[2023-03-15 21:01:44,350] [INFO] DFAST_QC pipeline started.
[2023-03-15 21:01:44,350] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 21:01:44,351] [INFO] DQC Reference Directory: /var/lib/cwl/stgac03bff2-3f91-4f1f-ae69-6645c7513b08/dqc_reference
[2023-03-15 21:01:45,597] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 21:01:45,597] [INFO] Task started: Prodigal
[2023-03-15 21:01:45,597] [INFO] Running command: cat /var/lib/cwl/stg14754f9b-ea45-4cfd-9b54-0ef85ad33831/OceanDNA-b31566.fa | prodigal -d OceanDNA-b31566/cds.fna -a OceanDNA-b31566/protein.faa -g 11 -q > /dev/null
[2023-03-15 21:01:54,645] [INFO] Task succeeded: Prodigal
[2023-03-15 21:01:54,645] [INFO] Task started: HMMsearch
[2023-03-15 21:01:54,645] [INFO] Running command: hmmsearch --tblout OceanDNA-b31566/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgac03bff2-3f91-4f1f-ae69-6645c7513b08/dqc_reference/reference_markers.hmm OceanDNA-b31566/protein.faa > /dev/null
[2023-03-15 21:01:54,813] [INFO] Task succeeded: HMMsearch
[2023-03-15 21:01:54,813] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg14754f9b-ea45-4cfd-9b54-0ef85ad33831/OceanDNA-b31566.fa]
[2023-03-15 21:01:54,827] [INFO] Query marker FASTA was written to OceanDNA-b31566/markers.fasta
[2023-03-15 21:01:54,828] [INFO] Task started: Blastn
[2023-03-15 21:01:54,828] [INFO] Running command: blastn -query OceanDNA-b31566/markers.fasta -db /var/lib/cwl/stgac03bff2-3f91-4f1f-ae69-6645c7513b08/dqc_reference/reference_markers.fasta -out OceanDNA-b31566/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 21:01:55,507] [INFO] Task succeeded: Blastn
[2023-03-15 21:01:55,508] [INFO] Selected 22 target genomes.
[2023-03-15 21:01:55,508] [INFO] Target genome list was writen to OceanDNA-b31566/target_genomes.txt
[2023-03-15 21:01:55,522] [INFO] Task started: fastANI
[2023-03-15 21:01:55,522] [INFO] Running command: fastANI --query /var/lib/cwl/stg14754f9b-ea45-4cfd-9b54-0ef85ad33831/OceanDNA-b31566.fa --refList OceanDNA-b31566/target_genomes.txt --output OceanDNA-b31566/fastani_result.tsv --threads 1
[2023-03-15 21:02:05,934] [INFO] Task succeeded: fastANI
[2023-03-15 21:02:05,935] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgac03bff2-3f91-4f1f-ae69-6645c7513b08/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 21:02:05,935] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgac03bff2-3f91-4f1f-ae69-6645c7513b08/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 21:02:05,947] [INFO] Found 22 fastANI hits (1 hits with ANI > threshold)
[2023-03-15 21:02:05,947] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-15 21:02:05,947] [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
Allopontixanthobacter confluentis	strain=KCTC 52259	GCA_009827615.1	1849021	1849021	type	True	98.0034	391	422	95	conclusive
Allopontixanthobacter sediminis	strain=KCTC 42453	GCA_009828115.1	1689985	1689985	type	True	78.3273	201	422	95	below_threshold
Croceibacterium atlanticum	strain=26DY36	GCA_001008165.2	1267766	1267766	type	True	77.8491	130	422	95	below_threshold
Croceibacterium atlanticum	strain=DSM 100738	GCA_014199315.1	1267766	1267766	type	True	77.7999	132	422	95	below_threshold
Croceibacterium xixiisoli	strain=S36	GCA_009827305.1	1476466	1476466	type	True	77.4111	128	422	95	below_threshold
Pontixanthobacter luteolus	strain=SW-109	GCA_009828095.1	295089	295089	type	True	77.3443	158	422	95	below_threshold
Pontixanthobacter aquaemixtae	strain=KCTC 52763	GCA_009827395.1	1958940	1958940	type	True	77.3012	141	422	95	below_threshold
Qipengyuania aestuarii	strain=GH1	GCA_019711535.1	2867241	2867241	type	True	77.1682	93	422	95	below_threshold
Croceicoccus hydrothermalis	strain=JLT1	GCA_022378335.1	2867964	2867964	type	True	77.135	75	422	95	below_threshold
Alteripontixanthobacter maritimus	strain=HME9302	GCA_003340475.1	2161824	2161824	type	True	77.1075	106	422	95	below_threshold
Pontixanthobacter gangjinensis	strain=JCM 17802	GCA_009827545.1	1028742	1028742	type	True	77.0628	94	422	95	below_threshold
Qipengyuania qiaonensis	strain=6D47A	GCA_019711515.1	2867240	2867240	type	True	77.0223	90	422	95	below_threshold
Qipengyuania huizhouensis	strain=YG19	GCA_019711635.1	2867245	2867245	type	True	76.8588	82	422	95	below_threshold
Erythrobacter ramosus	strain=JCM 10282	GCA_009828055.1	35811	35811	type	True	76.8583	96	422	95	below_threshold
Qipengyuania gaetbuli	strain=DSM 16225	GCA_009827315.1	266952	266952	type	True	76.8469	121	422	95	below_threshold
Qipengyuania sphaerica	strain=GH29	GCA_019711595.1	2867243	2867243	type	True	76.8349	99	422	95	below_threshold
Pelagerythrobacter rhizovicinus	strain=AY-3R	GCA_004135625.1	2268576	2268576	type	True	76.8169	80	422	95	below_threshold
Erythrobacter ramosus	strain=DSM 8510	GCA_014195675.1	35811	35811	type	True	76.811	98	422	95	below_threshold
Qipengyuania gelatinilytica	strain=1NDH1	GCA_019711315.1	2867231	2867231	type	True	76.7359	106	422	95	below_threshold
Pelagerythrobacter marinus	strain=H32	GCA_009827515.1	538382	538382	type	True	76.7162	106	422	95	below_threshold
Qipengyuania pacifica	strain=NZ-96	GCA_019857205.1	2860199	2860199	type	True	76.5837	90	422	95	below_threshold
Pelagerythrobacter aerophilus	strain=Ery1	GCA_003581645.1	2306995	2306995	type	True	76.4228	102	422	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 21:02:05,947] [INFO] DFAST Taxonomy check result was written to OceanDNA-b31566/tc_result.tsv
