[2023-03-18 01:08:39,194] [INFO] DFAST_QC pipeline started.
[2023-03-18 01:08:39,194] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 01:08:39,195] [INFO] DQC Reference Directory: /var/lib/cwl/stg5cab4af7-0b35-4cf8-b58b-34a039c064c9/dqc_reference
[2023-03-18 01:08:40,333] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 01:08:40,334] [INFO] Task started: Prodigal
[2023-03-18 01:08:40,334] [INFO] Running command: cat /var/lib/cwl/stga9e6c5a6-e946-4c36-a297-1d2d5ee00fa6/OceanDNA-b46880.fa | prodigal -d OceanDNA-b46880/cds.fna -a OceanDNA-b46880/protein.faa -g 11 -q > /dev/null
[2023-03-18 01:09:02,454] [INFO] Task succeeded: Prodigal
[2023-03-18 01:09:02,454] [INFO] Task started: HMMsearch
[2023-03-18 01:09:02,454] [INFO] Running command: hmmsearch --tblout OceanDNA-b46880/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5cab4af7-0b35-4cf8-b58b-34a039c064c9/dqc_reference/reference_markers.hmm OceanDNA-b46880/protein.faa > /dev/null
[2023-03-18 01:09:02,661] [INFO] Task succeeded: HMMsearch
[2023-03-18 01:09:02,662] [INFO] Found 6/6 markers.
[2023-03-18 01:09:02,684] [INFO] Query marker FASTA was written to OceanDNA-b46880/markers.fasta
[2023-03-18 01:09:02,685] [INFO] Task started: Blastn
[2023-03-18 01:09:02,685] [INFO] Running command: blastn -query OceanDNA-b46880/markers.fasta -db /var/lib/cwl/stg5cab4af7-0b35-4cf8-b58b-34a039c064c9/dqc_reference/reference_markers.fasta -out OceanDNA-b46880/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 01:09:03,214] [INFO] Task succeeded: Blastn
[2023-03-18 01:09:03,218] [INFO] Selected 20 target genomes.
[2023-03-18 01:09:03,219] [INFO] Target genome list was writen to OceanDNA-b46880/target_genomes.txt
[2023-03-18 01:09:03,232] [INFO] Task started: fastANI
[2023-03-18 01:09:03,232] [INFO] Running command: fastANI --query /var/lib/cwl/stga9e6c5a6-e946-4c36-a297-1d2d5ee00fa6/OceanDNA-b46880.fa --refList OceanDNA-b46880/target_genomes.txt --output OceanDNA-b46880/fastani_result.tsv --threads 1
[2023-03-18 01:09:13,793] [INFO] Task succeeded: fastANI
[2023-03-18 01:09:13,794] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5cab4af7-0b35-4cf8-b58b-34a039c064c9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 01:09:13,794] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5cab4af7-0b35-4cf8-b58b-34a039c064c9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 01:09:13,797] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 01:09:13,798] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 01:09:13,798] [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
Oceaniferula marina	strain=N1E253	GCA_013391475.1	2748318	2748318	type	True	76.2692	82	900	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 01:09:13,800] [INFO] DFAST Taxonomy check result was written to OceanDNA-b46880/tc_result.tsv
[2023-03-18 01:09:13,802] [INFO] ===== Taxonomy check completed =====
[2023-03-18 01:09:13,802] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 01:09:13,803] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5cab4af7-0b35-4cf8-b58b-34a039c064c9/dqc_reference/checkm_data
[2023-03-18 01:09:13,804] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 01:09:13,813] [INFO] Task started: CheckM
[2023-03-18 01:09:13,813] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b46880/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b46880/checkm_input OceanDNA-b46880/checkm_result
[2023-03-18 01:10:11,745] [INFO] Task succeeded: CheckM
[2023-03-18 01:10:11,745] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 01:10:11,748] [INFO] ===== Completeness check finished =====
[2023-03-18 01:10:11,748] [INFO] ===== Start GTDB Search =====
[2023-03-18 01:10:11,748] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b46880/markers.fasta)
[2023-03-18 01:10:11,749] [INFO] Task started: Blastn
[2023-03-18 01:10:11,749] [INFO] Running command: blastn -query OceanDNA-b46880/markers.fasta -db /var/lib/cwl/stg5cab4af7-0b35-4cf8-b58b-34a039c064c9/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b46880/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 01:10:12,489] [INFO] Task succeeded: Blastn
[2023-03-18 01:10:12,489] [INFO] Selected 26 target genomes.
[2023-03-18 01:10:12,490] [INFO] Target genome list was writen to OceanDNA-b46880/target_genomes_gtdb.txt
[2023-03-18 01:10:12,541] [INFO] Task started: fastANI
[2023-03-18 01:10:12,541] [INFO] Running command: fastANI --query /var/lib/cwl/stga9e6c5a6-e946-4c36-a297-1d2d5ee00fa6/OceanDNA-b46880.fa --refList OceanDNA-b46880/target_genomes_gtdb.txt --output OceanDNA-b46880/fastani_result_gtdb.tsv --threads 1
[2023-03-18 01:10:26,185] [INFO] Task succeeded: fastANI
[2023-03-18 01:10:26,189] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 01:10:26,190] [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_013041925.1	s__UBA985 sp013041925	77.0676	113	900	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__UBA985	95.0	100.00	100.00	1.00	1.00	2	-
GCA_016811075.1	s__UBA985 sp016811075	76.9297	112	900	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__UBA985	95.0	99.37	98.74	0.97	0.95	3	-
GCA_003527555.1	s__UBA985 sp003527555	76.6691	80	900	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__UBA985	95.0	98.70	97.71	0.76	0.72	4	-
GCA_018676385.1	s__UBA985 sp018676385	76.3223	78	900	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__UBA985	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013391475.1	s__UBA985 sp013391475	76.2649	81	900	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__UBA985	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 01:10:26,190] [INFO] GTDB search result was written to OceanDNA-b46880/result_gtdb.tsv
[2023-03-18 01:10:26,190] [INFO] ===== GTDB Search completed =====
[2023-03-18 01:10:26,191] [INFO] DFAST_QC result json was written to OceanDNA-b46880/dqc_result.json
[2023-03-18 01:10:26,191] [INFO] DFAST_QC completed!
[2023-03-18 01:10:26,191] [INFO] Total running time: 0h1m47s