[2023-03-14 10:55:58,906] [INFO] DFAST_QC pipeline started.
[2023-03-14 10:55:58,906] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 10:55:58,906] [INFO] DQC Reference Directory: /var/lib/cwl/stg81fcb19c-d527-4f2f-a8c6-52487a303e54/dqc_reference
[2023-03-14 10:56:00,753] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 10:56:00,753] [INFO] Task started: Prodigal
[2023-03-14 10:56:00,753] [INFO] Running command: cat /var/lib/cwl/stg67320bcb-0166-44dd-8eae-b4b31d965909/OceanDNA-b31714.fa | prodigal -d OceanDNA-b31714/cds.fna -a OceanDNA-b31714/protein.faa -g 11 -q > /dev/null
[2023-03-14 10:56:10,195] [INFO] Task succeeded: Prodigal
[2023-03-14 10:56:10,195] [INFO] Task started: HMMsearch
[2023-03-14 10:56:10,195] [INFO] Running command: hmmsearch --tblout OceanDNA-b31714/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg81fcb19c-d527-4f2f-a8c6-52487a303e54/dqc_reference/reference_markers.hmm OceanDNA-b31714/protein.faa > /dev/null
[2023-03-14 10:56:10,383] [INFO] Task succeeded: HMMsearch
[2023-03-14 10:56:10,383] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg67320bcb-0166-44dd-8eae-b4b31d965909/OceanDNA-b31714.fa]
[2023-03-14 10:56:10,398] [INFO] Query marker FASTA was written to OceanDNA-b31714/markers.fasta
[2023-03-14 10:56:10,398] [INFO] Task started: Blastn
[2023-03-14 10:56:10,398] [INFO] Running command: blastn -query OceanDNA-b31714/markers.fasta -db /var/lib/cwl/stg81fcb19c-d527-4f2f-a8c6-52487a303e54/dqc_reference/reference_markers.fasta -out OceanDNA-b31714/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 10:56:10,939] [INFO] Task succeeded: Blastn
[2023-03-14 10:56:10,940] [INFO] Selected 13 target genomes.
[2023-03-14 10:56:10,940] [INFO] Target genome list was writen to OceanDNA-b31714/target_genomes.txt
[2023-03-14 10:56:10,948] [INFO] Task started: fastANI
[2023-03-14 10:56:10,949] [INFO] Running command: fastANI --query /var/lib/cwl/stg67320bcb-0166-44dd-8eae-b4b31d965909/OceanDNA-b31714.fa --refList OceanDNA-b31714/target_genomes.txt --output OceanDNA-b31714/fastani_result.tsv --threads 1
[2023-03-14 10:56:17,729] [INFO] Task succeeded: fastANI
[2023-03-14 10:56:17,729] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg81fcb19c-d527-4f2f-a8c6-52487a303e54/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 10:56:17,729] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg81fcb19c-d527-4f2f-a8c6-52487a303e54/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 10:56:17,738] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 10:56:17,738] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-14 10:56:17,738] [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
Qipengyuania flava	strain=DSM 16421	GCA_011762005.1	192812	192812	type	True	81.2372	334	489	95	below_threshold
Qipengyuania qiaonensis	strain=6D47A	GCA_019711515.1	2867240	2867240	type	True	80.682	309	489	95	below_threshold
Qipengyuania proteolytica	strain=6B39	GCA_019711565.1	2867239	2867239	type	True	80.3758	306	489	95	below_threshold
Qipengyuania aurantiaca	strain=1NDH13	GCA_019711375.1	2867233	2867233	type	True	79.8746	275	489	95	below_threshold
Qipengyuania gaetbuli	strain=DSM 16225	GCA_009827315.1	266952	266952	type	True	79.7719	278	489	95	below_threshold
Qipengyuania aerophila	strain=GH25	GCA_019711555.1	2867242	2867242	type	True	79.7497	271	489	95	below_threshold
Qipengyuania pacifica	strain=NZ-96	GCA_019857205.1	2860199	2860199	type	True	79.6984	270	489	95	below_threshold
Qipengyuania polymorpha	strain=1NDH17	GCA_019711435.1	2867234	2867234	type	True	79.6522	255	489	95	below_threshold
Qipengyuania xiamenensis	strain=1XM1-15A	GCA_019711495.1	2867237	2867237	type	True	79.5766	259	489	95	below_threshold
Qipengyuania vesicularis	strain=1NDH10	GCA_019711415.1	2867232	2867232	type	True	79.2796	246	489	95	below_threshold
Qipengyuania seohaensis	strain=SW-135	GCA_002795865.1	266951	266951	type	True	79.1593	246	489	95	below_threshold
