[2023-03-18 06:02:58,279] [INFO] DFAST_QC pipeline started.
[2023-03-18 06:02:58,279] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 06:02:58,279] [INFO] DQC Reference Directory: /var/lib/cwl/stg502658a3-a194-496f-8346-b98f248d7324/dqc_reference
[2023-03-18 06:03:00,170] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 06:03:00,171] [INFO] Task started: Prodigal
[2023-03-18 06:03:00,171] [INFO] Running command: cat /var/lib/cwl/stg86ef8425-1023-4383-b6ab-30f6132bfb6e/OceanDNA-b31564.fa | prodigal -d OceanDNA-b31564/cds.fna -a OceanDNA-b31564/protein.faa -g 11 -q > /dev/null
[2023-03-18 06:03:12,139] [INFO] Task succeeded: Prodigal
[2023-03-18 06:03:12,140] [INFO] Task started: HMMsearch
[2023-03-18 06:03:12,140] [INFO] Running command: hmmsearch --tblout OceanDNA-b31564/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg502658a3-a194-496f-8346-b98f248d7324/dqc_reference/reference_markers.hmm OceanDNA-b31564/protein.faa > /dev/null
[2023-03-18 06:03:12,300] [INFO] Task succeeded: HMMsearch
[2023-03-18 06:03:12,301] [INFO] Found 6/6 markers.
[2023-03-18 06:03:12,316] [INFO] Query marker FASTA was written to OceanDNA-b31564/markers.fasta
[2023-03-18 06:03:12,317] [INFO] Task started: Blastn
[2023-03-18 06:03:12,317] [INFO] Running command: blastn -query OceanDNA-b31564/markers.fasta -db /var/lib/cwl/stg502658a3-a194-496f-8346-b98f248d7324/dqc_reference/reference_markers.fasta -out OceanDNA-b31564/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 06:03:12,913] [INFO] Task succeeded: Blastn
[2023-03-18 06:03:12,914] [INFO] Selected 27 target genomes.
[2023-03-18 06:03:12,914] [INFO] Target genome list was writen to OceanDNA-b31564/target_genomes.txt
[2023-03-18 06:03:13,185] [INFO] Task started: fastANI
[2023-03-18 06:03:13,185] [INFO] Running command: fastANI --query /var/lib/cwl/stg86ef8425-1023-4383-b6ab-30f6132bfb6e/OceanDNA-b31564.fa --refList OceanDNA-b31564/target_genomes.txt --output OceanDNA-b31564/fastani_result.tsv --threads 1
[2023-03-18 06:03:26,620] [INFO] Task succeeded: fastANI
[2023-03-18 06:03:26,621] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg502658a3-a194-496f-8346-b98f248d7324/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 06:03:26,621] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg502658a3-a194-496f-8346-b98f248d7324/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 06:03:26,635] [INFO] Found 26 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 06:03:26,635] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 06:03:26,636] [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
Altererythrobacter ishigakiensis	strain=NBRC 107699	GCA_001663155.1	476157	476157	type	True	81.6642	443	628	95	below_threshold
Altererythrobacter ishigakiensis	strain=ATCC BAA-2084	GCA_007830695.1	476157	476157	type	True	81.6135	439	628	95	below_threshold
Altererythrobacter lutimaris	strain=JGD-16	GCA_013371495.1	2743979	2743979	type	True	78.0931	220	628	95	below_threshold
Qipengyuania proteolytica	strain=6B39	GCA_019711565.1	2867239	2867239	type	True	77.5754	174	628	95	below_threshold
Qipengyuania xiamenensis	strain=1XM1-15A	GCA_019711495.1	2867237	2867237	type	True	77.5335	173	628	95	below_threshold
Parerythrobacter jejuensis	strain=JCM 16677	GCA_009827995.1	795812	795812	type	True	77.4916	198	628	95	below_threshold
Erythrobacter rubeus	strain=KMU-140	GCA_014705715.1	2760803	2760803	type	True	77.4289	210	628	95	below_threshold
Qipengyuania vesicularis	strain=1NDH10	GCA_019711415.1	2867232	2867232	type	True	77.4032	161	628	95	below_threshold
Erythrobacter dokdonensis	strain=DSM 17193	GCA_002155305.1	328225	328225	type	True	77.3331	184	628	95	below_threshold
Erythrobacter dokdonensis	strain=DSW-74	GCA_001677335.1	328225	328225	type	True	77.3047	187	628	95	below_threshold
Qipengyuania flava	strain=DSM 16421	GCA_011762005.1	192812	192812	type	True	77.3011	180	628	95	below_threshold
Alteraurantiacibacter aestuarii	strain=JCM 16339	GCA_009827405.1	650004	650004	type	True	77.279	81	628	95	below_threshold
Erythrobacter neustonensis	strain=DSM 9434	GCA_001663175.1	1112	1112	type	True	77.2085	181	628	95	below_threshold
Alteriqipengyuania abyssalis	strain=NZ-12B	GCA_019857185.1	2860200	2860200	type	True	77.1115	146	628	95	below_threshold
Erythrobacter cryptus	strain=DSM 12079	GCA_000422985.1	196588	196588	type	True	77.0474	139	628	95	below_threshold
Pelagerythrobacter aerophilus	strain=Ery1	GCA_003581645.1	2306995	2306995	type	True	76.9503	143	628	95	below_threshold
Erythrobacter insulae	strain=JBTF-M21	GCA_007004095.1	2584124	2584124	type	True	76.9462	168	628	95	below_threshold
Qipengyuania soli	strain=6D36	GCA_015529805.1	2782568	2782568	type	True	76.8834	158	628	95	below_threshold
Aurantiacibacter odishensis	strain=KCTC 23981	GCA_003605195.1	1155476	1155476	type	True	76.801	129	628	95	below_threshold
Pelagerythrobacter rhizovicinus	strain=AY-3R	GCA_004135625.1	2268576	2268576	type	True	76.7771	143	628	95	below_threshold
Croceibacterium atlanticum	strain=DSM 100738	GCA_014199315.1	1267766	1267766	type	True	76.6663	141	628	95	below_threshold
Croceibacterium atlanticum	strain=26DY36	GCA_001008165.2	1267766	1267766	type	True	76.6509	141	628	95	below_threshold
