[2023-03-15 16:25:57,003] [INFO] DFAST_QC pipeline started.
[2023-03-15 16:25:57,011] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 16:25:57,011] [INFO] DQC Reference Directory: /var/lib/cwl/stgb5e4dc89-2aa7-4eee-99e7-413d1a8f29a4/dqc_reference
[2023-03-15 16:25:58,598] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 16:25:58,598] [INFO] Task started: Prodigal
[2023-03-15 16:25:58,598] [INFO] Running command: cat /var/lib/cwl/stg853f284d-412b-4dc6-b9ce-37cc550cbf2f/OceanDNA-b31716.fa | prodigal -d OceanDNA-b31716/cds.fna -a OceanDNA-b31716/protein.faa -g 11 -q > /dev/null
[2023-03-15 16:26:18,021] [INFO] Task succeeded: Prodigal
[2023-03-15 16:26:18,021] [INFO] Task started: HMMsearch
[2023-03-15 16:26:18,021] [INFO] Running command: hmmsearch --tblout OceanDNA-b31716/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb5e4dc89-2aa7-4eee-99e7-413d1a8f29a4/dqc_reference/reference_markers.hmm OceanDNA-b31716/protein.faa > /dev/null
[2023-03-15 16:26:18,218] [INFO] Task succeeded: HMMsearch
[2023-03-15 16:26:18,219] [INFO] Found 6/6 markers.
[2023-03-15 16:26:18,293] [INFO] Query marker FASTA was written to OceanDNA-b31716/markers.fasta
[2023-03-15 16:26:18,293] [INFO] Task started: Blastn
[2023-03-15 16:26:18,293] [INFO] Running command: blastn -query OceanDNA-b31716/markers.fasta -db /var/lib/cwl/stgb5e4dc89-2aa7-4eee-99e7-413d1a8f29a4/dqc_reference/reference_markers.fasta -out OceanDNA-b31716/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 16:26:19,071] [INFO] Task succeeded: Blastn
[2023-03-15 16:26:19,082] [INFO] Selected 12 target genomes.
[2023-03-15 16:26:19,082] [INFO] Target genome list was writen to OceanDNA-b31716/target_genomes.txt
[2023-03-15 16:26:19,087] [INFO] Task started: fastANI
[2023-03-15 16:26:19,087] [INFO] Running command: fastANI --query /var/lib/cwl/stg853f284d-412b-4dc6-b9ce-37cc550cbf2f/OceanDNA-b31716.fa --refList OceanDNA-b31716/target_genomes.txt --output OceanDNA-b31716/fastani_result.tsv --threads 1
[2023-03-15 16:26:27,151] [INFO] Task succeeded: fastANI
[2023-03-15 16:26:27,151] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb5e4dc89-2aa7-4eee-99e7-413d1a8f29a4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 16:26:27,151] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb5e4dc89-2aa7-4eee-99e7-413d1a8f29a4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 16:26:27,159] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 16:26:27,159] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 16:26:27,159] [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	84.6974	763	1028	95	below_threshold
Qipengyuania proteolytica	strain=6B39	GCA_019711565.1	2867239	2867239	type	True	82.4258	656	1028	95	below_threshold
Qipengyuania qiaonensis	strain=6D47A	GCA_019711515.1	2867240	2867240	type	True	82.4125	657	1028	95	below_threshold
Qipengyuania pacifica	strain=NZ-96	GCA_019857205.1	2860199	2860199	type	True	81.8954	619	1028	95	below_threshold
Qipengyuania gaetbuli	strain=DSM 16225	GCA_009827315.1	266952	266952	type	True	81.6326	587	1028	95	below_threshold
Qipengyuania sphaerica	strain=GH29	GCA_019711595.1	2867243	2867243	type	True	81.5862	580	1028	95	below_threshold
Qipengyuania xiapuensis	strain=1NDW9	GCA_019711395.1	2867236	2867236	type	True	81.377	579	1028	95	below_threshold
Qipengyuania gelatinilytica	strain=1NDH1	GCA_019711315.1	2867231	2867231	type	True	81.3565	581	1028	95	below_threshold
Qipengyuania soli	strain=6D36	GCA_015529805.1	2782568	2782568	type	True	81.3106	564	1028	95	below_threshold
Qipengyuania aerophila	strain=GH25	GCA_019711555.1	2867242	2867242	type	True	81.3023	596	1028	95	below_threshold