Qipengyuania huizhouensis	strain=YG19	GCA_019711635.1	2867245	2867245	type	True	78.9777	220	489	95	below_threshold
Qipengyuania pelagi	strain=JCM 17468	GCA_009827295.1	994320	994320	type	True	78.8621	245	489	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-14 10:56:17,738] [INFO] DFAST Taxonomy check result was written to OceanDNA-b31714/tc_result.tsv
[2023-03-14 10:56:17,738] [INFO] ===== Taxonomy check completed =====
[2023-03-14 10:56:17,738] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 10:56:17,738] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg81fcb19c-d527-4f2f-a8c6-52487a303e54/dqc_reference/checkm_data
[2023-03-14 10:56:17,739] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 10:56:17,742] [INFO] Task started: CheckM
[2023-03-14 10:56:17,742] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b31714/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b31714/checkm_input OceanDNA-b31714/checkm_result
[2023-03-14 10:56:44,501] [INFO] Task succeeded: CheckM
[2023-03-14 10:56:44,501] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 43.58%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 10:56:44,503] [INFO] ===== Completeness check finished =====
[2023-03-14 10:56:44,503] [INFO] ===== Start GTDB Search =====
[2023-03-14 10:56:44,503] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b31714/markers.fasta)
[2023-03-14 10:56:44,503] [INFO] Task started: Blastn
[2023-03-14 10:56:44,503] [INFO] Running command: blastn -query OceanDNA-b31714/markers.fasta -db /var/lib/cwl/stg81fcb19c-d527-4f2f-a8c6-52487a303e54/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b31714/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 10:56:45,163] [INFO] Task succeeded: Blastn
[2023-03-14 10:56:45,164] [INFO] Selected 10 target genomes.
[2023-03-14 10:56:45,164] [INFO] Target genome list was writen to OceanDNA-b31714/target_genomes_gtdb.txt
[2023-03-14 10:56:45,175] [INFO] Task started: fastANI
[2023-03-14 10:56:45,175] [INFO] Running command: fastANI --query /var/lib/cwl/stg67320bcb-0166-44dd-8eae-b4b31d965909/OceanDNA-b31714.fa --refList OceanDNA-b31714/target_genomes_gtdb.txt --output OceanDNA-b31714/fastani_result_gtdb.tsv --threads 1
[2023-03-14 10:56:50,396] [INFO] Task succeeded: fastANI
[2023-03-14 10:56:50,403] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-14 10:56:50,403] [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_003355455.1	s__Qipengyuania aurea	91.7632	440	489	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	97.67	97.64	0.83	0.82	3	-
GCF_001542855.1	s__Qipengyuania sp001542855	83.1084	361	489	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	97.07	97.03	0.89	0.88	4	-
GCF_009828015.1	s__Qipengyuania citrea	81.6921	326	489	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	97.91	97.49	0.87	0.80	20	-
GCA_016764075.1	s__Qipengyuania sp016764075	81.6581	264	489	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011762005.1	s__Qipengyuania flava	81.2372	334	489	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	97.04	96.57	0.91	0.85	10	-
GCF_015767595.1	s__Qipengyuania sp002895025	79.7657	272	489	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	97.29	96.55	0.87	0.78	16	-
GCF_009827315.1	s__Qipengyuania gaetbuli	79.7535	279	489	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009827325.1	s__Qipengyuania vulgaris	78.8853	218	489	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009827295.1	s__Qipengyuania pelagi	78.8537	246	489	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011054555.1	s__Erythrobacter sp011054555	77.5495	158	489	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-14 10:56:50,403] [INFO] GTDB search result was written to OceanDNA-b31714/result_gtdb.tsv
[2023-03-14 10:56:50,403] [INFO] ===== GTDB Search completed =====
[2023-03-14 10:56:50,405] [INFO] DFAST_QC result json was written to OceanDNA-b31714/dqc_result.json
[2023-03-14 10:56:50,405] [INFO] DFAST_QC completed!
[2023-03-14 10:56:50,405] [INFO] Total running time: 0h0m51s