[2023-03-15 21:02:05,947] [INFO] ===== Taxonomy check completed =====
[2023-03-15 21:02:05,947] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 21:02:05,947] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgac03bff2-3f91-4f1f-ae69-6645c7513b08/dqc_reference/checkm_data
[2023-03-15 21:02:05,948] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 21:02:05,951] [INFO] Task started: CheckM
[2023-03-15 21:02:05,952] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b31566/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b31566/checkm_input OceanDNA-b31566/checkm_result
[2023-03-15 21:02:33,207] [INFO] Task succeeded: CheckM
[2023-03-15 21:02:33,207] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 56.25%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-15 21:02:33,209] [INFO] ===== Completeness check finished =====
[2023-03-15 21:02:33,209] [INFO] ===== Start GTDB Search =====
[2023-03-15 21:02:33,209] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b31566/markers.fasta)
[2023-03-15 21:02:33,211] [INFO] Task started: Blastn
[2023-03-15 21:02:33,211] [INFO] Running command: blastn -query OceanDNA-b31566/markers.fasta -db /var/lib/cwl/stgac03bff2-3f91-4f1f-ae69-6645c7513b08/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b31566/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 21:02:34,470] [INFO] Task succeeded: Blastn
[2023-03-15 21:02:34,470] [INFO] Selected 19 target genomes.
[2023-03-15 21:02:34,470] [INFO] Target genome list was writen to OceanDNA-b31566/target_genomes_gtdb.txt
[2023-03-15 21:02:34,731] [INFO] Task started: fastANI
[2023-03-15 21:02:34,732] [INFO] Running command: fastANI --query /var/lib/cwl/stg14754f9b-ea45-4cfd-9b54-0ef85ad33831/OceanDNA-b31566.fa --refList OceanDNA-b31566/target_genomes_gtdb.txt --output OceanDNA-b31566/fastani_result_gtdb.tsv --threads 1
[2023-03-15 21:02:44,231] [INFO] Task succeeded: fastANI
[2023-03-15 21:02:44,242] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 21:02:44,242] [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_009827615.1	s__Pseudopontixanthobacter_A confluentis	98.0034	391	422	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pseudopontixanthobacter_A	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_009828115.1	s__Pseudopontixanthobacter_A sediminis	78.3273	201	422	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pseudopontixanthobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001008165.2	s__Croceibacterium atlanticum	77.8229	131	422	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceibacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_005884405.1	s__Qipengyuania marisflavi	77.7988	152	422	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009828095.1	s__Pontixanthobacter luteolus	77.3443	158	422	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pontixanthobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013336795.1	s__Pseudopontixanthobacter muriae	77.3404	106	422	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pseudopontixanthobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014763545.1	s__JACXVD01 sp014763545	77.2406	145	422	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__JACXVD01	95.0	99.92	99.92	0.96	0.96	2	-
GCA_003724185.1	s__Erythrobacter sp003724185	77.1962	122	422	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001305965.1	s__Caenibius sp001305965	77.1236	123	422	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Caenibius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003340475.1	s__Alteripontixanthobacter maritimus	77.1204	107	422	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteripontixanthobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009827545.1	s__Pontixanthobacter gangjinensis	77.0914	93	422	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pontixanthobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002842735.1	s__Erythrobacter sp002842735	77.0482	133	422	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	95.33	95.33	0.91	0.91	2	-
GCF_009827315.1	s__Qipengyuania gaetbuli	76.8458	122	422	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018830415.1	s__Erythrobacter sp018830415	76.7252	108	422	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009827515.1	s__Pelagerythrobacter marinus	76.7162	106	422	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pelagerythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013260645.1	s__Qipengyuania mangrovi	76.6917	99	422	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009827655.1	s__Alteraurantiacibacter buctensis	76.6339	86	422	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001542855.1	s__Qipengyuania sp001542855	76.5913	112	422	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	97.07	97.03	0.89	0.88	4	-
GCF_016803135.1	s__Pelagerythrobacter sp016803135	76.5279	96	422	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pelagerythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 21:02:44,242] [INFO] GTDB search result was written to OceanDNA-b31566/result_gtdb.tsv
[2023-03-15 21:02:44,242] [INFO] ===== GTDB Search completed =====
[2023-03-15 21:02:44,244] [INFO] DFAST_QC result json was written to OceanDNA-b31566/dqc_result.json
[2023-03-15 21:02:44,245] [INFO] DFAST_QC completed!
[2023-03-15 21:02:44,245] [INFO] Total running time: 0h0m60s