[2023-03-17 06:30:49,100] [INFO] DFAST_QC pipeline started.
[2023-03-17 06:30:49,101] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 06:30:49,101] [INFO] DQC Reference Directory: /var/lib/cwl/stg6aa50930-a32b-4209-8470-e2d8c45646a0/dqc_reference
[2023-03-17 06:30:50,270] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 06:30:50,293] [INFO] Task started: Prodigal
[2023-03-17 06:30:50,293] [INFO] Running command: cat /var/lib/cwl/stgd279fa92-f6ea-43b9-a0b6-a98e144128d7/OceanDNA-b38872.fa | prodigal -d OceanDNA-b38872/cds.fna -a OceanDNA-b38872/protein.faa -g 11 -q > /dev/null
[2023-03-17 06:31:06,424] [INFO] Task succeeded: Prodigal
[2023-03-17 06:31:06,424] [INFO] Task started: HMMsearch
[2023-03-17 06:31:06,424] [INFO] Running command: hmmsearch --tblout OceanDNA-b38872/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6aa50930-a32b-4209-8470-e2d8c45646a0/dqc_reference/reference_markers.hmm OceanDNA-b38872/protein.faa > /dev/null
[2023-03-17 06:31:06,610] [INFO] Task succeeded: HMMsearch
[2023-03-17 06:31:06,610] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgd279fa92-f6ea-43b9-a0b6-a98e144128d7/OceanDNA-b38872.fa]
[2023-03-17 06:31:06,628] [INFO] Query marker FASTA was written to OceanDNA-b38872/markers.fasta
[2023-03-17 06:31:06,629] [INFO] Task started: Blastn
[2023-03-17 06:31:06,629] [INFO] Running command: blastn -query OceanDNA-b38872/markers.fasta -db /var/lib/cwl/stg6aa50930-a32b-4209-8470-e2d8c45646a0/dqc_reference/reference_markers.fasta -out OceanDNA-b38872/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 06:31:07,144] [INFO] Task succeeded: Blastn
[2023-03-17 06:31:07,145] [INFO] Selected 20 target genomes.
[2023-03-17 06:31:07,145] [INFO] Target genome list was writen to OceanDNA-b38872/target_genomes.txt
[2023-03-17 06:31:07,154] [INFO] Task started: fastANI
[2023-03-17 06:31:07,154] [INFO] Running command: fastANI --query /var/lib/cwl/stgd279fa92-f6ea-43b9-a0b6-a98e144128d7/OceanDNA-b38872.fa --refList OceanDNA-b38872/target_genomes.txt --output OceanDNA-b38872/fastani_result.tsv --threads 1
[2023-03-17 06:31:19,246] [INFO] Task succeeded: fastANI
[2023-03-17 06:31:19,246] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6aa50930-a32b-4209-8470-e2d8c45646a0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 06:31:19,246] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6aa50930-a32b-4209-8470-e2d8c45646a0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 06:31:19,253] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2023-03-17 06:31:19,253] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-17 06:31:19,253] [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
Neptuniibacter pectenicola	strain=LFT 1.8	GCA_001597735.1	1806669	1806669	type	True	99.079	919	969	95	conclusive
Neptuniibacter marinus	strain=ATR 1.1	GCA_001597725.1	1806670	1806670	type	True	83.8649	687	969	95	below_threshold
Neptuniibacter caesariensis	strain=MED92	GCA_000153345.1	207954	207954	type	True	78.235	192	969	95	below_threshold
Neptunomonas concharum	strain=JCM 17730	GCA_006148955.1	1031538	1031538	type	True	77.1262	63	969	95	below_threshold
Neptunomonas concharum	strain=JCM17730	GCA_008630635.1	1031538	1031538	type	True	77.0681	64	969	95	below_threshold
Amphritea japonica	strain=JCM 14782	GCA_024347275.1	452627	452627	type	True	76.9318	79	969	95	below_threshold
Amphritea ceti	strain=KCTC 42154	GCA_024347215.1	1524258	1524258	type	True	76.8079	59	969	95	below_threshold
Neptunomonas qingdaonensis	strain=CGMCC 1.10971	GCA_900113275.1	1045558	1045558	type	True	76.7038	66	969	95	below_threshold
