[2023-03-14 12:03:55,351] [INFO] DFAST_QC pipeline started.
[2023-03-14 12:03:55,352] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 12:03:55,352] [INFO] DQC Reference Directory: /var/lib/cwl/stg90a3d026-0273-4b37-9c1c-711f69ccf294/dqc_reference
[2023-03-14 12:03:56,865] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 12:03:56,865] [INFO] Task started: Prodigal
[2023-03-14 12:03:56,865] [INFO] Running command: cat /var/lib/cwl/stg8a3e93a8-8c41-4544-840d-6f3e0b07a1e3/OceanDNA-b31572.fa | prodigal -d OceanDNA-b31572/cds.fna -a OceanDNA-b31572/protein.faa -g 11 -q > /dev/null
[2023-03-14 12:04:10,090] [INFO] Task succeeded: Prodigal
[2023-03-14 12:04:10,090] [INFO] Task started: HMMsearch
[2023-03-14 12:04:10,090] [INFO] Running command: hmmsearch --tblout OceanDNA-b31572/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg90a3d026-0273-4b37-9c1c-711f69ccf294/dqc_reference/reference_markers.hmm OceanDNA-b31572/protein.faa > /dev/null
[2023-03-14 12:04:10,263] [INFO] Task succeeded: HMMsearch
[2023-03-14 12:04:10,263] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg8a3e93a8-8c41-4544-840d-6f3e0b07a1e3/OceanDNA-b31572.fa]
[2023-03-14 12:04:10,296] [INFO] Query marker FASTA was written to OceanDNA-b31572/markers.fasta
[2023-03-14 12:04:10,298] [INFO] Task started: Blastn
[2023-03-14 12:04:10,298] [INFO] Running command: blastn -query OceanDNA-b31572/markers.fasta -db /var/lib/cwl/stg90a3d026-0273-4b37-9c1c-711f69ccf294/dqc_reference/reference_markers.fasta -out OceanDNA-b31572/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 12:04:10,939] [INFO] Task succeeded: Blastn
[2023-03-14 12:04:10,941] [INFO] Selected 14 target genomes.
[2023-03-14 12:04:10,941] [INFO] Target genome list was writen to OceanDNA-b31572/target_genomes.txt
[2023-03-14 12:04:10,949] [INFO] Task started: fastANI
[2023-03-14 12:04:10,949] [INFO] Running command: fastANI --query /var/lib/cwl/stg8a3e93a8-8c41-4544-840d-6f3e0b07a1e3/OceanDNA-b31572.fa --refList OceanDNA-b31572/target_genomes.txt --output OceanDNA-b31572/fastani_result.tsv --threads 1
[2023-03-14 12:04:19,491] [INFO] Task succeeded: fastANI
[2023-03-14 12:04:19,492] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg90a3d026-0273-4b37-9c1c-711f69ccf294/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 12:04:19,492] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg90a3d026-0273-4b37-9c1c-711f69ccf294/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 12:04:19,501] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 12:04:19,502] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-14 12:04:19,502] [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	83.7824	554	705	95	below_threshold
Alteriqipengyuania lutimaris	strain=S-5	GCA_003363135.1	1538146	1538146	type	True	83.0652	545	705	95	below_threshold
Alteriqipengyuania lutimaris	strain=CECT 8624	GCA_014191645.1	1538146	1538146	type	True	83.0562	543	705	95	below_threshold
Qipengyuania proteolytica	strain=6B39	GCA_019711565.1	2867239	2867239	type	True	78.8073	330	705	95	below_threshold
Qipengyuania aurantiaca	strain=1NDH13	GCA_019711375.1	2867233	2867233	type	True	78.5991	316	705	95	below_threshold
Qipengyuania pelagi	strain=JCM 17468	GCA_009827295.1	994320	994320	type	True	78.4597	317	705	95	below_threshold
Qipengyuania gaetbuli	strain=DSM 16225	GCA_009827315.1	266952	266952	type	True	78.3728	323	705	95	below_threshold
Pelagerythrobacter rhizovicinus	strain=AY-3R	GCA_004135625.1	2268576	2268576	type	True	78.2328	302	705	95	below_threshold
Pelagerythrobacter aerophilus	strain=Ery1	GCA_003581645.1	2306995	2306995	type	True	78.1556	309	705	95	below_threshold
Erythrobacter dokdonensis	strain=DSW-74	GCA_001677335.1	328225	328225	type	True	78.135	266	705	95	below_threshold
Aurantiacibacter xanthus	strain=CCTCC AB 2015396	GCA_003584015.1	1784712	1784712	type	True	78.0455	237	705	95	below_threshold
Qipengyuania soli	strain=6D36	GCA_015529805.1	2782568	2782568	type	True	78.004	272	705	95	below_threshold
