[2023-03-14 10:55:58,905] [INFO] DFAST_QC pipeline started.
[2023-03-14 10:55:58,905] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 10:55:58,905] [INFO] DQC Reference Directory: /var/lib/cwl/stg34d67f9e-c4ea-4b3d-bb1a-0e6a6aced9a5/dqc_reference
[2023-03-14 10:56:00,685] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 10:56:00,685] [INFO] Task started: Prodigal
[2023-03-14 10:56:00,685] [INFO] Running command: cat /var/lib/cwl/stgd594721c-e946-4c36-937b-ee5e4be1b452/OceanDNA-b31575.fa | prodigal -d OceanDNA-b31575/cds.fna -a OceanDNA-b31575/protein.faa -g 11 -q > /dev/null
[2023-03-14 10:56:11,575] [INFO] Task succeeded: Prodigal
[2023-03-14 10:56:11,576] [INFO] Task started: HMMsearch
[2023-03-14 10:56:11,576] [INFO] Running command: hmmsearch --tblout OceanDNA-b31575/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg34d67f9e-c4ea-4b3d-bb1a-0e6a6aced9a5/dqc_reference/reference_markers.hmm OceanDNA-b31575/protein.faa > /dev/null
[2023-03-14 10:56:11,757] [INFO] Task succeeded: HMMsearch
[2023-03-14 10:56:11,757] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgd594721c-e946-4c36-937b-ee5e4be1b452/OceanDNA-b31575.fa]
[2023-03-14 10:56:11,771] [INFO] Query marker FASTA was written to OceanDNA-b31575/markers.fasta
[2023-03-14 10:56:11,772] [INFO] Task started: Blastn
[2023-03-14 10:56:11,772] [INFO] Running command: blastn -query OceanDNA-b31575/markers.fasta -db /var/lib/cwl/stg34d67f9e-c4ea-4b3d-bb1a-0e6a6aced9a5/dqc_reference/reference_markers.fasta -out OceanDNA-b31575/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 10:56:12,358] [INFO] Task succeeded: Blastn
[2023-03-14 10:56:12,359] [INFO] Selected 12 target genomes.
[2023-03-14 10:56:12,359] [INFO] Target genome list was writen to OceanDNA-b31575/target_genomes.txt
[2023-03-14 10:56:12,366] [INFO] Task started: fastANI
[2023-03-14 10:56:12,366] [INFO] Running command: fastANI --query /var/lib/cwl/stgd594721c-e946-4c36-937b-ee5e4be1b452/OceanDNA-b31575.fa --refList OceanDNA-b31575/target_genomes.txt --output OceanDNA-b31575/fastani_result.tsv --threads 1
[2023-03-14 10:56:19,595] [INFO] Task succeeded: fastANI
[2023-03-14 10:56:19,595] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg34d67f9e-c4ea-4b3d-bb1a-0e6a6aced9a5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 10:56:19,596] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg34d67f9e-c4ea-4b3d-bb1a-0e6a6aced9a5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 10:56:19,603] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 10:56:19,604] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-14 10:56:19,604] [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	84.5039	492	582	95	below_threshold
Alteriqipengyuania lutimaris	strain=CECT 8624	GCA_014191645.1	1538146	1538146	type	True	84.4446	484	582	95	below_threshold
Alteriqipengyuania lutimaris	strain=S-5	GCA_003363135.1	1538146	1538146	type	True	84.4257	486	582	95	below_threshold
Qipengyuania proteolytica	strain=6B39	GCA_019711565.1	2867239	2867239	type	True	79.1677	288	582	95	below_threshold
Pelagerythrobacter marinus	strain=H32	GCA_009827515.1	538382	538382	type	True	78.748	310	582	95	below_threshold
Pelagerythrobacter rhizovicinus	strain=AY-3R	GCA_004135625.1	2268576	2268576	type	True	78.5267	281	582	95	below_threshold
Qipengyuania gelatinilytica	strain=1NDH1	GCA_019711315.1	2867231	2867231	type	True	78.4948	255	582	95	below_threshold
Qipengyuania nanhaisediminis	strain=CGMCC 1.7715	GCA_900115585.1	604088	604088	type	True	78.338	237	582	95	below_threshold
Qipengyuania algicida	strain=KEMB 9005-328	GCA_009828025.1	1836209	1836209	type	True	78.13	213	582	95	below_threshold
Qipengyuania intermedia	strain=GH38	GCA_019711615.1	2867244	2867244	type	True	78.1108	228	582	95	below_threshold
Qipengyuania seohaensis	strain=SW-135	GCA_002795865.1	266951	266951	type	True	78.0134	222	582	95	below_threshold
