[2023-03-19 03:50:07,836] [INFO] DFAST_QC pipeline started.
[2023-03-19 03:50:07,836] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 03:50:07,836] [INFO] DQC Reference Directory: /var/lib/cwl/stg503f4806-e7dd-4fe7-99b3-2df1f335c45f/dqc_reference
[2023-03-19 03:50:09,609] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 03:50:09,609] [INFO] Task started: Prodigal
[2023-03-19 03:50:09,609] [INFO] Running command: cat /var/lib/cwl/stgc20d1ed2-7aab-42b2-b2d9-da503c14d316/OceanDNA-b31816.fa | prodigal -d OceanDNA-b31816/cds.fna -a OceanDNA-b31816/protein.faa -g 11 -q > /dev/null
[2023-03-19 03:50:21,268] [INFO] Task succeeded: Prodigal
[2023-03-19 03:50:21,269] [INFO] Task started: HMMsearch
[2023-03-19 03:50:21,269] [INFO] Running command: hmmsearch --tblout OceanDNA-b31816/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg503f4806-e7dd-4fe7-99b3-2df1f335c45f/dqc_reference/reference_markers.hmm OceanDNA-b31816/protein.faa > /dev/null
[2023-03-19 03:50:21,494] [INFO] Task succeeded: HMMsearch
[2023-03-19 03:50:21,494] [INFO] Found 6/6 markers.
[2023-03-19 03:50:21,510] [INFO] Query marker FASTA was written to OceanDNA-b31816/markers.fasta
[2023-03-19 03:50:21,511] [INFO] Task started: Blastn
[2023-03-19 03:50:21,511] [INFO] Running command: blastn -query OceanDNA-b31816/markers.fasta -db /var/lib/cwl/stg503f4806-e7dd-4fe7-99b3-2df1f335c45f/dqc_reference/reference_markers.fasta -out OceanDNA-b31816/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 03:50:22,191] [INFO] Task succeeded: Blastn
[2023-03-19 03:50:22,192] [INFO] Selected 14 target genomes.
[2023-03-19 03:50:22,192] [INFO] Target genome list was writen to OceanDNA-b31816/target_genomes.txt
[2023-03-19 03:50:22,200] [INFO] Task started: fastANI
[2023-03-19 03:50:22,200] [INFO] Running command: fastANI --query /var/lib/cwl/stgc20d1ed2-7aab-42b2-b2d9-da503c14d316/OceanDNA-b31816.fa --refList OceanDNA-b31816/target_genomes.txt --output OceanDNA-b31816/fastani_result.tsv --threads 1
[2023-03-19 03:50:30,048] [INFO] Task succeeded: fastANI
[2023-03-19 03:50:30,049] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg503f4806-e7dd-4fe7-99b3-2df1f335c45f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 03:50:30,049] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg503f4806-e7dd-4fe7-99b3-2df1f335c45f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 03:50:30,058] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2023-03-19 03:50:30,058] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-19 03:50:30,058] [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	97.0619	590	609	95	conclusive
Qipengyuania qiaonensis	strain=6D47A	GCA_019711515.1	2867240	2867240	type	True	81.3023	426	609	95	below_threshold
Qipengyuania proteolytica	strain=6B39	GCA_019711565.1	2867239	2867239	type	True	81.2625	430	609	95	below_threshold
Qipengyuania aurantiaca	strain=1NDH13	GCA_019711375.1	2867233	2867233	type	True	80.7157	377	609	95	below_threshold
Qipengyuania sphaerica	strain=GH29	GCA_019711595.1	2867243	2867243	type	True	80.678	369	609	95	below_threshold
Qipengyuania gaetbuli	strain=DSM 16225	GCA_009827315.1	266952	266952	type	True	80.5766	398	609	95	below_threshold
Qipengyuania xiapuensis	strain=1NDW9	GCA_019711395.1	2867236	2867236	type	True	80.5372	382	609	95	below_threshold
Qipengyuania gelatinilytica	strain=1NDH1	GCA_019711315.1	2867231	2867231	type	True	80.4377	383	609	95	below_threshold
Qipengyuania polymorpha	strain=1NDH17	GCA_019711435.1	2867234	2867234	type	True	80.366	387	609	95	below_threshold
Qipengyuania aerophila	strain=GH25	GCA_019711555.1	2867242	2867242	type	True	80.301	390	609	95	below_threshold
Qipengyuania pacifica	strain=NZ-96	GCA_019857205.1	2860199	2860199	type	True	80.2419	398	609	95	below_threshold
Qipengyuania vesicularis	strain=1NDH10	GCA_019711415.1	2867232	2867232	type	True	80.1073	356	609	95	below_threshold
Qipengyuania soli	strain=6D36	GCA_015529805.1	2782568	2782568	type	True	80.1017	390	609	95	below_threshold
Qipengyuania aquimaris	strain=JCM 12189	GCA_009827445.1	255984	255984	suspected-type	True	79.7761	353	609	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 03:50:30,058] [INFO] DFAST Taxonomy check result was written to OceanDNA-b31816/tc_result.tsv
