[2023-03-18 09:41:09,155] [INFO] DFAST_QC pipeline started.
[2023-03-18 09:41:09,155] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 09:41:09,156] [INFO] DQC Reference Directory: /var/lib/cwl/stge906fd13-2153-4d70-b3fe-53e02ec37a08/dqc_reference
[2023-03-18 09:41:10,324] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 09:41:10,324] [INFO] Task started: Prodigal
[2023-03-18 09:41:10,324] [INFO] Running command: cat /var/lib/cwl/stg2206687d-b586-47ee-8bbf-e1d93d669c62/OceanDNA-b38873.fa | prodigal -d OceanDNA-b38873/cds.fna -a OceanDNA-b38873/protein.faa -g 11 -q > /dev/null
[2023-03-18 09:41:28,977] [INFO] Task succeeded: Prodigal
[2023-03-18 09:41:28,977] [INFO] Task started: HMMsearch
[2023-03-18 09:41:28,977] [INFO] Running command: hmmsearch --tblout OceanDNA-b38873/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge906fd13-2153-4d70-b3fe-53e02ec37a08/dqc_reference/reference_markers.hmm OceanDNA-b38873/protein.faa > /dev/null
[2023-03-18 09:41:29,204] [INFO] Task succeeded: HMMsearch
[2023-03-18 09:41:29,204] [INFO] Found 6/6 markers.
[2023-03-18 09:41:29,226] [INFO] Query marker FASTA was written to OceanDNA-b38873/markers.fasta
[2023-03-18 09:41:29,226] [INFO] Task started: Blastn
[2023-03-18 09:41:29,226] [INFO] Running command: blastn -query OceanDNA-b38873/markers.fasta -db /var/lib/cwl/stge906fd13-2153-4d70-b3fe-53e02ec37a08/dqc_reference/reference_markers.fasta -out OceanDNA-b38873/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 09:41:29,784] [INFO] Task succeeded: Blastn
[2023-03-18 09:41:29,785] [INFO] Selected 23 target genomes.
[2023-03-18 09:41:29,785] [INFO] Target genome list was writen to OceanDNA-b38873/target_genomes.txt
[2023-03-18 09:41:29,801] [INFO] Task started: fastANI
[2023-03-18 09:41:29,801] [INFO] Running command: fastANI --query /var/lib/cwl/stg2206687d-b586-47ee-8bbf-e1d93d669c62/OceanDNA-b38873.fa --refList OceanDNA-b38873/target_genomes.txt --output OceanDNA-b38873/fastani_result.tsv --threads 1
[2023-03-18 09:41:44,707] [INFO] Task succeeded: fastANI
[2023-03-18 09:41:44,708] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge906fd13-2153-4d70-b3fe-53e02ec37a08/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 09:41:44,708] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge906fd13-2153-4d70-b3fe-53e02ec37a08/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 09:41:44,717] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 09:41:44,717] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 09:41:44,718] [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	79.5578	334	1161	95	below_threshold
Neptuniibacter marinus	strain=ATR 1.1	GCA_001597725.1	1806670	1806670	type	True	79.5005	354	1161	95	below_threshold
Neptuniibacter caesariensis	strain=MED92	GCA_000153345.1	207954	207954	type	True	78.1517	246	1161	95	below_threshold
Amphritea japonica	strain=ATCC BAA-1530	GCA_016592435.1	452627	452627	type	True	77.3426	75	1161	95	below_threshold
Amphritea pacifica	strain=ZJ14W	GCA_016924145.1	2811233	2811233	type	True	77.0235	59	1161	95	below_threshold
Amphritea ceti	strain=KCTC 42154	GCA_024347215.1	1524258	1524258	type	True	77.0153	62	1161	95	below_threshold
Marinobacterium jannaschii	strain=DSM 6295	GCA_000620085.1	64970	64970	type	True	76.9631	65	1161	95	below_threshold
Neptunomonas concharum	strain=JCM 17730	GCA_006148955.1	1031538	1031538	type	True	76.9187	76	1161	95	below_threshold
Neptunomonas concharum	strain=JCM17730	GCA_008630635.1	1031538	1031538	type	True	76.8947	77	1161	95	below_threshold
Neptunomonas qingdaonensis	strain=CGMCC 1.10971	GCA_900113275.1	1045558	1045558	type	True	76.8557	67	1161	95	below_threshold
Neptunomonas antarctica	strain=DSM 22306	GCA_900156635.1	619304	619304	type	True	76.8083	73	1161	95	below_threshold
Neptunomonas marina	strain=HPM-16	GCA_004005935.1	1815562	1815562	type	True	76.7511	75	1161	95	below_threshold
Neptunomonas qingdaonensis	strain=P10-2-4	GCA_016082375.1	1045558	1045558	type	True	76.6863	70	1161	95	below_threshold
Neptunomonas antarctica	strain=S3-22	GCA_001305295.1	619304	619304	type	True	76.6605	71	1161	95	below_threshold
Amphritea spongicola	strain=JCM 16668	GCA_017051665.1	707589	707589	type	True	76.478	62	1161	95	below_threshold