Qipengyuania aerophila	strain=GH25	GCA_019711555.1	2867242	2867242	type	True	77.4902	216	705	95	below_threshold
Croceibacterium atlanticum	strain=26DY36	GCA_001008165.2	1267766	1267766	type	True	76.9379	210	705	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-14 12:04:19,505] [INFO] DFAST Taxonomy check result was written to OceanDNA-b31572/tc_result.tsv
[2023-03-14 12:04:19,505] [INFO] ===== Taxonomy check completed =====
[2023-03-14 12:04:19,505] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 12:04:19,505] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg90a3d026-0273-4b37-9c1c-711f69ccf294/dqc_reference/checkm_data
[2023-03-14 12:04:19,506] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 12:04:19,511] [INFO] Task started: CheckM
[2023-03-14 12:04:19,512] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b31572/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b31572/checkm_input OceanDNA-b31572/checkm_result
[2023-03-14 12:04:55,475] [INFO] Task succeeded: CheckM
[2023-03-14 12:04:55,476] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 55.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 12:04:55,519] [INFO] ===== Completeness check finished =====
[2023-03-14 12:04:55,520] [INFO] ===== Start GTDB Search =====
[2023-03-14 12:04:55,520] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b31572/markers.fasta)
[2023-03-14 12:04:55,521] [INFO] Task started: Blastn
[2023-03-14 12:04:55,521] [INFO] Running command: blastn -query OceanDNA-b31572/markers.fasta -db /var/lib/cwl/stg90a3d026-0273-4b37-9c1c-711f69ccf294/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b31572/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 12:04:56,549] [INFO] Task succeeded: Blastn
[2023-03-14 12:04:56,553] [INFO] Selected 8 target genomes.
[2023-03-14 12:04:56,553] [INFO] Target genome list was writen to OceanDNA-b31572/target_genomes_gtdb.txt
[2023-03-14 12:04:56,569] [INFO] Task started: fastANI
[2023-03-14 12:04:56,569] [INFO] Running command: fastANI --query /var/lib/cwl/stg8a3e93a8-8c41-4544-840d-6f3e0b07a1e3/OceanDNA-b31572.fa --refList OceanDNA-b31572/target_genomes_gtdb.txt --output OceanDNA-b31572/fastani_result_gtdb.tsv --threads 1
[2023-03-14 12:05:01,356] [INFO] Task succeeded: fastANI
[2023-03-14 12:05:01,362] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-14 12:05:01,362] [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_000176355.1	s__Alteriqipengyuania bathyomarina	83.7579	546	705	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	83.6584	559	705	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	83.5786	571	705	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteriqipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002729695.1	s__Alteriqipengyuania sp002729695	83.4903	537	705	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteriqipengyuania	95.0	99.53	99.11	0.93	0.90	4	-
GCA_002377695.1	s__Alteriqipengyuania sp002377695	83.2329	551	705	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteriqipengyuania	95.0	99.97	99.97	1.00	1.00	2	-
GCF_003363135.1	s__Alteriqipengyuania lutimaris	83.0495	546	705	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteriqipengyuania	95.0	100.00	100.00	1.00	1.00	2	-
GCA_009993635.1	s__Alteriqipengyuania sp009993635	82.9823	582	705	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteriqipengyuania	95.0	99.91	99.91	0.97	0.97	2	-
GCA_002712945.1	s__Alteriqipengyuania sp002712945	82.6965	297	705	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteriqipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-14 12:05:01,365] [INFO] GTDB search result was written to OceanDNA-b31572/result_gtdb.tsv
[2023-03-14 12:05:01,365] [INFO] ===== GTDB Search completed =====
[2023-03-14 12:05:01,369] [INFO] DFAST_QC result json was written to OceanDNA-b31572/dqc_result.json
[2023-03-14 12:05:01,369] [INFO] DFAST_QC completed!
[2023-03-14 12:05:01,369] [INFO] Total running time: 0h1m6s