[2023-03-19 03:50:30,059] [INFO] ===== Taxonomy check completed =====
[2023-03-19 03:50:30,059] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 03:50:30,059] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg503f4806-e7dd-4fe7-99b3-2df1f335c45f/dqc_reference/checkm_data
[2023-03-19 03:50:30,059] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 03:50:30,063] [INFO] Task started: CheckM
[2023-03-19 03:50:30,063] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b31816/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b31816/checkm_input OceanDNA-b31816/checkm_result
[2023-03-19 03:51:02,269] [INFO] Task succeeded: CheckM
[2023-03-19 03:51:02,269] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 70.83%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 03:51:02,272] [INFO] ===== Completeness check finished =====
[2023-03-19 03:51:02,272] [INFO] ===== Start GTDB Search =====
[2023-03-19 03:51:02,272] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b31816/markers.fasta)
[2023-03-19 03:51:02,272] [INFO] Task started: Blastn
[2023-03-19 03:51:02,272] [INFO] Running command: blastn -query OceanDNA-b31816/markers.fasta -db /var/lib/cwl/stg503f4806-e7dd-4fe7-99b3-2df1f335c45f/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b31816/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 03:51:03,348] [INFO] Task succeeded: Blastn
[2023-03-19 03:51:03,349] [INFO] Selected 14 target genomes.
[2023-03-19 03:51:03,350] [INFO] Target genome list was writen to OceanDNA-b31816/target_genomes_gtdb.txt
[2023-03-19 03:51:03,362] [INFO] Task started: fastANI
[2023-03-19 03:51:03,362] [INFO] Running command: fastANI --query /var/lib/cwl/stgc20d1ed2-7aab-42b2-b2d9-da503c14d316/OceanDNA-b31816.fa --refList OceanDNA-b31816/target_genomes_gtdb.txt --output OceanDNA-b31816/fastani_result_gtdb.tsv --threads 1
[2023-03-19 03:51:11,478] [INFO] Task succeeded: fastANI
[2023-03-19 03:51:11,487] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-19 03:51:11,487] [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_011762005.1	s__Qipengyuania flava	97.0619	590	609	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	97.04	96.57	0.91	0.85	10	conclusive
GCF_009828015.1	s__Qipengyuania citrea	84.691	502	609	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	83.9801	400	609	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001542855.1	s__Qipengyuania sp001542855	82.3412	468	609	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	97.07	97.03	0.89	0.88	4	-
GCF_003355455.1	s__Qipengyuania aurea	81.8485	437	609	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	97.67	97.64	0.83	0.82	3	-
GCF_009827315.1	s__Qipengyuania gaetbuli	80.5766	398	609	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015767595.1	s__Qipengyuania sp002895025	80.5577	395	609	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	97.29	96.55	0.87	0.78	16	-
GCF_000181515.1	s__Qipengyuania sp000181515	80.3006	380	609	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	80.0877	391	609	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	80.0234	300	609	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009827445.1	s__Qipengyuania aquimaris	79.762	354	609	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	79.744	336	609	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001635685.1	s__Qipengyuania sp001635685	79.2706	338	609	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	99.58	97.35	0.92	0.89	12	-
GCF_015999305.1	s__Alteriqipengyuania sp015999305	78.7311	333	609	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteriqipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 03:51:11,487] [INFO] GTDB search result was written to OceanDNA-b31816/result_gtdb.tsv
[2023-03-19 03:51:11,488] [INFO] ===== GTDB Search completed =====
[2023-03-19 03:51:11,489] [INFO] DFAST_QC result json was written to OceanDNA-b31816/dqc_result.json
[2023-03-19 03:51:11,489] [INFO] DFAST_QC completed!
[2023-03-19 03:51:11,489] [INFO] Total running time: 0h1m4s