Neptunomonas japonica	strain=DSM 18939	GCA_000422765.1	417574	417574	type	True	76.6086	79	969	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 06:31:19,253] [INFO] DFAST Taxonomy check result was written to OceanDNA-b38872/tc_result.tsv
[2023-03-17 06:31:19,253] [INFO] ===== Taxonomy check completed =====
[2023-03-17 06:31:19,253] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 06:31:19,253] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6aa50930-a32b-4209-8470-e2d8c45646a0/dqc_reference/checkm_data
[2023-03-17 06:31:19,254] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 06:31:19,258] [INFO] Task started: CheckM
[2023-03-17 06:31:19,258] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b38872/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b38872/checkm_input OceanDNA-b38872/checkm_result
[2023-03-17 06:32:01,671] [INFO] Task succeeded: CheckM
[2023-03-17 06:32:01,671] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 06:32:01,673] [INFO] ===== Completeness check finished =====
[2023-03-17 06:32:01,674] [INFO] ===== Start GTDB Search =====
[2023-03-17 06:32:01,674] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b38872/markers.fasta)
[2023-03-17 06:32:01,674] [INFO] Task started: Blastn
[2023-03-17 06:32:01,674] [INFO] Running command: blastn -query OceanDNA-b38872/markers.fasta -db /var/lib/cwl/stg6aa50930-a32b-4209-8470-e2d8c45646a0/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b38872/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 06:32:02,400] [INFO] Task succeeded: Blastn
[2023-03-17 06:32:02,400] [INFO] Selected 15 target genomes.
[2023-03-17 06:32:02,400] [INFO] Target genome list was writen to OceanDNA-b38872/target_genomes_gtdb.txt
[2023-03-17 06:32:02,535] [INFO] Task started: fastANI
[2023-03-17 06:32:02,535] [INFO] Running command: fastANI --query /var/lib/cwl/stgd279fa92-f6ea-43b9-a0b6-a98e144128d7/OceanDNA-b38872.fa --refList OceanDNA-b38872/target_genomes_gtdb.txt --output OceanDNA-b38872/fastani_result_gtdb.tsv --threads 1
[2023-03-17 06:32:12,779] [INFO] Task succeeded: fastANI
[2023-03-17 06:32:12,784] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 06:32:12,784] [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_001597735.1	s__Neptuniibacter pectenicola	99.079	919	969	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Neptuniibacter	95.0	98.78	98.78	0.91	0.91	2	conclusive
GCF_001597725.1	s__Neptuniibacter marinus	83.8649	687	969	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Neptuniibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002435145.1	s__Neptuniibacter sp002435145	79.3141	304	969	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Neptuniibacter	95.0	99.91	99.87	0.93	0.93	3	-
GCF_000153345.1	s__Neptuniibacter caesariensis	78.235	192	969	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Neptuniibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015209595.1	s__Pontibacterium sp015209595	77.5143	94	969	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Pontibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008630635.1	s__Neptunomonas concharum	77.0681	64	969	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Neptunomonas	95.0	100.00	100.00	0.98	0.98	2	-
GCA_016744175.1	s__Neptunomonas sp016744175	76.5715	66	969	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Neptunomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 06:32:12,784] [INFO] GTDB search result was written to OceanDNA-b38872/result_gtdb.tsv
[2023-03-17 06:32:12,784] [INFO] ===== GTDB Search completed =====
[2023-03-17 06:32:12,785] [INFO] DFAST_QC result json was written to OceanDNA-b38872/dqc_result.json
[2023-03-17 06:32:12,786] [INFO] DFAST_QC completed!
[2023-03-17 06:32:12,786] [INFO] Total running time: 0h1m24s