[2023-03-15 05:08:43,829] [INFO] DFAST_QC pipeline started.
[2023-03-15 05:08:43,829] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 05:08:43,829] [INFO] DQC Reference Directory: /var/lib/cwl/stg143fbbc3-6973-4cdb-bf53-af80b679842a/dqc_reference
[2023-03-15 05:08:50,118] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 05:08:50,120] [INFO] Task started: Prodigal
[2023-03-15 05:08:50,120] [INFO] Running command: cat /var/lib/cwl/stgd098f65a-1b0d-4fbd-8132-7e49bb12a193/OceanDNA-b31570.fa | prodigal -d OceanDNA-b31570/cds.fna -a OceanDNA-b31570/protein.faa -g 11 -q > /dev/null
[2023-03-15 05:09:04,763] [INFO] Task succeeded: Prodigal
[2023-03-15 05:09:04,763] [INFO] Task started: HMMsearch
[2023-03-15 05:09:04,763] [INFO] Running command: hmmsearch --tblout OceanDNA-b31570/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg143fbbc3-6973-4cdb-bf53-af80b679842a/dqc_reference/reference_markers.hmm OceanDNA-b31570/protein.faa > /dev/null
[2023-03-15 05:09:05,016] [INFO] Task succeeded: HMMsearch
[2023-03-15 05:09:05,017] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgd098f65a-1b0d-4fbd-8132-7e49bb12a193/OceanDNA-b31570.fa]
[2023-03-15 05:09:05,047] [INFO] Query marker FASTA was written to OceanDNA-b31570/markers.fasta
[2023-03-15 05:09:05,049] [INFO] Task started: Blastn
[2023-03-15 05:09:05,049] [INFO] Running command: blastn -query OceanDNA-b31570/markers.fasta -db /var/lib/cwl/stg143fbbc3-6973-4cdb-bf53-af80b679842a/dqc_reference/reference_markers.fasta -out OceanDNA-b31570/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 05:09:08,912] [INFO] Task succeeded: Blastn
[2023-03-15 05:09:08,915] [INFO] Selected 22 target genomes.
[2023-03-15 05:09:08,915] [INFO] Target genome list was writen to OceanDNA-b31570/target_genomes.txt
[2023-03-15 05:09:08,969] [INFO] Task started: fastANI
[2023-03-15 05:09:08,969] [INFO] Running command: fastANI --query /var/lib/cwl/stgd098f65a-1b0d-4fbd-8132-7e49bb12a193/OceanDNA-b31570.fa --refList OceanDNA-b31570/target_genomes.txt --output OceanDNA-b31570/fastani_result.tsv --threads 1
[2023-03-15 05:09:21,252] [INFO] Task succeeded: fastANI
[2023-03-15 05:09:21,252] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg143fbbc3-6973-4cdb-bf53-af80b679842a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 05:09:21,253] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg143fbbc3-6973-4cdb-bf53-af80b679842a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 05:09:21,313] [INFO] Found 22 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 05:09:21,313] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 05:09:21,313] [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
Alteriqipengyuania lutimaris	strain=CECT 8624	GCA_014191645.1	1538146	1538146	type	True	83.8354	572	785	95	below_threshold
Alteriqipengyuania lutimaris	strain=S-5	GCA_003363135.1	1538146	1538146	type	True	83.8294	569	785	95	below_threshold
Alteriqipengyuania abyssalis	strain=NZ-12B	GCA_019857185.1	2860200	2860200	type	True	83.7928	545	785	95	below_threshold
Qipengyuania proteolytica	strain=6B39	GCA_019711565.1	2867239	2867239	type	True	78.3497	327	785	95	below_threshold
Qipengyuania pelagi	strain=JCM 17468	GCA_009827295.1	994320	994320	type	True	78.3205	327	785	95	below_threshold
Erythrobacter donghaensis	strain=DSM 16220	GCA_002155425.1	267135	267135	suspected-type	True	78.1379	330	785	95	below_threshold
Qipengyuania sphaerica	strain=GH29	GCA_019711595.1	2867243	2867243	type	True	78.0552	282	785	95	below_threshold
Aurantiacibacter luteus	strain=KA37	GCA_001010945.1	1581420	1581420	type	True	77.9884	307	785	95	below_threshold
Qipengyuania aurantiaca	strain=1NDH13	GCA_019711375.1	2867233	2867233	type	True	77.9845	308	785	95	below_threshold
Pelagerythrobacter rhizovicinus	strain=AY-3R	GCA_004135625.1	2268576	2268576	type	True	77.9799	291	785	95	below_threshold
Qipengyuania polymorpha	strain=1NDH17	GCA_019711435.1	2867234	2867234	type	True	77.9487	278	785	95	below_threshold
Erythrobacter litoralis	strain=DSM 8509	GCA_001719165.1	39960	39960	type	True	77.9484	294	785	95	below_threshold
Pelagerythrobacter aerophilus	strain=Ery1	GCA_003581645.1	2306995	2306995	type	True	77.9482	304	785	95	below_threshold
Aurantiacibacter odishensis	strain=KCTC 23981	GCA_003605195.1	1155476	1155476	type	True	77.8543	266	785	95	below_threshold
Qipengyuania flava	strain=DSM 16421	GCA_011762005.1	192812	192812	type	True	77.8405	299	785	95	below_threshold
Aurantiacibacter xanthus	strain=CCTCC AB 2015396	GCA_003584015.1	1784712	1784712	type	True	77.7719	259	785	95	below_threshold
Erythrobacter dokdonensis	strain=DSW-74	GCA_001677335.1	328225	328225	type	True	77.7605	278	785	95	below_threshold
