[2023-03-16 04:38:30,102] [INFO] DFAST_QC pipeline started.
[2023-03-16 04:38:30,103] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 04:38:30,103] [INFO] DQC Reference Directory: /var/lib/cwl/stg36e9abf0-e17f-43f2-b194-4b8e65ceacac/dqc_reference
[2023-03-16 04:38:31,202] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 04:38:31,202] [INFO] Task started: Prodigal
[2023-03-16 04:38:31,203] [INFO] Running command: cat /var/lib/cwl/stg316c8132-562b-4239-a249-62b3c0e8a2e1/OceanDNA-b13510.fa | prodigal -d OceanDNA-b13510/cds.fna -a OceanDNA-b13510/protein.faa -g 11 -q > /dev/null
[2023-03-16 04:38:38,239] [INFO] Task succeeded: Prodigal
[2023-03-16 04:38:38,240] [INFO] Task started: HMMsearch
[2023-03-16 04:38:38,240] [INFO] Running command: hmmsearch --tblout OceanDNA-b13510/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg36e9abf0-e17f-43f2-b194-4b8e65ceacac/dqc_reference/reference_markers.hmm OceanDNA-b13510/protein.faa > /dev/null
[2023-03-16 04:38:38,441] [INFO] Task succeeded: HMMsearch
[2023-03-16 04:38:38,442] [INFO] Found 6/6 markers.
[2023-03-16 04:38:38,455] [INFO] Query marker FASTA was written to OceanDNA-b13510/markers.fasta
[2023-03-16 04:38:38,455] [INFO] Task started: Blastn
[2023-03-16 04:38:38,455] [INFO] Running command: blastn -query OceanDNA-b13510/markers.fasta -db /var/lib/cwl/stg36e9abf0-e17f-43f2-b194-4b8e65ceacac/dqc_reference/reference_markers.fasta -out OceanDNA-b13510/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 04:38:38,973] [INFO] Task succeeded: Blastn
[2023-03-16 04:38:38,974] [INFO] Selected 10 target genomes.
[2023-03-16 04:38:38,974] [INFO] Target genome list was writen to OceanDNA-b13510/target_genomes.txt
[2023-03-16 04:38:38,980] [INFO] Task started: fastANI
[2023-03-16 04:38:38,980] [INFO] Running command: fastANI --query /var/lib/cwl/stg316c8132-562b-4239-a249-62b3c0e8a2e1/OceanDNA-b13510.fa --refList OceanDNA-b13510/target_genomes.txt --output OceanDNA-b13510/fastani_result.tsv --threads 1
[2023-03-16 04:38:42,319] [INFO] Task succeeded: fastANI
[2023-03-16 04:38:42,320] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg36e9abf0-e17f-43f2-b194-4b8e65ceacac/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 04:38:42,320] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg36e9abf0-e17f-43f2-b194-4b8e65ceacac/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 04:38:42,320] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 04:38:42,320] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 04:38:42,320] [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
--------------------------------------------------------------------------------
[2023-03-16 04:38:42,320] [INFO] DFAST Taxonomy check result was written to OceanDNA-b13510/tc_result.tsv
[2023-03-16 04:38:42,320] [INFO] ===== Taxonomy check completed =====
[2023-03-16 04:38:42,321] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 04:38:42,321] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg36e9abf0-e17f-43f2-b194-4b8e65ceacac/dqc_reference/checkm_data
[2023-03-16 04:38:42,331] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 04:38:42,334] [INFO] Task started: CheckM
[2023-03-16 04:38:42,334] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b13510/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b13510/checkm_input OceanDNA-b13510/checkm_result
[2023-03-16 04:39:05,369] [INFO] Task succeeded: CheckM
[2023-03-16 04:39:05,370] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 80.98%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 04:39:05,371] [INFO] ===== Completeness check finished =====
[2023-03-16 04:39:05,371] [INFO] ===== Start GTDB Search =====
[2023-03-16 04:39:05,372] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b13510/markers.fasta)
[2023-03-16 04:39:05,373] [INFO] Task started: Blastn
[2023-03-16 04:39:05,373] [INFO] Running command: blastn -query OceanDNA-b13510/markers.fasta -db /var/lib/cwl/stg36e9abf0-e17f-43f2-b194-4b8e65ceacac/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b13510/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 04:39:06,177] [INFO] Task succeeded: Blastn
[2023-03-16 04:39:06,178] [INFO] Selected 14 target genomes.
[2023-03-16 04:39:06,178] [INFO] Target genome list was writen to OceanDNA-b13510/target_genomes_gtdb.txt
[2023-03-16 04:39:06,187] [INFO] Task started: fastANI
[2023-03-16 04:39:06,187] [INFO] Running command: fastANI --query /var/lib/cwl/stg316c8132-562b-4239-a249-62b3c0e8a2e1/OceanDNA-b13510.fa --refList OceanDNA-b13510/target_genomes_gtdb.txt --output OceanDNA-b13510/fastani_result_gtdb.tsv --threads 1
[2023-03-16 04:39:11,978] [INFO] Task succeeded: fastANI
[2023-03-16 04:39:11,981] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 04:39:11,982] [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	88.3264	351	415	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	87.2393	372	415	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	81.8184	296	415	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__UBA11657;g__UBA11657	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 04:39:11,982] [INFO] GTDB search result was written to OceanDNA-b13510/result_gtdb.tsv
[2023-03-16 04:39:11,982] [INFO] ===== GTDB Search completed =====
[2023-03-16 04:39:11,982] [INFO] DFAST_QC result json was written to OceanDNA-b13510/dqc_result.json
[2023-03-16 04:39:11,982] [INFO] DFAST_QC completed!
[2023-03-16 04:39:11,983] [INFO] Total running time: 0h0m42s