[2023-03-15 16:03:34,273] [INFO] DFAST_QC pipeline started.
[2023-03-15 16:03:34,274] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 16:03:34,274] [INFO] DQC Reference Directory: /var/lib/cwl/stgf6b1dcba-472f-4880-a03d-08ac8e6b3df5/dqc_reference
[2023-03-15 16:03:35,745] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 16:03:35,745] [INFO] Task started: Prodigal
[2023-03-15 16:03:35,745] [INFO] Running command: cat /var/lib/cwl/stg50ec1a56-8d44-4036-8d9a-e4688e03a6c9/OceanDNA-b33321.fa | prodigal -d OceanDNA-b33321/cds.fna -a OceanDNA-b33321/protein.faa -g 11 -q > /dev/null
[2023-03-15 16:03:57,835] [INFO] Task succeeded: Prodigal
[2023-03-15 16:03:57,835] [INFO] Task started: HMMsearch
[2023-03-15 16:03:57,835] [INFO] Running command: hmmsearch --tblout OceanDNA-b33321/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf6b1dcba-472f-4880-a03d-08ac8e6b3df5/dqc_reference/reference_markers.hmm OceanDNA-b33321/protein.faa > /dev/null
[2023-03-15 16:03:58,053] [INFO] Task succeeded: HMMsearch
[2023-03-15 16:03:58,053] [INFO] Found 6/6 markers.
[2023-03-15 16:03:58,078] [INFO] Query marker FASTA was written to OceanDNA-b33321/markers.fasta
[2023-03-15 16:03:58,080] [INFO] Task started: Blastn
[2023-03-15 16:03:58,080] [INFO] Running command: blastn -query OceanDNA-b33321/markers.fasta -db /var/lib/cwl/stgf6b1dcba-472f-4880-a03d-08ac8e6b3df5/dqc_reference/reference_markers.fasta -out OceanDNA-b33321/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 16:03:58,802] [INFO] Task succeeded: Blastn
[2023-03-15 16:03:58,804] [INFO] Selected 29 target genomes.
[2023-03-15 16:03:58,804] [INFO] Target genome list was writen to OceanDNA-b33321/target_genomes.txt
[2023-03-15 16:03:58,824] [INFO] Task started: fastANI
[2023-03-15 16:03:58,824] [INFO] Running command: fastANI --query /var/lib/cwl/stg50ec1a56-8d44-4036-8d9a-e4688e03a6c9/OceanDNA-b33321.fa --refList OceanDNA-b33321/target_genomes.txt --output OceanDNA-b33321/fastani_result.tsv --threads 1
[2023-03-15 16:04:22,791] [INFO] Task succeeded: fastANI
[2023-03-15 16:04:22,792] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf6b1dcba-472f-4880-a03d-08ac8e6b3df5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 16:04:22,792] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf6b1dcba-472f-4880-a03d-08ac8e6b3df5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 16:04:22,797] [INFO] Found 5 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 16:04:22,797] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 16:04:22,797] [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
Limnobacter alexandrii	strain=LZ-4	GCA_005871185.1	2570352	2570352	type	True	82.5808	774	1081	95	below_threshold
Limnobacter humi	strain=NBRC 111650	GCA_024518835.1	1778671	1778671	type	True	78.0319	303	1081	95	below_threshold
Herbaspirillum camelliae	strain=WT00C	GCA_001929405.1	1892903	1892903	type	True	75.9391	54	1081	95	below_threshold
Pseudoduganella lutea	strain=DSM 17473	GCA_004209755.1	321985	321985	type	True	75.7627	50	1081	95	below_threshold
Noviherbaspirillum aerium	strain=122213-3	GCA_008929045.1	2588497	2588497	type	True	75.483	51	1081	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 16:04:22,798] [INFO] DFAST Taxonomy check result was written to OceanDNA-b33321/tc_result.tsv
[2023-03-15 16:04:22,798] [INFO] ===== Taxonomy check completed =====
[2023-03-15 16:04:22,798] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 16:04:22,798] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf6b1dcba-472f-4880-a03d-08ac8e6b3df5/dqc_reference/checkm_data
[2023-03-15 16:04:22,799] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 16:04:23,030] [INFO] Task started: CheckM
[2023-03-15 16:04:23,030] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b33321/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b33321/checkm_input OceanDNA-b33321/checkm_result
[2023-03-15 16:05:20,314] [INFO] Task succeeded: CheckM
[2023-03-15 16:05:20,314] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 16:05:20,322] [INFO] ===== Completeness check finished =====
[2023-03-15 16:05:20,322] [INFO] ===== Start GTDB Search =====
[2023-03-15 16:05:20,322] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b33321/markers.fasta)
[2023-03-15 16:05:20,323] [INFO] Task started: Blastn
[2023-03-15 16:05:20,323] [INFO] Running command: blastn -query OceanDNA-b33321/markers.fasta -db /var/lib/cwl/stgf6b1dcba-472f-4880-a03d-08ac8e6b3df5/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b33321/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 16:05:21,593] [INFO] Task succeeded: Blastn
[2023-03-15 16:05:21,595] [INFO] Selected 11 target genomes.
[2023-03-15 16:05:21,595] [INFO] Target genome list was writen to OceanDNA-b33321/target_genomes_gtdb.txt
[2023-03-15 16:05:21,635] [INFO] Task started: fastANI
[2023-03-15 16:05:21,635] [INFO] Running command: fastANI --query /var/lib/cwl/stg50ec1a56-8d44-4036-8d9a-e4688e03a6c9/OceanDNA-b33321.fa --refList OceanDNA-b33321/target_genomes_gtdb.txt --output OceanDNA-b33321/fastani_result_gtdb.tsv --threads 1
[2023-03-15 16:05:29,699] [INFO] Task succeeded: fastANI
[2023-03-15 16:05:29,705] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 16:05:29,705] [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_000170915.1	s__Limnobacter sp000170915	83.2503	737	1081	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnobacter	95.0	98.10	98.01	0.88	0.86	5	-
GCF_005871185.1	s__Limnobacter alexandrii	82.5757	774	1081	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902506325.1	s__Limnobacter sp902506325	82.5572	737	1081	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013004065.1	s__Limnobacter sp002954425	82.5475	755	1081	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnobacter	95.0	97.67	96.02	0.92	0.87	19	-
GCA_018815245.1	s__Limnobacter sp018815245	82.4802	750	1081	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnobacter	95.0	99.98	99.93	0.99	0.98	9	-
GCA_001601825.1	s__Limnobacter sp001601825	81.7131	673	1081	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018812945.1	s__Limnobacter sp018812945	81.2879	618	1081	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004291335.1	s__Limnobacter thiooxidans	80.9829	611	1081	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 16:05:29,706] [INFO] GTDB search result was written to OceanDNA-b33321/result_gtdb.tsv
[2023-03-15 16:05:29,707] [INFO] ===== GTDB Search completed =====
[2023-03-15 16:05:29,709] [INFO] DFAST_QC result json was written to OceanDNA-b33321/dqc_result.json
[2023-03-15 16:05:29,709] [INFO] DFAST_QC completed!
[2023-03-15 16:05:29,709] [INFO] Total running time: 0h1m55s