[2023-03-15 12:44:24,470] [INFO] DFAST_QC pipeline started.
[2023-03-15 12:44:24,471] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 12:44:24,471] [INFO] DQC Reference Directory: /var/lib/cwl/stg5a6f2544-2c6a-4efc-95d5-8b43acdbbe67/dqc_reference
[2023-03-15 12:44:26,208] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 12:44:26,208] [INFO] Task started: Prodigal
[2023-03-15 12:44:26,208] [INFO] Running command: cat /var/lib/cwl/stg3c5c354e-e81d-4f8d-9f59-bd0f01f04d9e/OceanDNA-b31725.fa | prodigal -d OceanDNA-b31725/cds.fna -a OceanDNA-b31725/protein.faa -g 11 -q > /dev/null
[2023-03-15 12:44:37,725] [INFO] Task succeeded: Prodigal
[2023-03-15 12:44:37,725] [INFO] Task started: HMMsearch
[2023-03-15 12:44:37,725] [INFO] Running command: hmmsearch --tblout OceanDNA-b31725/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5a6f2544-2c6a-4efc-95d5-8b43acdbbe67/dqc_reference/reference_markers.hmm OceanDNA-b31725/protein.faa > /dev/null
[2023-03-15 12:44:37,935] [INFO] Task succeeded: HMMsearch
[2023-03-15 12:44:37,936] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg3c5c354e-e81d-4f8d-9f59-bd0f01f04d9e/OceanDNA-b31725.fa]
[2023-03-15 12:44:37,953] [INFO] Query marker FASTA was written to OceanDNA-b31725/markers.fasta
[2023-03-15 12:44:37,954] [INFO] Task started: Blastn
[2023-03-15 12:44:37,954] [INFO] Running command: blastn -query OceanDNA-b31725/markers.fasta -db /var/lib/cwl/stg5a6f2544-2c6a-4efc-95d5-8b43acdbbe67/dqc_reference/reference_markers.fasta -out OceanDNA-b31725/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 12:44:38,743] [INFO] Task succeeded: Blastn
[2023-03-15 12:44:38,744] [INFO] Selected 14 target genomes.
[2023-03-15 12:44:38,744] [INFO] Target genome list was writen to OceanDNA-b31725/target_genomes.txt
[2023-03-15 12:44:38,753] [INFO] Task started: fastANI
[2023-03-15 12:44:38,753] [INFO] Running command: fastANI --query /var/lib/cwl/stg3c5c354e-e81d-4f8d-9f59-bd0f01f04d9e/OceanDNA-b31725.fa --refList OceanDNA-b31725/target_genomes.txt --output OceanDNA-b31725/fastani_result.tsv --threads 1
[2023-03-15 12:44:46,484] [INFO] Task succeeded: fastANI
[2023-03-15 12:44:46,484] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5a6f2544-2c6a-4efc-95d5-8b43acdbbe67/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 12:44:46,484] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5a6f2544-2c6a-4efc-95d5-8b43acdbbe67/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 12:44:46,493] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 12:44:46,493] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 12:44:46,493] [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 qiaonensis	strain=6D47A	GCA_019711515.1	2867240	2867240	type	True	83.6642	464	614	95	below_threshold
Qipengyuania flava	strain=DSM 16421	GCA_011762005.1	192812	192812	type	True	81.6936	397	614	95	below_threshold
Qipengyuania pacifica	strain=NZ-96	GCA_019857205.1	2860199	2860199	type	True	81.686	433	614	95	below_threshold
Qipengyuania proteolytica	strain=6B39	GCA_019711565.1	2867239	2867239	type	True	81.5521	388	614	95	below_threshold
Qipengyuania aerophila	strain=GH25	GCA_019711555.1	2867242	2867242	type	True	81.3695	398	614	95	below_threshold
Qipengyuania gaetbuli	strain=DSM 16225	GCA_009827315.1	266952	266952	type	True	80.773	361	614	95	below_threshold
Qipengyuania polymorpha	strain=1NDH17	GCA_019711435.1	2867234	2867234	type	True	80.6204	348	614	95	below_threshold
Qipengyuania sphaerica	strain=GH29	GCA_019711595.1	2867243	2867243	type	True	80.5215	361	614	95	below_threshold
Qipengyuania gelatinilytica	strain=1NDH1	GCA_019711315.1	2867231	2867231	type	True	80.4704	343	614	95	below_threshold
Qipengyuania xiapuensis	strain=1NDW9	GCA_019711395.1	2867236	2867236	type	True	80.4276	355	614	95	below_threshold
Qipengyuania soli	strain=6D36	GCA_015529805.1	2782568	2782568	type	True	80.3625	373	614	95	below_threshold
Qipengyuania nanhaisediminis	strain=CGMCC 1.7715	GCA_900115585.1	604088	604088	type	True	80.0173	326	614	95	below_threshold
Qipengyuania vesicularis	strain=1NDH10	GCA_019711415.1	2867232	2867232	type	True	79.8885	344	614	95	below_threshold