Qipengyuania qiaonensis	strain=6D47A	GCA_019711515.1	2867240	2867240	type	True	77.7294	226	785	95	below_threshold
Pelagerythrobacter marensis	strain=DSM 21428	GCA_001461885.1	543877	543877	type	True	77.708	271	785	95	below_threshold
Erythrobacter dokdonensis	strain=DSM 17193	GCA_002155305.1	328225	328225	type	True	77.7047	281	785	95	below_threshold
Pelagerythrobacter marensis	strain=KCTC 22370	GCA_001028625.1	543877	543877	type	True	77.6866	271	785	95	below_threshold
Qipengyuania huizhouensis	strain=YG19	GCA_019711635.1	2867245	2867245	type	True	77.34	196	785	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 05:09:21,317] [INFO] DFAST Taxonomy check result was written to OceanDNA-b31570/tc_result.tsv
[2023-03-15 05:09:21,325] [INFO] ===== Taxonomy check completed =====
[2023-03-15 05:09:21,325] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 05:09:21,325] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg143fbbc3-6973-4cdb-bf53-af80b679842a/dqc_reference/checkm_data
[2023-03-15 05:09:21,326] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 05:09:21,336] [INFO] Task started: CheckM
[2023-03-15 05:09:21,337] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b31570/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b31570/checkm_input OceanDNA-b31570/checkm_result
[2023-03-15 05:10:05,106] [INFO] Task succeeded: CheckM
[2023-03-15 05:10:05,107] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 47.52%
Contamintation: 9.72%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-15 05:10:05,109] [INFO] ===== Completeness check finished =====
[2023-03-15 05:10:05,110] [INFO] ===== Start GTDB Search =====
[2023-03-15 05:10:05,110] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b31570/markers.fasta)
[2023-03-15 05:10:05,112] [INFO] Task started: Blastn
[2023-03-15 05:10:05,112] [INFO] Running command: blastn -query OceanDNA-b31570/markers.fasta -db /var/lib/cwl/stg143fbbc3-6973-4cdb-bf53-af80b679842a/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b31570/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 05:10:06,646] [INFO] Task succeeded: Blastn
[2023-03-15 05:10:06,673] [INFO] Selected 8 target genomes.
[2023-03-15 05:10:06,674] [INFO] Target genome list was writen to OceanDNA-b31570/target_genomes_gtdb.txt
[2023-03-15 05:10:06,731] [INFO] Task started: fastANI
[2023-03-15 05:10:06,731] [INFO] Running command: fastANI --query /var/lib/cwl/stgd098f65a-1b0d-4fbd-8132-7e49bb12a193/OceanDNA-b31570.fa --refList OceanDNA-b31570/target_genomes_gtdb.txt --output OceanDNA-b31570/fastani_result_gtdb.tsv --threads 1
[2023-03-15 05:10:11,663] [INFO] Task succeeded: fastANI
[2023-03-15 05:10:11,669] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 05:10:11,669] [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_003363135.1	s__Alteriqipengyuania lutimaris	83.8294	569	785	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteriqipengyuania	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000186705.1	s__Alteriqipengyuania sp000186705	83.6623	561	785	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteriqipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015999305.1	s__Alteriqipengyuania sp015999305	83.6248	550	785	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteriqipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000176355.1	s__Alteriqipengyuania bathyomarina	83.6071	541	785	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteriqipengyuania	95.0	98.10	96.53	0.93	0.90	11	-
GCA_002377695.1	s__Alteriqipengyuania sp002377695	83.4202	521	785	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteriqipengyuania	95.0	99.97	99.97	1.00	1.00	2	-
GCA_002712945.1	s__Alteriqipengyuania sp002712945	83.2516	307	785	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteriqipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009993635.1	s__Alteriqipengyuania sp009993635	83.0873	537	785	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteriqipengyuania	95.0	99.91	99.91	0.97	0.97	2	-
GCA_002729695.1	s__Alteriqipengyuania sp002729695	83.0581	515	785	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteriqipengyuania	95.0	99.53	99.11	0.93	0.90	4	-
--------------------------------------------------------------------------------
[2023-03-15 05:10:11,671] [INFO] GTDB search result was written to OceanDNA-b31570/result_gtdb.tsv
[2023-03-15 05:10:11,675] [INFO] ===== GTDB Search completed =====
[2023-03-15 05:10:11,681] [INFO] DFAST_QC result json was written to OceanDNA-b31570/dqc_result.json
[2023-03-15 05:10:11,681] [INFO] DFAST_QC completed!
[2023-03-15 05:10:11,681] [INFO] Total running time: 0h1m28s