[2023-03-19 02:56:19,910] [INFO] DFAST_QC pipeline started.
[2023-03-19 02:56:19,911] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 02:56:19,911] [INFO] DQC Reference Directory: /var/lib/cwl/stge0c8b905-d784-4370-97e3-fd09dc621c08/dqc_reference
[2023-03-19 02:56:21,032] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 02:56:21,032] [INFO] Task started: Prodigal
[2023-03-19 02:56:21,032] [INFO] Running command: cat /var/lib/cwl/stga8b7cb1b-6dec-4057-aa57-6c314fa3875b/OceanDNA-b13508.fa | prodigal -d OceanDNA-b13508/cds.fna -a OceanDNA-b13508/protein.faa -g 11 -q > /dev/null
[2023-03-19 02:56:24,773] [INFO] Task succeeded: Prodigal
[2023-03-19 02:56:24,773] [INFO] Task started: HMMsearch
[2023-03-19 02:56:24,773] [INFO] Running command: hmmsearch --tblout OceanDNA-b13508/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge0c8b905-d784-4370-97e3-fd09dc621c08/dqc_reference/reference_markers.hmm OceanDNA-b13508/protein.faa > /dev/null
[2023-03-19 02:56:24,937] [INFO] Task succeeded: HMMsearch
[2023-03-19 02:56:24,937] [WARNING] Found 5/6 markers. [/var/lib/cwl/stga8b7cb1b-6dec-4057-aa57-6c314fa3875b/OceanDNA-b13508.fa]
[2023-03-19 02:56:24,946] [INFO] Query marker FASTA was written to OceanDNA-b13508/markers.fasta
[2023-03-19 02:56:24,947] [INFO] Task started: Blastn
[2023-03-19 02:56:24,948] [INFO] Running command: blastn -query OceanDNA-b13508/markers.fasta -db /var/lib/cwl/stge0c8b905-d784-4370-97e3-fd09dc621c08/dqc_reference/reference_markers.fasta -out OceanDNA-b13508/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 02:56:25,533] [INFO] Task succeeded: Blastn
[2023-03-19 02:56:25,534] [INFO] Selected 10 target genomes.
[2023-03-19 02:56:25,534] [INFO] Target genome list was writen to OceanDNA-b13508/target_genomes.txt
[2023-03-19 02:56:25,542] [INFO] Task started: fastANI
[2023-03-19 02:56:25,543] [INFO] Running command: fastANI --query /var/lib/cwl/stga8b7cb1b-6dec-4057-aa57-6c314fa3875b/OceanDNA-b13508.fa --refList OceanDNA-b13508/target_genomes.txt --output OceanDNA-b13508/fastani_result.tsv --threads 1
[2023-03-19 02:56:29,340] [INFO] Task succeeded: fastANI
[2023-03-19 02:56:29,340] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge0c8b905-d784-4370-97e3-fd09dc621c08/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 02:56:29,341] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge0c8b905-d784-4370-97e3-fd09dc621c08/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 02:56:29,341] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 02:56:29,341] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 02:56:29,341] [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
--------------------------------------------------------------------------------
[2023-03-19 02:56:29,341] [INFO] DFAST Taxonomy check result was written to OceanDNA-b13508/tc_result.tsv
[2023-03-19 02:56:29,341] [INFO] ===== Taxonomy check completed =====
[2023-03-19 02:56:29,341] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 02:56:29,341] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge0c8b905-d784-4370-97e3-fd09dc621c08/dqc_reference/checkm_data
[2023-03-19 02:56:29,394] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 02:56:29,396] [INFO] Task started: CheckM
[2023-03-19 02:56:29,396] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b13508/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b13508/checkm_input OceanDNA-b13508/checkm_result
[2023-03-19 02:56:46,075] [INFO] Task succeeded: CheckM
[2023-03-19 02:56:46,075] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 61.14%
Contamintation: 0.38%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-19 02:56:46,077] [INFO] ===== Completeness check finished =====
[2023-03-19 02:56:46,077] [INFO] ===== Start GTDB Search =====
[2023-03-19 02:56:46,077] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b13508/markers.fasta)
[2023-03-19 02:56:46,078] [INFO] Task started: Blastn
[2023-03-19 02:56:46,079] [INFO] Running command: blastn -query OceanDNA-b13508/markers.fasta -db /var/lib/cwl/stge0c8b905-d784-4370-97e3-fd09dc621c08/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b13508/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 02:56:46,827] [INFO] Task succeeded: Blastn
[2023-03-19 02:56:46,827] [INFO] Selected 13 target genomes.
[2023-03-19 02:56:46,827] [INFO] Target genome list was writen to OceanDNA-b13508/target_genomes_gtdb.txt
[2023-03-19 02:56:46,891] [INFO] Task started: fastANI
[2023-03-19 02:56:46,891] [INFO] Running command: fastANI --query /var/lib/cwl/stga8b7cb1b-6dec-4057-aa57-6c314fa3875b/OceanDNA-b13508.fa --refList OceanDNA-b13508/target_genomes_gtdb.txt --output OceanDNA-b13508/fastani_result_gtdb.tsv --threads 1
[2023-03-19 02:56:52,009] [INFO] Task succeeded: fastANI
[2023-03-19 02:56:52,012] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 02:56:52,012] [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_002346435.1	s__UBA11657 sp002346435	87.3281	157	188	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__UBA11657;g__UBA11657	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002377585.1	s__UBA11657 sp002377585	86.0626	166	188	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__UBA11657;g__UBA11657	95.0	99.07	98.64	0.89	0.85	4	-
GCA_002311455.1	s__UBA11657 sp002311455	80.8917	136	188	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__UBA11657;g__UBA11657	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 02:56:52,012] [INFO] GTDB search result was written to OceanDNA-b13508/result_gtdb.tsv
[2023-03-19 02:56:52,012] [INFO] ===== GTDB Search completed =====
[2023-03-19 02:56:52,013] [INFO] DFAST_QC result json was written to OceanDNA-b13508/dqc_result.json
[2023-03-19 02:56:52,013] [INFO] DFAST_QC completed!
[2023-03-19 02:56:52,013] [INFO] Total running time: 0h0m32s