[2023-03-18 08:17:17,732] [INFO] DFAST_QC pipeline started.
[2023-03-18 08:17:17,732] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 08:17:17,732] [INFO] DQC Reference Directory: /var/lib/cwl/stg0107d4bf-906a-47bf-8189-f1464bf9eb1e/dqc_reference
[2023-03-18 08:17:18,942] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 08:17:18,943] [INFO] Task started: Prodigal
[2023-03-18 08:17:18,943] [INFO] Running command: cat /var/lib/cwl/stg5d9e8f19-dcb2-449d-b60e-a709bd6ed343/OceanDNA-b31949.fa | prodigal -d OceanDNA-b31949/cds.fna -a OceanDNA-b31949/protein.faa -g 11 -q > /dev/null
[2023-03-18 08:17:28,495] [INFO] Task succeeded: Prodigal
[2023-03-18 08:17:28,496] [INFO] Task started: HMMsearch
[2023-03-18 08:17:28,496] [INFO] Running command: hmmsearch --tblout OceanDNA-b31949/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0107d4bf-906a-47bf-8189-f1464bf9eb1e/dqc_reference/reference_markers.hmm OceanDNA-b31949/protein.faa > /dev/null
[2023-03-18 08:17:28,661] [INFO] Task succeeded: HMMsearch
[2023-03-18 08:17:28,662] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg5d9e8f19-dcb2-449d-b60e-a709bd6ed343/OceanDNA-b31949.fa]
[2023-03-18 08:17:28,676] [INFO] Query marker FASTA was written to OceanDNA-b31949/markers.fasta
[2023-03-18 08:17:28,676] [INFO] Task started: Blastn
[2023-03-18 08:17:28,676] [INFO] Running command: blastn -query OceanDNA-b31949/markers.fasta -db /var/lib/cwl/stg0107d4bf-906a-47bf-8189-f1464bf9eb1e/dqc_reference/reference_markers.fasta -out OceanDNA-b31949/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 08:17:29,143] [INFO] Task succeeded: Blastn
[2023-03-18 08:17:29,144] [INFO] Selected 15 target genomes.
[2023-03-18 08:17:29,144] [INFO] Target genome list was writen to OceanDNA-b31949/target_genomes.txt
[2023-03-18 08:17:29,153] [INFO] Task started: fastANI
[2023-03-18 08:17:29,153] [INFO] Running command: fastANI --query /var/lib/cwl/stg5d9e8f19-dcb2-449d-b60e-a709bd6ed343/OceanDNA-b31949.fa --refList OceanDNA-b31949/target_genomes.txt --output OceanDNA-b31949/fastani_result.tsv --threads 1
[2023-03-18 08:17:37,034] [INFO] Task succeeded: fastANI
[2023-03-18 08:17:37,034] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0107d4bf-906a-47bf-8189-f1464bf9eb1e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 08:17:37,035] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0107d4bf-906a-47bf-8189-f1464bf9eb1e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 08:17:37,043] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 08:17:37,043] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 08:17:37,043] [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
Aurantiacibacter odishensis	strain=KCTC 23981	GCA_003605195.1	1155476	1155476	type	True	82.1265	349	480	95	below_threshold
Aurantiacibacter zhengii	strain=V18	GCA_003584125.1	2307003	2307003	type	True	81.701	336	480	95	below_threshold
Aurantiacibacter rhizosphaerae	strain=GH3-10	GCA_009807005.1	2691582	2691582	type	True	79.9781	310	480	95	below_threshold
Aurantiacibacter gangjinensis	strain=K7-2	GCA_001010925.1	502682	502682	type	True	78.495	228	480	95	below_threshold
Aurantiacibacter gangjinensis	strain=CGMCC 1.15024	GCA_001886695.1	502682	502682	type	True	78.4752	230	480	95	below_threshold
Aurantiacibacter arachoides	strain=CGMCC 1.15507	GCA_014643415.1	1850444	1850444	type	True	77.7963	199	480	95	below_threshold
Aurantiacibacter sediminis	strain=JGD-13	GCA_016019885.1	2793064	2793064	type	True	77.5896	177	480	95	below_threshold
Alteriqipengyuania lutimaris	strain=S-5	GCA_003363135.1	1538146	1538146	type	True	77.1276	103	480	95	below_threshold
Erythrobacter dokdonensis	strain=DSW-74	GCA_001677335.1	328225	328225	type	True	76.9389	117	480	95	below_threshold
Erythrobacter dokdonensis	strain=DSM 17193	GCA_002155305.1	328225	328225	type	True	76.8934	121	480	95	below_threshold
Croceibacterium mercuriale	strain=Coronado	GCA_000802385.1	1572751	1572751	type	True	76.8131	113	480	95	below_threshold
Novosphingobium guangzhouense	strain=SA925	GCA_002896965.1	1850347	1850347	type	True	76.6204	103	480	95	below_threshold
Tsuneonella deserti	strain=CGMCC 1.15959	GCA_014644315.1	2035528	2035528	type	True	76.5802	82	480	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 08:17:37,043] [INFO] DFAST Taxonomy check result was written to OceanDNA-b31949/tc_result.tsv
[2023-03-18 08:17:37,043] [INFO] ===== Taxonomy check completed =====
