[2023-03-14 12:25:41,467] [INFO] DFAST_QC pipeline started.
[2023-03-14 12:25:41,467] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 12:25:41,467] [INFO] DQC Reference Directory: /var/lib/cwl/stg40bc7a31-4ccd-400b-8770-852c6c2cd941/dqc_reference
[2023-03-14 12:25:42,668] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 12:25:42,668] [INFO] Task started: Prodigal
[2023-03-14 12:25:42,668] [INFO] Running command: cat /var/lib/cwl/stg0619f85d-7cd7-49f5-816d-24596de8b669/OceanDNA-b31678.fa | prodigal -d OceanDNA-b31678/cds.fna -a OceanDNA-b31678/protein.faa -g 11 -q > /dev/null
[2023-03-14 12:25:59,584] [INFO] Task succeeded: Prodigal
[2023-03-14 12:25:59,584] [INFO] Task started: HMMsearch
[2023-03-14 12:25:59,584] [INFO] Running command: hmmsearch --tblout OceanDNA-b31678/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg40bc7a31-4ccd-400b-8770-852c6c2cd941/dqc_reference/reference_markers.hmm OceanDNA-b31678/protein.faa > /dev/null
[2023-03-14 12:25:59,784] [INFO] Task succeeded: HMMsearch
[2023-03-14 12:25:59,785] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg0619f85d-7cd7-49f5-816d-24596de8b669/OceanDNA-b31678.fa]
[2023-03-14 12:25:59,800] [INFO] Query marker FASTA was written to OceanDNA-b31678/markers.fasta
[2023-03-14 12:25:59,801] [INFO] Task started: Blastn
[2023-03-14 12:25:59,801] [INFO] Running command: blastn -query OceanDNA-b31678/markers.fasta -db /var/lib/cwl/stg40bc7a31-4ccd-400b-8770-852c6c2cd941/dqc_reference/reference_markers.fasta -out OceanDNA-b31678/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 12:26:00,465] [INFO] Task succeeded: Blastn
[2023-03-14 12:26:00,465] [INFO] Selected 23 target genomes.
[2023-03-14 12:26:00,466] [INFO] Target genome list was writen to OceanDNA-b31678/target_genomes.txt
[2023-03-14 12:26:00,480] [INFO] Task started: fastANI
[2023-03-14 12:26:00,480] [INFO] Running command: fastANI --query /var/lib/cwl/stg0619f85d-7cd7-49f5-816d-24596de8b669/OceanDNA-b31678.fa --refList OceanDNA-b31678/target_genomes.txt --output OceanDNA-b31678/fastani_result.tsv --threads 1
[2023-03-14 12:26:13,835] [INFO] Task succeeded: fastANI
[2023-03-14 12:26:13,836] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg40bc7a31-4ccd-400b-8770-852c6c2cd941/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 12:26:13,836] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg40bc7a31-4ccd-400b-8770-852c6c2cd941/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 12:26:13,848] [INFO] Found 23 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 12:26:13,848] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-14 12:26:13,849] [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 litoralis	strain=DSM 8509	GCA_001719165.1	39960	39960	type	True	78.3792	387	864	95	below_threshold
Erythrobacter sanguineus	strain=JCM 20691	GCA_002155655.1	198312	198312	type	True	78.3416	395	864	95	below_threshold
Erythrobacter litoralis	strain=DSM 8509	GCA_000714795.1	39960	39960	type	True	78.3158	399	864	95	below_threshold
Erythrobacter rubeus	strain=KMU-140	GCA_014705715.1	2760803	2760803	type	True	78.0441	373	864	95	below_threshold
Erythrobacter neustonensis	strain=DSM 9434	GCA_001663175.1	1112	1112	type	True	78.0401	354	864	95	below_threshold
Erythrobacter donghaensis	strain=DSM 16220	GCA_002155425.1	267135	267135	suspected-type	True	77.9739	371	864	95	below_threshold
Erythrobacter tepidarius	strain=DSM 10594	GCA_002155695.1	60454	60454	type	True	77.8615	322	864	95	below_threshold
Erythrobacter longus	strain=DSM 6997	GCA_000715015.1	1044	1044	type	True	77.7467	317	864	95	below_threshold
Qipengyuania intermedia	strain=GH38	GCA_019711615.1	2867244	2867244	type	True	77.7005	213	864	95	below_threshold
Erythrobacter colymbi	strain=JCM 18338	GCA_002155685.1	1161202	1161202	type	True	77.6593	329	864	95	below_threshold
Qipengyuania vesicularis	strain=1NDH10	GCA_019711415.1	2867232	2867232	type	True	77.5715	217	864	95	below_threshold
Qipengyuania pelagi	strain=JCM 17468	GCA_009827295.1	994320	994320	type	True	77.3334	221	864	95	below_threshold
Aurantiacibacter suaedae	strain=GH3-15	GCA_005434915.1	2545755	2545755	type	True	77.1786	152	864	95	below_threshold
Aurantiacibacter xanthus	strain=CCTCC AB 2015396	GCA_003584015.1	1784712	1784712	type	True	77.1646	178	864	95	below_threshold
Altererythrobacter lutimaris	strain=JGD-16	GCA_013371495.1	2743979	2743979	type	True	77.1119	234	864	95	below_threshold
Pontixanthobacter aquaemixtae	strain=KCTC 52763	GCA_009827395.1	1958940	1958940	type	True	77.0998	220	864	95	below_threshold
Croceibacterium xixiisoli	strain=S36	GCA_009827305.1	1476466	1476466	type	True	77.0466	151	864	95	below_threshold
Pelagerythrobacter rhizovicinus	strain=AY-3R	GCA_004135625.1	2268576	2268576	type	True	76.8806	172	864	95	below_threshold
Aurantiacibacter luteus	strain=KA37	GCA_001010945.1	1581420	1581420	type	True	76.8039	143	864	95	below_threshold
Novosphingobium sediminis	strain=NBRC 106119	GCA_007991615.1	707214	707214	type	True	76.6164	158	864	95	below_threshold
