[2023-03-15 13:55:37,497] [INFO] DFAST_QC pipeline started.
[2023-03-15 13:55:37,498] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 13:55:37,498] [INFO] DQC Reference Directory: /var/lib/cwl/stg5e8f98da-1518-4ef8-aa6c-94f87a286085/dqc_reference
[2023-03-15 13:55:38,608] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 13:55:38,608] [INFO] Task started: Prodigal
[2023-03-15 13:55:38,609] [INFO] Running command: cat /var/lib/cwl/stg4bc7f562-6ca4-44e7-ad00-63047b5664b4/OceanDNA-b31574.fa | prodigal -d OceanDNA-b31574/cds.fna -a OceanDNA-b31574/protein.faa -g 11 -q > /dev/null
[2023-03-15 13:55:55,173] [INFO] Task succeeded: Prodigal
[2023-03-15 13:55:55,173] [INFO] Task started: HMMsearch
[2023-03-15 13:55:55,173] [INFO] Running command: hmmsearch --tblout OceanDNA-b31574/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5e8f98da-1518-4ef8-aa6c-94f87a286085/dqc_reference/reference_markers.hmm OceanDNA-b31574/protein.faa > /dev/null
[2023-03-15 13:55:55,369] [INFO] Task succeeded: HMMsearch
[2023-03-15 13:55:55,370] [INFO] Found 6/6 markers.
[2023-03-15 13:55:55,388] [INFO] Query marker FASTA was written to OceanDNA-b31574/markers.fasta
[2023-03-15 13:55:55,389] [INFO] Task started: Blastn
[2023-03-15 13:55:55,389] [INFO] Running command: blastn -query OceanDNA-b31574/markers.fasta -db /var/lib/cwl/stg5e8f98da-1518-4ef8-aa6c-94f87a286085/dqc_reference/reference_markers.fasta -out OceanDNA-b31574/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 13:55:56,252] [INFO] Task succeeded: Blastn
[2023-03-15 13:55:56,253] [INFO] Selected 18 target genomes.
[2023-03-15 13:55:56,253] [INFO] Target genome list was writen to OceanDNA-b31574/target_genomes.txt
[2023-03-15 13:55:56,292] [INFO] Task started: fastANI
[2023-03-15 13:55:56,292] [INFO] Running command: fastANI --query /var/lib/cwl/stg4bc7f562-6ca4-44e7-ad00-63047b5664b4/OceanDNA-b31574.fa --refList OceanDNA-b31574/target_genomes.txt --output OceanDNA-b31574/fastani_result.tsv --threads 1
[2023-03-15 13:56:07,692] [INFO] Task succeeded: fastANI
[2023-03-15 13:56:07,693] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5e8f98da-1518-4ef8-aa6c-94f87a286085/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 13:56:07,693] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5e8f98da-1518-4ef8-aa6c-94f87a286085/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 13:56:07,703] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 13:56:07,703] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 13:56:07,703] [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 abyssalis	strain=NZ-12B	GCA_019857185.1	2860200	2860200	type	True	84.8397	683	896	95	below_threshold
Alteriqipengyuania lutimaris	strain=S-5	GCA_003363135.1	1538146	1538146	type	True	84.788	689	896	95	below_threshold
Alteriqipengyuania lutimaris	strain=CECT 8624	GCA_014191645.1	1538146	1538146	type	True	84.7494	697	896	95	below_threshold
Qipengyuania proteolytica	strain=6B39	GCA_019711565.1	2867239	2867239	type	True	79.4596	426	896	95	below_threshold
Qipengyuania polymorpha	strain=1NDH17	GCA_019711435.1	2867234	2867234	type	True	79.2101	379	896	95	below_threshold
Qipengyuania gaetbuli	strain=DSM 16225	GCA_009827315.1	266952	266952	type	True	79.1899	385	896	95	below_threshold
Qipengyuania pelagi	strain=JCM 17468	GCA_009827295.1	994320	994320	type	True	79.0465	428	896	95	below_threshold
Pelagerythrobacter aerophilus	strain=Ery1	GCA_003581645.1	2306995	2306995	type	True	79.0132	397	896	95	below_threshold
Qipengyuania xiapuensis	strain=1NDW9	GCA_019711395.1	2867236	2867236	type	True	78.8046	395	896	95	below_threshold
Erythrobacter donghaensis	strain=DSM 16220	GCA_002155425.1	267135	267135	suspected-type	True	78.734	421	896	95	below_threshold
Qipengyuania intermedia	strain=GH38	GCA_019711615.1	2867244	2867244	type	True	78.6856	343	896	95	below_threshold
Pelagerythrobacter rhizovicinus	strain=AY-3R	GCA_004135625.1	2268576	2268576	type	True	78.6651	407	896	95	below_threshold
Qipengyuania qiaonensis	strain=6D47A	GCA_019711515.1	2867240	2867240	type	True	78.6329	343	896	95	below_threshold