Novosphingobium acidiphilum	strain=DSM 19966	GCA_000429005.1	505248	505248	type	True	76.3897	100	628	95	below_threshold
Sphingopyxis soli	strain=BL03	GCA_018682675.1	592051	592051	type	True	76.2609	75	628	95	below_threshold
Sphingopyxis solisilvae	strain=R366	GCA_015475875.1	1886788	1886788	type	True	76.0377	90	628	95	below_threshold
Sphingopyxis alaskensis	strain=RB2256	GCA_000013985.1	117207	117207	type	True	75.9516	79	628	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 06:03:26,636] [INFO] DFAST Taxonomy check result was written to OceanDNA-b31564/tc_result.tsv
[2023-03-18 06:03:26,636] [INFO] ===== Taxonomy check completed =====
[2023-03-18 06:03:26,637] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 06:03:26,637] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg502658a3-a194-496f-8346-b98f248d7324/dqc_reference/checkm_data
[2023-03-18 06:03:26,637] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 06:03:26,648] [INFO] Task started: CheckM
[2023-03-18 06:03:26,648] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b31564/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b31564/checkm_input OceanDNA-b31564/checkm_result
[2023-03-18 06:03:59,918] [INFO] Task succeeded: CheckM
[2023-03-18 06:03:59,918] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 72.92%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 06:03:59,920] [INFO] ===== Completeness check finished =====
[2023-03-18 06:03:59,920] [INFO] ===== Start GTDB Search =====
[2023-03-18 06:03:59,920] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b31564/markers.fasta)
[2023-03-18 06:03:59,921] [INFO] Task started: Blastn
[2023-03-18 06:03:59,922] [INFO] Running command: blastn -query OceanDNA-b31564/markers.fasta -db /var/lib/cwl/stg502658a3-a194-496f-8346-b98f248d7324/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b31564/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 06:04:00,830] [INFO] Task succeeded: Blastn
[2023-03-18 06:04:00,831] [INFO] Selected 18 target genomes.
[2023-03-18 06:04:00,831] [INFO] Target genome list was writen to OceanDNA-b31564/target_genomes_gtdb.txt
[2023-03-18 06:04:01,564] [INFO] Task started: fastANI
[2023-03-18 06:04:01,565] [INFO] Running command: fastANI --query /var/lib/cwl/stg86ef8425-1023-4383-b6ab-30f6132bfb6e/OceanDNA-b31564.fa --refList OceanDNA-b31564/target_genomes_gtdb.txt --output OceanDNA-b31564/fastani_result_gtdb.tsv --threads 1
[2023-03-18 06:04:10,468] [INFO] Task succeeded: fastANI
[2023-03-18 06:04:10,479] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 06:04:10,479] [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_003149575.1	s__Erythrobacter sp003149575	98.775	612	628	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	98.16	98.16	0.93	0.93	2	conclusive
GCA_013002295.1	s__Erythrobacter sp013002295	86.8694	419	628	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	99.14	98.90	0.85	0.82	4	-
GCF_001663155.1	s__Erythrobacter ishigakiensis	81.6637	443	628	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	97.03	96.25	0.95	0.94	6	-
GCF_011047315.1	s__Erythrobacter sp011047315	78.72	328	628	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013371495.1	s__Erythrobacter sp013371495	78.0931	220	628	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001515985.1	s__Erythrobacter sp001515985	77.9817	236	628	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900177715.1	s__Erythrobacter xiamenensis	77.8703	251	628	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001281485.1	s__Erythrobacter epoxidivorans	77.604	198	628	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014983025.1	s__Erythrobacter sp014983025	77.4369	177	628	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001677335.1	s__Erythrobacter dokdonensis	77.3047	187	628	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCA_001724215.1	s__Erythrobacter sp001724215	77.2625	172	628	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011524425.1	s__Erythrobacter sp011524425	77.1718	120	628	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005434975.1	s__Parerythrobacter lutipelagi	77.0755	195	628	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Parerythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002215495.1	s__Erythrobacter sp002215495	76.9604	158	628	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009905735.1	s__Erythrobacter sp009905735	76.8753	201	628	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015529805.1	s__Qipengyuania soli	76.869	159	628	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001542875.1	s__Erythrobacter sp001542875	76.6885	147	628	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001008165.2	s__Croceibacterium atlanticum	76.6509	141	628	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceibacterium	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2023-03-18 06:04:10,479] [INFO] GTDB search result was written to OceanDNA-b31564/result_gtdb.tsv
[2023-03-18 06:04:10,479] [INFO] ===== GTDB Search completed =====
[2023-03-18 06:04:10,481] [INFO] DFAST_QC result json was written to OceanDNA-b31564/dqc_result.json
[2023-03-18 06:04:10,482] [INFO] DFAST_QC completed!
[2023-03-18 06:04:10,482] [INFO] Total running time: 0h1m12s