[2023-03-17 09:41:39,969] [INFO] DFAST_QC pipeline started.
[2023-03-17 09:41:39,969] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 09:41:39,970] [INFO] DQC Reference Directory: /var/lib/cwl/stg96735bbd-0ab1-4a72-af0b-18fb21ec5541/dqc_reference
[2023-03-17 09:41:41,756] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 09:41:41,756] [INFO] Task started: Prodigal
[2023-03-17 09:41:41,756] [INFO] Running command: cat /var/lib/cwl/stg21d605cd-654a-4982-8eb3-0f5514c45a32/OceanDNA-b24171.fa | prodigal -d OceanDNA-b24171/cds.fna -a OceanDNA-b24171/protein.faa -g 11 -q > /dev/null
[2023-03-17 09:41:49,871] [INFO] Task succeeded: Prodigal
[2023-03-17 09:41:49,871] [INFO] Task started: HMMsearch
[2023-03-17 09:41:49,872] [INFO] Running command: hmmsearch --tblout OceanDNA-b24171/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg96735bbd-0ab1-4a72-af0b-18fb21ec5541/dqc_reference/reference_markers.hmm OceanDNA-b24171/protein.faa > /dev/null
[2023-03-17 09:41:50,013] [INFO] Task succeeded: HMMsearch
[2023-03-17 09:41:50,014] [WARNING] Found 1/6 markers. [/var/lib/cwl/stg21d605cd-654a-4982-8eb3-0f5514c45a32/OceanDNA-b24171.fa]
[2023-03-17 09:41:50,039] [INFO] Query marker FASTA was written to OceanDNA-b24171/markers.fasta
[2023-03-17 09:41:50,039] [INFO] Task started: Blastn
[2023-03-17 09:41:50,039] [INFO] Running command: blastn -query OceanDNA-b24171/markers.fasta -db /var/lib/cwl/stg96735bbd-0ab1-4a72-af0b-18fb21ec5541/dqc_reference/reference_markers.fasta -out OceanDNA-b24171/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 09:41:50,459] [INFO] Task succeeded: Blastn
[2023-03-17 09:41:50,464] [INFO] Selected 5 target genomes.
[2023-03-17 09:41:50,464] [INFO] Target genome list was writen to OceanDNA-b24171/target_genomes.txt
[2023-03-17 09:41:50,500] [INFO] Task started: fastANI
[2023-03-17 09:41:50,500] [INFO] Running command: fastANI --query /var/lib/cwl/stg21d605cd-654a-4982-8eb3-0f5514c45a32/OceanDNA-b24171.fa --refList OceanDNA-b24171/target_genomes.txt --output OceanDNA-b24171/fastani_result.tsv --threads 1
[2023-03-17 09:41:55,315] [INFO] Task succeeded: fastANI
[2023-03-17 09:41:55,316] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg96735bbd-0ab1-4a72-af0b-18fb21ec5541/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 09:41:55,316] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg96735bbd-0ab1-4a72-af0b-18fb21ec5541/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 09:41:55,320] [INFO] Found 4 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 09:41:55,320] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 09:41:55,321] [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
Stella humosa	strain=ATCC 43930	GCA_006738645.1	94	94	type	True	83.4517	245	283	95	below_threshold
Stella humosa	strain=DSM 5900	GCA_003751345.1	94	94	type	True	83.4421	247	283	95	below_threshold
Azospirillum thiophilum	strain=DSM 21654	GCA_000960825.1	528244	528244	type	True	77.0597	80	283	95	below_threshold
Reyranella soli	strain=NBRC 108950	GCA_007992495.1	1230389	1230389	type	True	76.5797	95	283	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 09:41:55,322] [INFO] DFAST Taxonomy check result was written to OceanDNA-b24171/tc_result.tsv
[2023-03-17 09:41:55,322] [INFO] ===== Taxonomy check completed =====
[2023-03-17 09:41:55,322] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 09:41:55,323] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg96735bbd-0ab1-4a72-af0b-18fb21ec5541/dqc_reference/checkm_data
[2023-03-17 09:41:55,323] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 09:41:55,382] [INFO] Task started: CheckM
[2023-03-17 09:41:55,382] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b24171/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b24171/checkm_input OceanDNA-b24171/checkm_result
[2023-03-17 09:42:20,528] [INFO] Task succeeded: CheckM
[2023-03-17 09:42:20,529] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 38.02%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 09:42:20,553] [INFO] ===== Completeness check finished =====
[2023-03-17 09:42:20,553] [INFO] ===== Start GTDB Search =====
[2023-03-17 09:42:20,553] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b24171/markers.fasta)
[2023-03-17 09:42:20,555] [INFO] Task started: Blastn
[2023-03-17 09:42:20,555] [INFO] Running command: blastn -query OceanDNA-b24171/markers.fasta -db /var/lib/cwl/stg96735bbd-0ab1-4a72-af0b-18fb21ec5541/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b24171/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 09:42:20,940] [INFO] Task succeeded: Blastn
[2023-03-17 09:42:20,943] [INFO] Selected 5 target genomes.
[2023-03-17 09:42:20,943] [INFO] Target genome list was writen to OceanDNA-b24171/target_genomes_gtdb.txt
[2023-03-17 09:42:21,082] [INFO] Task started: fastANI
[2023-03-17 09:42:21,082] [INFO] Running command: fastANI --query /var/lib/cwl/stg21d605cd-654a-4982-8eb3-0f5514c45a32/OceanDNA-b24171.fa --refList OceanDNA-b24171/target_genomes_gtdb.txt --output OceanDNA-b24171/fastani_result_gtdb.tsv --threads 1
[2023-03-17 09:42:24,743] [INFO] Task succeeded: fastANI
[2023-03-17 09:42:24,746] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 09:42:24,746] [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_006738865.1	s__Stella sp006738865	94.7875	276	283	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__ATCC43930;f__Stellaceae;g__Stella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_006739055.1	s__Stella vacuolata	83.8246	248	283	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__ATCC43930;f__Stellaceae;g__Stella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006738645.1	s__Stella humosa	83.4517	245	283	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__ATCC43930;f__Stellaceae;g__Stella	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2023-03-17 09:42:24,748] [INFO] GTDB search result was written to OceanDNA-b24171/result_gtdb.tsv
[2023-03-17 09:42:24,749] [INFO] ===== GTDB Search completed =====
[2023-03-17 09:42:24,752] [INFO] DFAST_QC result json was written to OceanDNA-b24171/dqc_result.json
[2023-03-17 09:42:24,752] [INFO] DFAST_QC completed!
[2023-03-17 09:42:24,752] [INFO] Total running time: 0h0m45s