Aurantiacibacter zhengii	strain=V18	GCA_003584125.1	2307003	2307003	type	True	78.5593	331	896	95	below_threshold
Aurantiacibacter luteus	strain=KA37	GCA_001010945.1	1581420	1581420	type	True	78.4748	373	896	95	below_threshold
Aurantiacibacter odishensis	strain=KCTC 23981	GCA_003605195.1	1155476	1155476	type	True	78.2778	332	896	95	below_threshold
Qipengyuania aerophila	strain=GH25	GCA_019711555.1	2867242	2867242	type	True	78.1005	290	896	95	below_threshold
Qipengyuania pacifica	strain=NZ-96	GCA_019857205.1	2860199	2860199	type	True	77.9751	294	896	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 13:56:07,704] [INFO] DFAST Taxonomy check result was written to OceanDNA-b31574/tc_result.tsv
[2023-03-15 13:56:07,704] [INFO] ===== Taxonomy check completed =====
[2023-03-15 13:56:07,704] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 13:56:07,704] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5e8f98da-1518-4ef8-aa6c-94f87a286085/dqc_reference/checkm_data
[2023-03-15 13:56:07,705] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 13:56:07,813] [INFO] Task started: CheckM
[2023-03-15 13:56:07,813] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b31574/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b31574/checkm_input OceanDNA-b31574/checkm_result
[2023-03-15 13:56:50,596] [INFO] Task succeeded: CheckM
[2023-03-15 13:56:50,597] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 82.95%
Contamintation: 2.08%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-15 13:56:50,849] [INFO] ===== Completeness check finished =====
[2023-03-15 13:56:50,849] [INFO] ===== Start GTDB Search =====
[2023-03-15 13:56:50,849] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b31574/markers.fasta)
[2023-03-15 13:56:50,850] [INFO] Task started: Blastn
[2023-03-15 13:56:50,850] [INFO] Running command: blastn -query OceanDNA-b31574/markers.fasta -db /var/lib/cwl/stg5e8f98da-1518-4ef8-aa6c-94f87a286085/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b31574/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 13:56:52,545] [INFO] Task succeeded: Blastn
[2023-03-15 13:56:52,547] [INFO] Selected 8 target genomes.
[2023-03-15 13:56:52,547] [INFO] Target genome list was writen to OceanDNA-b31574/target_genomes_gtdb.txt
[2023-03-15 13:56:52,569] [INFO] Task started: fastANI
[2023-03-15 13:56:52,569] [INFO] Running command: fastANI --query /var/lib/cwl/stg4bc7f562-6ca4-44e7-ad00-63047b5664b4/OceanDNA-b31574.fa --refList OceanDNA-b31574/target_genomes_gtdb.txt --output OceanDNA-b31574/fastani_result_gtdb.tsv --threads 1
[2023-03-15 13:56:57,802] [INFO] Task succeeded: fastANI
[2023-03-15 13:56:57,808] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 13:56:57,808] [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	84.788	689	896	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteriqipengyuania	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000176355.1	s__Alteriqipengyuania bathyomarina	84.6805	684	896	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteriqipengyuania	95.0	98.10	96.53	0.93	0.90	11	-
GCF_015999305.1	s__Alteriqipengyuania sp015999305	84.6655	692	896	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteriqipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000186705.1	s__Alteriqipengyuania sp000186705	84.318	689	896	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteriqipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002377695.1	s__Alteriqipengyuania sp002377695	84.2388	664	896	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	84.0627	370	896	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	83.8429	677	896	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	83.7349	644	896	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 13:56:57,809] [INFO] GTDB search result was written to OceanDNA-b31574/result_gtdb.tsv
[2023-03-15 13:56:57,809] [INFO] ===== GTDB Search completed =====
[2023-03-15 13:56:57,812] [INFO] DFAST_QC result json was written to OceanDNA-b31574/dqc_result.json
[2023-03-15 13:56:57,812] [INFO] DFAST_QC completed!
[2023-03-15 13:56:57,812] [INFO] Total running time: 0h1m20s