[2023-03-17 11:29:30,394] [INFO] DFAST_QC pipeline started.
[2023-03-17 11:29:30,394] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 11:29:30,394] [INFO] DQC Reference Directory: /var/lib/cwl/stge081bc48-f826-4107-9ab6-33449221df29/dqc_reference
[2023-03-17 11:29:31,493] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 11:29:31,494] [INFO] Task started: Prodigal
[2023-03-17 11:29:31,494] [INFO] Running command: cat /var/lib/cwl/stg35791d53-bdb3-4185-8323-19555b1d6074/OceanDNA-b6200.fa | prodigal -d OceanDNA-b6200/cds.fna -a OceanDNA-b6200/protein.faa -g 11 -q > /dev/null
[2023-03-17 11:29:46,682] [INFO] Task succeeded: Prodigal
[2023-03-17 11:29:46,682] [INFO] Task started: HMMsearch
[2023-03-17 11:29:46,682] [INFO] Running command: hmmsearch --tblout OceanDNA-b6200/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge081bc48-f826-4107-9ab6-33449221df29/dqc_reference/reference_markers.hmm OceanDNA-b6200/protein.faa > /dev/null
[2023-03-17 11:29:46,853] [INFO] Task succeeded: HMMsearch
[2023-03-17 11:29:46,854] [INFO] Found 6/6 markers.
[2023-03-17 11:29:46,868] [INFO] Query marker FASTA was written to OceanDNA-b6200/markers.fasta
[2023-03-17 11:29:46,870] [INFO] Task started: Blastn
[2023-03-17 11:29:46,870] [INFO] Running command: blastn -query OceanDNA-b6200/markers.fasta -db /var/lib/cwl/stge081bc48-f826-4107-9ab6-33449221df29/dqc_reference/reference_markers.fasta -out OceanDNA-b6200/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 11:29:47,410] [INFO] Task succeeded: Blastn
[2023-03-17 11:29:47,411] [INFO] Selected 29 target genomes.
[2023-03-17 11:29:47,411] [INFO] Target genome list was writen to OceanDNA-b6200/target_genomes.txt
[2023-03-17 11:29:47,507] [INFO] Task started: fastANI
[2023-03-17 11:29:47,507] [INFO] Running command: fastANI --query /var/lib/cwl/stg35791d53-bdb3-4185-8323-19555b1d6074/OceanDNA-b6200.fa --refList OceanDNA-b6200/target_genomes.txt --output OceanDNA-b6200/fastani_result.tsv --threads 1
[2023-03-17 11:30:04,266] [INFO] Task succeeded: fastANI
[2023-03-17 11:30:04,267] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge081bc48-f826-4107-9ab6-33449221df29/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 11:30:04,267] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge081bc48-f826-4107-9ab6-33449221df29/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 11:30:04,271] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 11:30:04,271] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 11:30:04,271] [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
Lutibacter citreus	strain=1KV19	GCA_003260195.1	2138210	2138210	type	True	76.5266	55	657	95	below_threshold
Lutibacter oceani	strain=JCM30924	GCA_003426875.1	1853311	1853311	type	True	76.5121	57	657	95	below_threshold
Lutibacter oceani	strain=325-5	GCA_003384935.1	1853311	1853311	type	True	76.4777	58	657	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 11:30:04,272] [INFO] DFAST Taxonomy check result was written to OceanDNA-b6200/tc_result.tsv
[2023-03-17 11:30:04,272] [INFO] ===== Taxonomy check completed =====
[2023-03-17 11:30:04,272] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 11:30:04,272] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge081bc48-f826-4107-9ab6-33449221df29/dqc_reference/checkm_data
[2023-03-17 11:30:04,273] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 11:30:04,649] [INFO] Task started: CheckM
[2023-03-17 11:30:04,649] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b6200/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b6200/checkm_input OceanDNA-b6200/checkm_result
[2023-03-17 11:30:45,759] [INFO] Task succeeded: CheckM
[2023-03-17 11:30:45,760] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 11:30:45,782] [INFO] ===== Completeness check finished =====
[2023-03-17 11:30:45,782] [INFO] ===== Start GTDB Search =====
[2023-03-17 11:30:45,782] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b6200/markers.fasta)
[2023-03-17 11:30:45,783] [INFO] Task started: Blastn
[2023-03-17 11:30:45,783] [INFO] Running command: blastn -query OceanDNA-b6200/markers.fasta -db /var/lib/cwl/stge081bc48-f826-4107-9ab6-33449221df29/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b6200/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 11:30:46,541] [INFO] Task succeeded: Blastn
[2023-03-17 11:30:46,548] [INFO] Selected 32 target genomes.
[2023-03-17 11:30:46,548] [INFO] Target genome list was writen to OceanDNA-b6200/target_genomes_gtdb.txt
[2023-03-17 11:30:46,602] [INFO] Task started: fastANI
[2023-03-17 11:30:46,602] [INFO] Running command: fastANI --query /var/lib/cwl/stg35791d53-bdb3-4185-8323-19555b1d6074/OceanDNA-b6200.fa --refList OceanDNA-b6200/target_genomes_gtdb.txt --output OceanDNA-b6200/fastani_result_gtdb.tsv --threads 1
[2023-03-17 11:31:03,445] [INFO] Task succeeded: fastANI
[2023-03-17 11:31:03,449] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 11:31:03,449] [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
GCF_012524075.1	s__Lutibacter sp012524075	76.6731	58	657	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016342705.1	s__Lutibacter sp016342705	76.6276	50	657	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003260195.1	s__Lutibacter citreus	76.5266	55	657	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003384935.1	s__Lutibacter oceani	76.4777	58	657	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCA_001800975.1	s__Lutibacter sp001800975	76.38	50	657	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 11:31:03,449] [INFO] GTDB search result was written to OceanDNA-b6200/result_gtdb.tsv
[2023-03-17 11:31:03,449] [INFO] ===== GTDB Search completed =====
[2023-03-17 11:31:03,450] [INFO] DFAST_QC result json was written to OceanDNA-b6200/dqc_result.json
[2023-03-17 11:31:03,450] [INFO] DFAST_QC completed!
[2023-03-17 11:31:03,450] [INFO] Total running time: 0h1m33s