Qipengyuania seohaensis	strain=SW-135	GCA_002795865.1	266951	266951	type	True	79.8246	312	614	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 12:44:46,493] [INFO] DFAST Taxonomy check result was written to OceanDNA-b31725/tc_result.tsv
[2023-03-15 12:44:46,494] [INFO] ===== Taxonomy check completed =====
[2023-03-15 12:44:46,494] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 12:44:46,494] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5a6f2544-2c6a-4efc-95d5-8b43acdbbe67/dqc_reference/checkm_data
[2023-03-15 12:44:46,495] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 12:44:46,498] [INFO] Task started: CheckM
[2023-03-15 12:44:46,498] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b31725/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b31725/checkm_input OceanDNA-b31725/checkm_result
[2023-03-15 12:45:18,781] [INFO] Task succeeded: CheckM
[2023-03-15 12:45:18,782] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 47.92%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 12:45:18,784] [INFO] ===== Completeness check finished =====
[2023-03-15 12:45:18,784] [INFO] ===== Start GTDB Search =====
[2023-03-15 12:45:18,784] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b31725/markers.fasta)
[2023-03-15 12:45:18,784] [INFO] Task started: Blastn
[2023-03-15 12:45:18,784] [INFO] Running command: blastn -query OceanDNA-b31725/markers.fasta -db /var/lib/cwl/stg5a6f2544-2c6a-4efc-95d5-8b43acdbbe67/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b31725/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 12:45:20,276] [INFO] Task succeeded: Blastn
[2023-03-15 12:45:20,276] [INFO] Selected 14 target genomes.
[2023-03-15 12:45:20,276] [INFO] Target genome list was writen to OceanDNA-b31725/target_genomes_gtdb.txt
[2023-03-15 12:45:20,319] [INFO] Task started: fastANI
[2023-03-15 12:45:20,319] [INFO] Running command: fastANI --query /var/lib/cwl/stg3c5c354e-e81d-4f8d-9f59-bd0f01f04d9e/OceanDNA-b31725.fa --refList OceanDNA-b31725/target_genomes_gtdb.txt --output OceanDNA-b31725/fastani_result_gtdb.tsv --threads 1
[2023-03-15 12:45:27,904] [INFO] Task succeeded: fastANI
[2023-03-15 12:45:27,912] [INFO] Found 14 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 12:45:27,912] [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_001542855.1	s__Qipengyuania sp001542855	82.5273	426	614	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	81.9698	413	614	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	81.9048	333	614	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003355455.1	s__Qipengyuania aurea	81.8025	424	614	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	97.67	97.64	0.83	0.82	3	-
GCF_011762005.1	s__Qipengyuania flava	81.6936	397	614	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	81.405	416	614	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	80.773	361	614	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015529805.1	s__Qipengyuania soli	80.3465	374	614	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000756795.1	s__Qipengyuania vulgaris_A	80.2492	346	614	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013260645.1	s__Qipengyuania mangrovi	80.1845	332	614	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013001165.1	s__Qipengyuania sp013001165	80.0575	278	614	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900115585.1	s__Qipengyuania nanhaisediminis	80.0173	326	614	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002795865.1	s__Qipengyuania seohaensis	79.8246	312	614	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	79.251	309	614	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 12:45:27,912] [INFO] GTDB search result was written to OceanDNA-b31725/result_gtdb.tsv
[2023-03-15 12:45:27,913] [INFO] ===== GTDB Search completed =====
[2023-03-15 12:45:27,914] [INFO] DFAST_QC result json was written to OceanDNA-b31725/dqc_result.json
[2023-03-15 12:45:27,914] [INFO] DFAST_QC completed!
[2023-03-15 12:45:27,914] [INFO] Total running time: 0h1m3s