[2023-03-18 08:17:37,043] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 08:17:37,043] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0107d4bf-906a-47bf-8189-f1464bf9eb1e/dqc_reference/checkm_data
[2023-03-18 08:17:37,044] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 08:17:37,061] [INFO] Task started: CheckM
[2023-03-18 08:17:37,061] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b31949/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b31949/checkm_input OceanDNA-b31949/checkm_result
[2023-03-18 08:18:05,229] [INFO] Task succeeded: CheckM
[2023-03-18 08:18:05,230] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 37.15%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 08:18:05,231] [INFO] ===== Completeness check finished =====
[2023-03-18 08:18:05,232] [INFO] ===== Start GTDB Search =====
[2023-03-18 08:18:05,232] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b31949/markers.fasta)
[2023-03-18 08:18:05,232] [INFO] Task started: Blastn
[2023-03-18 08:18:05,232] [INFO] Running command: blastn -query OceanDNA-b31949/markers.fasta -db /var/lib/cwl/stg0107d4bf-906a-47bf-8189-f1464bf9eb1e/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b31949/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 08:18:05,764] [INFO] Task succeeded: Blastn
[2023-03-18 08:18:05,765] [INFO] Selected 16 target genomes.
[2023-03-18 08:18:05,765] [INFO] Target genome list was writen to OceanDNA-b31949/target_genomes_gtdb.txt
[2023-03-18 08:18:05,779] [INFO] Task started: fastANI
[2023-03-18 08:18:05,779] [INFO] Running command: fastANI --query /var/lib/cwl/stg5d9e8f19-dcb2-449d-b60e-a709bd6ed343/OceanDNA-b31949.fa --refList OceanDNA-b31949/target_genomes_gtdb.txt --output OceanDNA-b31949/fastani_result_gtdb.tsv --threads 1
[2023-03-18 08:18:14,463] [INFO] Task succeeded: fastANI
[2023-03-18 08:18:14,473] [INFO] Found 16 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 08:18:14,473] [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_003605195.1	s__Alteraurantiacibacter odishensis	82.1307	349	480	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003584125.1	s__Alteraurantiacibacter zhengii	81.6871	337	480	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009807005.1	s__Alteraurantiacibacter rhizosphaerae	79.9781	310	480	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001886695.1	s__Alteraurantiacibacter gangjinensis	78.4752	230	480	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_902498745.1	s__Alteraurantiacibacter sp902498745	78.0593	196	480	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003605475.1	s__Alteraurantiacibacter aquimixticola_A	77.9092	178	480	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016019885.1	s__Alteraurantiacibacter sp016019885	77.5896	177	480	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002729695.1	s__Alteriqipengyuania sp002729695	77.151	116	480	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteriqipengyuania	95.0	99.53	99.11	0.93	0.90	4	-
GCF_002952215.1	s__Erythrobacter sp002952215	77.1317	111	480	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001677335.1	s__Erythrobacter dokdonensis	76.9389	117	480	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000802385.1	s__Croceibacterium mercuriale	76.8131	113	480	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001683845.1	s__Croceibacterium sp001683845	76.6755	100	480	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002712945.1	s__Alteriqipengyuania sp002712945	76.651	70	480	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteriqipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002896965.1	s__Novosphingobium guangzhouense	76.6204	103	480	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014644315.1	s__Tsuneonella deserti	76.5802	82	480	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Tsuneonella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013370205.1	s__Actirhodobacter atriluteus	76.1646	78	480	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Actirhodobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 08:18:14,473] [INFO] GTDB search result was written to OceanDNA-b31949/result_gtdb.tsv
[2023-03-18 08:18:14,473] [INFO] ===== GTDB Search completed =====
[2023-03-18 08:18:14,475] [INFO] DFAST_QC result json was written to OceanDNA-b31949/dqc_result.json
[2023-03-18 08:18:14,475] [INFO] DFAST_QC completed!
[2023-03-18 08:18:14,475] [INFO] Total running time: 0h0m57s