Novosphingobium silvae	strain=FGD1	GCA_009856825.1	2692619	2692619	type	True	77.0856	127	582	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-14 10:56:19,604] [INFO] DFAST Taxonomy check result was written to OceanDNA-b31575/tc_result.tsv
[2023-03-14 10:56:19,604] [INFO] ===== Taxonomy check completed =====
[2023-03-14 10:56:19,604] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 10:56:19,604] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg34d67f9e-c4ea-4b3d-bb1a-0e6a6aced9a5/dqc_reference/checkm_data
[2023-03-14 10:56:19,605] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 10:56:19,608] [INFO] Task started: CheckM
[2023-03-14 10:56:19,608] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b31575/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b31575/checkm_input OceanDNA-b31575/checkm_result
[2023-03-14 10:56:50,067] [INFO] Task succeeded: CheckM
[2023-03-14 10:56:50,067] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 59.72%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 10:56:50,069] [INFO] ===== Completeness check finished =====
[2023-03-14 10:56:50,069] [INFO] ===== Start GTDB Search =====
[2023-03-14 10:56:50,069] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b31575/markers.fasta)
[2023-03-14 10:56:50,069] [INFO] Task started: Blastn
[2023-03-14 10:56:50,069] [INFO] Running command: blastn -query OceanDNA-b31575/markers.fasta -db /var/lib/cwl/stg34d67f9e-c4ea-4b3d-bb1a-0e6a6aced9a5/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b31575/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 10:56:50,926] [INFO] Task succeeded: Blastn
[2023-03-14 10:56:50,927] [INFO] Selected 8 target genomes.
[2023-03-14 10:56:50,927] [INFO] Target genome list was writen to OceanDNA-b31575/target_genomes_gtdb.txt
[2023-03-14 10:56:50,936] [INFO] Task started: fastANI
[2023-03-14 10:56:50,937] [INFO] Running command: fastANI --query /var/lib/cwl/stgd594721c-e946-4c36-937b-ee5e4be1b452/OceanDNA-b31575.fa --refList OceanDNA-b31575/target_genomes_gtdb.txt --output OceanDNA-b31575/fastani_result_gtdb.tsv --threads 1
[2023-03-14 10:56:55,590] [INFO] Task succeeded: fastANI
[2023-03-14 10:56:55,596] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-14 10:56:55,596] [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_015999305.1	s__Alteriqipengyuania sp015999305	84.6	494	582	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteriqipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003363135.1	s__Alteriqipengyuania lutimaris	84.4257	486	582	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteriqipengyuania	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000176355.1	s__Alteriqipengyuania bathyomarina	84.3526	489	582	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteriqipengyuania	95.0	98.10	96.53	0.93	0.90	11	-
GCF_000186705.1	s__Alteriqipengyuania sp000186705	84.0459	480	582	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteriqipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009993635.1	s__Alteriqipengyuania sp009993635	83.7695	484	582	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	83.7402	251	582	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteriqipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002377695.1	s__Alteriqipengyuania sp002377695	83.5767	481	582	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteriqipengyuania	95.0	99.97	99.97	1.00	1.00	2	-
GCA_002729695.1	s__Alteriqipengyuania sp002729695	83.5705	471	582	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteriqipengyuania	95.0	99.53	99.11	0.93	0.90	4	-
--------------------------------------------------------------------------------
[2023-03-14 10:56:55,597] [INFO] GTDB search result was written to OceanDNA-b31575/result_gtdb.tsv
[2023-03-14 10:56:55,597] [INFO] ===== GTDB Search completed =====
[2023-03-14 10:56:55,598] [INFO] DFAST_QC result json was written to OceanDNA-b31575/dqc_result.json
[2023-03-14 10:56:55,598] [INFO] DFAST_QC completed!
[2023-03-14 10:56:55,598] [INFO] Total running time: 0h0m57s