Qipengyuania vesicularis	strain=1NDH10	GCA_019711415.1	2867232	2867232	type	True	81.0512	528	1028	95	below_threshold
Qipengyuania aquimaris	strain=JCM 12189	GCA_009827445.1	255984	255984	suspected-type	True	80.6245	532	1028	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 16:26:27,168] [INFO] DFAST Taxonomy check result was written to OceanDNA-b31716/tc_result.tsv
[2023-03-15 16:26:27,181] [INFO] ===== Taxonomy check completed =====
[2023-03-15 16:26:27,182] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 16:26:27,182] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb5e4dc89-2aa7-4eee-99e7-413d1a8f29a4/dqc_reference/checkm_data
[2023-03-15 16:26:27,183] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 16:26:27,193] [INFO] Task started: CheckM
[2023-03-15 16:26:27,193] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b31716/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b31716/checkm_input OceanDNA-b31716/checkm_result
[2023-03-15 16:27:15,891] [INFO] Task succeeded: CheckM
[2023-03-15 16:27:15,891] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 16:27:15,937] [INFO] ===== Completeness check finished =====
[2023-03-15 16:27:15,937] [INFO] ===== Start GTDB Search =====
[2023-03-15 16:27:15,937] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b31716/markers.fasta)
[2023-03-15 16:27:15,939] [INFO] Task started: Blastn
[2023-03-15 16:27:15,939] [INFO] Running command: blastn -query OceanDNA-b31716/markers.fasta -db /var/lib/cwl/stgb5e4dc89-2aa7-4eee-99e7-413d1a8f29a4/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b31716/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 16:27:17,240] [INFO] Task succeeded: Blastn
[2023-03-15 16:27:17,255] [INFO] Selected 9 target genomes.
[2023-03-15 16:27:17,255] [INFO] Target genome list was writen to OceanDNA-b31716/target_genomes_gtdb.txt
[2023-03-15 16:27:17,265] [INFO] Task started: fastANI
[2023-03-15 16:27:17,265] [INFO] Running command: fastANI --query /var/lib/cwl/stg853f284d-412b-4dc6-b9ce-37cc550cbf2f/OceanDNA-b31716.fa --refList OceanDNA-b31716/target_genomes_gtdb.txt --output OceanDNA-b31716/fastani_result_gtdb.tsv --threads 1
[2023-03-15 16:27:23,409] [INFO] Task succeeded: fastANI
[2023-03-15 16:27:23,415] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 16:27:23,415] [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
GCA_016764075.1	s__Qipengyuania sp016764075	96.3264	661	1028	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_009828015.1	s__Qipengyuania citrea	87.8758	767	1028	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	97.91	97.49	0.87	0.80	20	-
GCF_011762005.1	s__Qipengyuania flava	84.6974	763	1028	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	97.04	96.57	0.91	0.85	10	-
GCF_001542855.1	s__Qipengyuania sp001542855	84.1846	751	1028	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	82.9645	691	1028	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	81.6407	586	1028	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	81.6288	617	1028	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	97.29	96.55	0.87	0.78	16	-
GCF_015529805.1	s__Qipengyuania soli	81.322	563	1028	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	81.1434	570	1028	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 16:27:23,419] [INFO] GTDB search result was written to OceanDNA-b31716/result_gtdb.tsv
[2023-03-15 16:27:23,424] [INFO] ===== GTDB Search completed =====
[2023-03-15 16:27:23,430] [INFO] DFAST_QC result json was written to OceanDNA-b31716/dqc_result.json
[2023-03-15 16:27:23,430] [INFO] DFAST_QC completed!
[2023-03-15 16:27:23,430] [INFO] Total running time: 0h1m26s