Novosphingobium ovatum	strain=FSY-8	GCA_009909235.1	1908523	1908523	type	True	76.6159	118	864	95	below_threshold
Novosphingobium marinum	strain=CGMCC 1.12918	GCA_014640055.1	1514948	1514948	type	True	76.5457	127	864	95	below_threshold
Novosphingobium ginsenosidimutans	strain=FW-6	GCA_007954425.1	1176536	1176536	type	True	76.5402	166	864	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-14 12:26:13,849] [INFO] DFAST Taxonomy check result was written to OceanDNA-b31678/tc_result.tsv
[2023-03-14 12:26:13,849] [INFO] ===== Taxonomy check completed =====
[2023-03-14 12:26:13,849] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 12:26:13,849] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg40bc7a31-4ccd-400b-8770-852c6c2cd941/dqc_reference/checkm_data
[2023-03-14 12:26:13,850] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 12:26:13,867] [INFO] Task started: CheckM
[2023-03-14 12:26:13,867] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b31678/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b31678/checkm_input OceanDNA-b31678/checkm_result
[2023-03-14 12:26:57,923] [INFO] Task succeeded: CheckM
[2023-03-14 12:26:57,924] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 58.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 12:26:57,929] [INFO] ===== Completeness check finished =====
[2023-03-14 12:26:57,929] [INFO] ===== Start GTDB Search =====
[2023-03-14 12:26:57,929] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b31678/markers.fasta)
[2023-03-14 12:26:57,930] [INFO] Task started: Blastn
[2023-03-14 12:26:57,930] [INFO] Running command: blastn -query OceanDNA-b31678/markers.fasta -db /var/lib/cwl/stg40bc7a31-4ccd-400b-8770-852c6c2cd941/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b31678/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 12:26:58,809] [INFO] Task succeeded: Blastn
[2023-03-14 12:26:58,810] [INFO] Selected 22 target genomes.
[2023-03-14 12:26:58,810] [INFO] Target genome list was writen to OceanDNA-b31678/target_genomes_gtdb.txt
[2023-03-14 12:26:58,848] [INFO] Task started: fastANI
[2023-03-14 12:26:58,848] [INFO] Running command: fastANI --query /var/lib/cwl/stg0619f85d-7cd7-49f5-816d-24596de8b669/OceanDNA-b31678.fa --refList OceanDNA-b31678/target_genomes_gtdb.txt --output OceanDNA-b31678/fastani_result_gtdb.tsv --threads 1
[2023-03-14 12:27:11,847] [INFO] Task succeeded: fastANI
[2023-03-14 12:27:11,859] [INFO] Found 22 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-14 12:27:11,859] [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_000714765.1	s__Erythrobacter sp000714765	79.4562	501	864	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	78.9639	414	864	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018205975.1	s__Erythrobacter sp018205975	78.6713	444	864	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000152865.1	s__Erythrobacter sp000152865	78.6197	422	864	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	78.6013	300	864	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	78.2581	255	864	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009363635.1	s__Erythrobacter sp009363635	78.1963	366	864	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001724215.1	s__Erythrobacter sp001724215	78.1801	321	864	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001720465.1	s__Erythrobacter sp001720465	78.1307	364	864	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000744895.1	s__Erythrobacter sp000744895	78.0975	389	864	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002952215.1	s__Erythrobacter sp002952215	78.0916	349	864	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014705715.1	s__Erythrobacter sp014705715	78.0441	373	864	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	78.0008	343	864	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	77.9991	294	864	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006542605.1	s__Erythrobacter sp006542605	77.9504	352	864	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	77.8425	312	864	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018991295.1	s__Erythrobacter sp018991295	77.7999	264	864	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002155685.1	s__Erythrobacter colymbi	77.6684	328	864	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014763545.1	s__JACXVD01 sp014763545	77.5586	222	864	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__JACXVD01	95.0	99.92	99.92	0.96	0.96	2	-
GCF_001281485.1	s__Erythrobacter epoxidivorans	77.555	246	864	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900149685.1	s__Erythrobacter sp900149685	77.3911	270	864	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	77.1119	234	864	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-14 12:27:11,859] [INFO] GTDB search result was written to OceanDNA-b31678/result_gtdb.tsv
[2023-03-14 12:27:11,859] [INFO] ===== GTDB Search completed =====
[2023-03-14 12:27:11,862] [INFO] DFAST_QC result json was written to OceanDNA-b31678/dqc_result.json
[2023-03-14 12:27:11,862] [INFO] DFAST_QC completed!
[2023-03-14 12:27:11,862] [INFO] Total running time: 0h1m30s