Neptunomonas phycophila	strain=CECT 8716	GCA_001922575.1	1572645	1572645	type	True	76.3829	64	1161	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 09:41:44,718] [INFO] DFAST Taxonomy check result was written to OceanDNA-b38873/tc_result.tsv
[2023-03-18 09:41:44,718] [INFO] ===== Taxonomy check completed =====
[2023-03-18 09:41:44,718] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 09:41:44,718] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge906fd13-2153-4d70-b3fe-53e02ec37a08/dqc_reference/checkm_data
[2023-03-18 09:41:44,719] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 09:41:44,724] [INFO] Task started: CheckM
[2023-03-18 09:41:44,724] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b38873/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b38873/checkm_input OceanDNA-b38873/checkm_result
[2023-03-18 09:42:32,541] [INFO] Task succeeded: CheckM
[2023-03-18 09:42:32,542] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 66.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 09:42:32,556] [INFO] ===== Completeness check finished =====
[2023-03-18 09:42:32,556] [INFO] ===== Start GTDB Search =====
[2023-03-18 09:42:32,556] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b38873/markers.fasta)
[2023-03-18 09:42:32,557] [INFO] Task started: Blastn
[2023-03-18 09:42:32,558] [INFO] Running command: blastn -query OceanDNA-b38873/markers.fasta -db /var/lib/cwl/stge906fd13-2153-4d70-b3fe-53e02ec37a08/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b38873/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 09:42:33,349] [INFO] Task succeeded: Blastn
[2023-03-18 09:42:33,350] [INFO] Selected 17 target genomes.
[2023-03-18 09:42:33,350] [INFO] Target genome list was writen to OceanDNA-b38873/target_genomes_gtdb.txt
[2023-03-18 09:42:33,393] [INFO] Task started: fastANI
[2023-03-18 09:42:33,393] [INFO] Running command: fastANI --query /var/lib/cwl/stg2206687d-b586-47ee-8bbf-e1d93d669c62/OceanDNA-b38873.fa --refList OceanDNA-b38873/target_genomes_gtdb.txt --output OceanDNA-b38873/fastani_result_gtdb.tsv --threads 1
[2023-03-18 09:42:44,219] [INFO] Task succeeded: fastANI
[2023-03-18 09:42:44,226] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 09:42:44,226] [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_002435145.1	s__Neptuniibacter sp002435145	99.9044	1080	1161	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Neptuniibacter	95.0	99.91	99.87	0.93	0.93	3	conclusive
GCF_001597735.1	s__Neptuniibacter pectenicola	79.5729	333	1161	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Neptuniibacter	95.0	98.78	98.78	0.91	0.91	2	-
GCF_001597725.1	s__Neptuniibacter marinus	79.5024	355	1161	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Neptuniibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000153345.1	s__Neptuniibacter caesariensis	78.1517	246	1161	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	77.3569	95	1161	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Pontibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000620085.1	s__Marinobacterium_B jannaschii	76.9631	65	1161	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008630635.1	s__Neptunomonas concharum	76.927	76	1161	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Neptunomonas	95.0	100.00	100.00	0.98	0.98	2	-
GCF_900113275.1	s__Neptunomonas qingdaonensis	76.8574	68	1161	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Neptunomonas	95.0	99.99	99.99	0.99	0.99	2	-
GCF_001305295.1	s__Neptunomonas antarctica	76.6354	73	1161	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Neptunomonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001922575.1	s__Neptunomonas phycophila	76.3615	66	1161	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Neptunomonas	95.0	98.55	98.14	0.96	0.94	4	-
--------------------------------------------------------------------------------
[2023-03-18 09:42:44,226] [INFO] GTDB search result was written to OceanDNA-b38873/result_gtdb.tsv
[2023-03-18 09:42:44,226] [INFO] ===== GTDB Search completed =====
[2023-03-18 09:42:44,227] [INFO] DFAST_QC result json was written to OceanDNA-b38873/dqc_result.json
[2023-03-18 09:42:44,228] [INFO] DFAST_QC completed!
[2023-03-18 09:42:44,228] [INFO] Total running time: 0h1m35s