[2023-03-16 06:12:34,989] [INFO] DFAST_QC pipeline started.
[2023-03-16 06:12:34,989] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 06:12:34,989] [INFO] DQC Reference Directory: /var/lib/cwl/stg8d0b5f2d-ee2b-49d3-beb4-b5d2bf6d7169/dqc_reference
[2023-03-16 06:12:36,624] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 06:12:36,625] [INFO] Task started: Prodigal
[2023-03-16 06:12:36,625] [INFO] Running command: cat /var/lib/cwl/stg6e75b47c-6e38-47e7-8703-da5a89ddbbfd/OceanDNA-b31664.fa | prodigal -d OceanDNA-b31664/cds.fna -a OceanDNA-b31664/protein.faa -g 11 -q > /dev/null
[2023-03-16 06:12:48,234] [INFO] Task succeeded: Prodigal
[2023-03-16 06:12:48,234] [INFO] Task started: HMMsearch
[2023-03-16 06:12:48,234] [INFO] Running command: hmmsearch --tblout OceanDNA-b31664/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8d0b5f2d-ee2b-49d3-beb4-b5d2bf6d7169/dqc_reference/reference_markers.hmm OceanDNA-b31664/protein.faa > /dev/null
[2023-03-16 06:12:48,498] [INFO] Task succeeded: HMMsearch
[2023-03-16 06:12:48,499] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg6e75b47c-6e38-47e7-8703-da5a89ddbbfd/OceanDNA-b31664.fa]
[2023-03-16 06:12:48,526] [INFO] Query marker FASTA was written to OceanDNA-b31664/markers.fasta
[2023-03-16 06:12:48,527] [INFO] Task started: Blastn
[2023-03-16 06:12:48,527] [INFO] Running command: blastn -query OceanDNA-b31664/markers.fasta -db /var/lib/cwl/stg8d0b5f2d-ee2b-49d3-beb4-b5d2bf6d7169/dqc_reference/reference_markers.fasta -out OceanDNA-b31664/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 06:12:49,064] [INFO] Task succeeded: Blastn
[2023-03-16 06:12:49,067] [INFO] Selected 19 target genomes.
[2023-03-16 06:12:49,068] [INFO] Target genome list was writen to OceanDNA-b31664/target_genomes.txt
[2023-03-16 06:12:49,080] [INFO] Task started: fastANI
[2023-03-16 06:12:49,080] [INFO] Running command: fastANI --query /var/lib/cwl/stg6e75b47c-6e38-47e7-8703-da5a89ddbbfd/OceanDNA-b31664.fa --refList OceanDNA-b31664/target_genomes.txt --output OceanDNA-b31664/fastani_result.tsv --threads 1
[2023-03-16 06:12:59,741] [INFO] Task succeeded: fastANI
[2023-03-16 06:12:59,741] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8d0b5f2d-ee2b-49d3-beb4-b5d2bf6d7169/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 06:12:59,742] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8d0b5f2d-ee2b-49d3-beb4-b5d2bf6d7169/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 06:12:59,748] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 06:12:59,748] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 06:12:59,748] [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
Erythrobacter longus	strain=DSM 6997	GCA_000715015.1	1044	1044	type	True	78.8163	322	600	95	below_threshold
Erythrobacter rubeus	strain=KMU-140	GCA_014705715.1	2760803	2760803	type	True	77.3566	109	600	95	below_threshold
Erythrobacter insulae	strain=JBTF-M21	GCA_007004095.1	2584124	2584124	type	True	77.1752	99	600	95	below_threshold
Qipengyuania intermedia	strain=GH38	GCA_019711615.1	2867244	2867244	type	True	76.935	68	600	95	below_threshold
Altererythrobacter lutimaris	strain=JGD-16	GCA_013371495.1	2743979	2743979	type	True	76.7322	99	600	95	below_threshold
Qipengyuania huizhouensis	strain=YG19	GCA_019711635.1	2867245	2867245	type	True	76.4824	62	600	95	below_threshold
Qipengyuania vesicularis	strain=1NDH10	GCA_019711415.1	2867232	2867232	type	True	76.4695	71	600	95	below_threshold
Erythrobacter neustonensis	strain=DSM 9434	GCA_001663175.1	1112	1112	type	True	76.2205	99	600	95	below_threshold
Qipengyuania qiaonensis	strain=6D47A	GCA_019711515.1	2867240	2867240	type	True	75.9155	63	600	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 06:12:59,751] [INFO] DFAST Taxonomy check result was written to OceanDNA-b31664/tc_result.tsv
[2023-03-16 06:12:59,755] [INFO] ===== Taxonomy check completed =====
