:25,063] [INFO] Target genome list was writen to OceanDNA-b22054/target_genomes_gtdb.txt
[2023-03-14 13:00:25,073] [INFO] Task started: fastANI
[2023-03-14 13:00:25,074] [INFO] Running command: fastANI --query /var/lib/cwl/stg35272119-30ac-4571-8cc5-cf53c90d794c/OceanDNA-b22054.fa --refList OceanDNA-b22054/target_genomes_gtdb.txt --output OceanDNA-b22054/fastani_result_gtdb.tsv --threads 1
[2023-03-14 13:00:31,316] [INFO] Task succeeded: fastANI
[2023-03-14 13:00:31,321] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-14 13:00:31,322] [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_007859995.1	s__Scalindua rubra_B	84.177	193	319	d__Bacteria;p__Planctomycetota;c__Brocadiae;o__Brocadiales;f__Scalinduaceae;g__Scalindua	95.0	99.90	99.85	0.94	0.91	3	-
GCA_018648405.1	s__Scalindua sp018648405	84.1409	204	319	d__Bacteria;p__Planctomycetota;c__Brocadiae;o__Brocadiales;f__Scalinduaceae;g__Scalindua	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018670825.1	s__Scalindua sp018670825	82.52	240	319	d__Bacteria;p__Planctomycetota;c__Brocadiae;o__Brocadiales;f__Scalinduaceae;g__Scalindua	95.0	99.80	99.75	0.89	0.87	5	-
GCF_002443295.1	s__Scalindua japonica	79.6347	204	319	d__Bacteria;p__Planctomycetota;c__Brocadiae;o__Brocadiales;f__Scalinduaceae;g__Scalindua	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018263435.1	s__Scalindua arabica	77.8442	105	319	d__Bacteria;p__Planctomycetota;c__Brocadiae;o__Brocadiales;f__Scalinduaceae;g__Scalindua	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001828595.1	s__Scalindua sp001828595	77.4825	91	319	d__Bacteria;p__Planctomycetota;c__Brocadiae;o__Brocadiales;f__Scalinduaceae;g__Scalindua	95.0	99.23	99.13	0.79	0.77	3	-
GCA_001723765.1	s__Scalindua rubra_A	76.7382	76	319	d__Bacteria;p__Planctomycetota;c__Brocadiae;o__Brocadiales;f__Scalinduaceae;g__Scalindua	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-14 13:00:31,322] [INFO] GTDB search result was written to OceanDNA-b22054/result_gtdb.tsv
[2023-03-14 13:00:31,322] [INFO] ===== GTDB Search completed =====
[2023-03-14 13:00:31,323] [INFO] DFAST_QC result json was written to OceanDNA-b22054/dqc_result.json
[2023-03-14 13:00:31,323] [INFO] DFAST_QC completed!
[2023-03-14 13:00:31,323] [INFO] Total running time: 0h0m45s