[2023-03-14 12:19:39,622] [INFO] DFAST_QC pipeline started.
[2023-03-14 12:19:39,623] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 12:19:39,623] [INFO] DQC Reference Directory: /var/lib/cwl/stgf9100e9c-1824-4077-9c97-3c2e6d24b954/dqc_reference
[2023-03-14 12:19:40,764] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 12:19:40,764] [INFO] Task started: Prodigal
[2023-03-14 12:19:40,764] [INFO] Running command: cat /var/lib/cwl/stga75b5824-a41f-461c-9b35-2a6a49bd5501/OceanDNA-b31948.fa | prodigal -d OceanDNA-b31948/cds.fna -a OceanDNA-b31948/protein.faa -g 11 -q > /dev/null
[2023-03-14 12:19:55,352] [INFO] Task succeeded: Prodigal
[2023-03-14 12:19:55,352] [INFO] Task started: HMMsearch
[2023-03-14 12:19:55,352] [INFO] Running command: hmmsearch --tblout OceanDNA-b31948/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf9100e9c-1824-4077-9c97-3c2e6d24b954/dqc_reference/reference_markers.hmm OceanDNA-b31948/protein.faa > /dev/null
[2023-03-14 12:19:55,523] [INFO] Task succeeded: HMMsearch
[2023-03-14 12:19:55,524] [WARNING] Found 4/6 markers. [/var/lib/cwl/stga75b5824-a41f-461c-9b35-2a6a49bd5501/OceanDNA-b31948.fa]
[2023-03-14 12:19:55,546] [INFO] Query marker FASTA was written to OceanDNA-b31948/markers.fasta
[2023-03-14 12:19:55,547] [INFO] Task started: Blastn
[2023-03-14 12:19:55,547] [INFO] Running command: blastn -query OceanDNA-b31948/markers.fasta -db /var/lib/cwl/stgf9100e9c-1824-4077-9c97-3c2e6d24b954/dqc_reference/reference_markers.fasta -out OceanDNA-b31948/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 12:19:56,204] [INFO] Task succeeded: Blastn
[2023-03-14 12:19:56,207] [INFO] Selected 12 target genomes.
[2023-03-14 12:19:56,207] [INFO] Target genome list was writen to OceanDNA-b31948/target_genomes.txt
[2023-03-14 12:19:56,214] [INFO] Task started: fastANI
[2023-03-14 12:19:56,214] [INFO] Running command: fastANI --query /var/lib/cwl/stga75b5824-a41f-461c-9b35-2a6a49bd5501/OceanDNA-b31948.fa --refList OceanDNA-b31948/target_genomes.txt --output OceanDNA-b31948/fastani_result.tsv --threads 1
[2023-03-14 12:20:03,521] [INFO] Task succeeded: fastANI
[2023-03-14 12:20:03,522] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf9100e9c-1824-4077-9c97-3c2e6d24b954/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 12:20:03,522] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf9100e9c-1824-4077-9c97-3c2e6d24b954/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 12:20:03,530] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 12:20:03,530] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-14 12:20:03,530] [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
Aurantiacibacter odishensis	strain=KCTC 23981	GCA_003605195.1	1155476	1155476	type	True	90.9579	648	767	95	below_threshold
Aurantiacibacter zhengii	strain=V18	GCA_003584125.1	2307003	2307003	type	True	83.9552	525	767	95	below_threshold
Aurantiacibacter rhizosphaerae	strain=GH3-10	GCA_009807005.1	2691582	2691582	type	True	81.3499	518	767	95	below_threshold
Aurantiacibacter luteus	strain=KA37	GCA_001010945.1	1581420	1581420	type	True	80.233	430	767	95	below_threshold
Aurantiacibacter gangjinensis	strain=CGMCC 1.15024	GCA_001886695.1	502682	502682	type	True	79.3981	390	767	95	below_threshold
Aurantiacibacter gangjinensis	strain=K7-2	GCA_001010925.1	502682	502682	type	True	79.3799	393	767	95	below_threshold
Aurantiacibacter sediminis	strain=JGD-13	GCA_016019885.1	2793064	2793064	type	True	78.5707	297	767	95	below_threshold
Qipengyuania aurantiaca	strain=1NDH13	GCA_019711375.1	2867233	2867233	type	True	78.1428	272	767	95	below_threshold
Croceibacterium ferulae	strain=SX2RGS8	GCA_003660445.1	1854641	1854641	type	True	78.0967	215	767	95	below_threshold
Qipengyuania gelatinilytica	strain=1NDH1	GCA_019711315.1	2867231	2867231	type	True	77.9657	258	767	95	below_threshold
Qipengyuania xiamenensis	strain=1XM1-15A	GCA_019711495.1	2867237	2867237	type	True	77.938	244	767	95	below_threshold