[2023-03-16 06:12:59,755] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 06:12:59,755] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8d0b5f2d-ee2b-49d3-beb4-b5d2bf6d7169/dqc_reference/checkm_data
[2023-03-16 06:12:59,756] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 06:12:59,768] [INFO] Task started: CheckM
[2023-03-16 06:12:59,768] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b31664/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b31664/checkm_input OceanDNA-b31664/checkm_result
[2023-03-16 06:13:32,802] [INFO] Task succeeded: CheckM
[2023-03-16 06:13:32,803] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 77.14%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 06:13:32,896] [INFO] ===== Completeness check finished =====
[2023-03-16 06:13:32,896] [INFO] ===== Start GTDB Search =====
[2023-03-16 06:13:32,896] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b31664/markers.fasta)
[2023-03-16 06:13:32,897] [INFO] Task started: Blastn
[2023-03-16 06:13:32,897] [INFO] Running command: blastn -query OceanDNA-b31664/markers.fasta -db /var/lib/cwl/stg8d0b5f2d-ee2b-49d3-beb4-b5d2bf6d7169/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b31664/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 06:13:33,606] [INFO] Task succeeded: Blastn
[2023-03-16 06:13:33,614] [INFO] Selected 20 target genomes.
[2023-03-16 06:13:33,614] [INFO] Target genome list was writen to OceanDNA-b31664/target_genomes_gtdb.txt
[2023-03-16 06:13:33,657] [INFO] Task started: fastANI
[2023-03-16 06:13:33,657] [INFO] Running command: fastANI --query /var/lib/cwl/stg6e75b47c-6e38-47e7-8703-da5a89ddbbfd/OceanDNA-b31664.fa --refList OceanDNA-b31664/target_genomes_gtdb.txt --output OceanDNA-b31664/fastani_result_gtdb.tsv --threads 1
[2023-03-16 06:13:44,482] [INFO] Task succeeded: fastANI
[2023-03-16 06:13:44,490] [INFO] Found 14 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 06:13:44,491] [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_000715015.1	s__Erythrobacter longus	78.8163	322	600	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013214365.1	s__Erythrobacter sp013214365	77.683	123	600	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003264115.1	s__Erythrobacter sp003264115	77.4018	157	600	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000714765.1	s__Erythrobacter sp000714765	77.2964	147	600	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001542875.1	s__Erythrobacter sp001542875	77.1521	113	600	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019204025.1	s__Erythrobacter sp019204025	76.7487	99	600	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	76.7322	99	600	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002706445.1	s__Erythrobacter sp002706445	76.6574	104	600	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019204045.1	s__Erythrobacter sp019204045	76.6177	98	600	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011047315.1	s__Erythrobacter sp011047315	76.5111	75	600	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013002295.1	s__Erythrobacter sp013002295	76.4959	59	600	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	99.14	98.90	0.85	0.82	4	-
GCA_001464915.1	s__Erythrobacter sp001464915	76.3871	96	600	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	76.3166	76	600	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002215495.1	s__Erythrobacter sp002215495	76.2884	108	600	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 06:13:44,492] [INFO] GTDB search result was written to OceanDNA-b31664/result_gtdb.tsv
[2023-03-16 06:13:44,495] [INFO] ===== GTDB Search completed =====
[2023-03-16 06:13:44,499] [INFO] DFAST_QC result json was written to OceanDNA-b31664/dqc_result.json
[2023-03-16 06:13:44,499] [INFO] DFAST_QC completed!
[2023-03-16 06:13:44,499] [INFO] Total running time: 0h1m10s