Qipengyuania sphaerica	strain=GH29	GCA_019711595.1	2867243	2867243	type	True	77.9062	259	767	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-14 12:20:03,531] [INFO] DFAST Taxonomy check result was written to OceanDNA-b31948/tc_result.tsv
[2023-03-14 12:20:03,532] [INFO] ===== Taxonomy check completed =====
[2023-03-14 12:20:03,532] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 12:20:03,532] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf9100e9c-1824-4077-9c97-3c2e6d24b954/dqc_reference/checkm_data
[2023-03-14 12:20:03,533] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 12:20:03,545] [INFO] Task started: CheckM
[2023-03-14 12:20:03,546] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b31948/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b31948/checkm_input OceanDNA-b31948/checkm_result
[2023-03-14 12:20:42,476] [INFO] Task succeeded: CheckM
[2023-03-14 12:20:42,476] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 68.18%
Contamintation: 20.83%
Strain heterogeneity: 60.00%
--------------------------------------------------------------------------------
[2023-03-14 12:20:42,495] [INFO] ===== Completeness check finished =====
[2023-03-14 12:20:42,495] [INFO] ===== Start GTDB Search =====
[2023-03-14 12:20:42,495] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b31948/markers.fasta)
[2023-03-14 12:20:42,496] [INFO] Task started: Blastn
[2023-03-14 12:20:42,497] [INFO] Running command: blastn -query OceanDNA-b31948/markers.fasta -db /var/lib/cwl/stgf9100e9c-1824-4077-9c97-3c2e6d24b954/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b31948/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 12:20:43,620] [INFO] Task succeeded: Blastn
[2023-03-14 12:20:43,622] [INFO] Selected 11 target genomes.
[2023-03-14 12:20:43,622] [INFO] Target genome list was writen to OceanDNA-b31948/target_genomes_gtdb.txt
[2023-03-14 12:20:43,635] [INFO] Task started: fastANI
[2023-03-14 12:20:43,635] [INFO] Running command: fastANI --query /var/lib/cwl/stga75b5824-a41f-461c-9b35-2a6a49bd5501/OceanDNA-b31948.fa --refList OceanDNA-b31948/target_genomes_gtdb.txt --output OceanDNA-b31948/fastani_result_gtdb.tsv --threads 1
[2023-03-14 12:20:51,292] [INFO] Task succeeded: fastANI
[2023-03-14 12:20:51,299] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-14 12:20:51,299] [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_003605195.1	s__Alteraurantiacibacter odishensis	90.9579	648	767	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003584125.1	s__Alteraurantiacibacter zhengii	83.9552	525	767	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009807005.1	s__Alteraurantiacibacter rhizosphaerae	81.3499	518	767	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004965515.1	s__Alteraurantiacibacter aquimixticola	79.5656	402	767	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001886695.1	s__Alteraurantiacibacter gangjinensis	79.3855	391	767	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_902498745.1	s__Alteraurantiacibacter sp902498745	79.1281	339	767	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003605475.1	s__Alteraurantiacibacter aquimixticola_A	78.8938	336	767	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009827655.1	s__Alteraurantiacibacter buctensis	78.8927	405	767	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016019885.1	s__Alteraurantiacibacter sp016019885	78.5703	297	767	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003569745.1	s__Croceibacterium sp003569745	78.3191	319	767	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003660445.1	s__Croceibacterium ferulae	78.0967	215	767	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceibacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-14 12:20:51,301] [INFO] GTDB search result was written to OceanDNA-b31948/result_gtdb.tsv
[2023-03-14 12:20:51,303] [INFO] ===== GTDB Search completed =====
[2023-03-14 12:20:51,306] [INFO] DFAST_QC result json was written to OceanDNA-b31948/dqc_result.json
[2023-03-14 12:20:51,307] [INFO] DFAST_QC completed!
[2023-03-14 12:20:51,307] [INFO] Total running time: 0h1m12s