[2023-03-17 05:59:11,055] [INFO] DFAST_QC pipeline started.
[2023-03-17 05:59:11,055] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 05:59:11,055] [INFO] DQC Reference Directory: /var/lib/cwl/stg8d2ede56-482a-4d56-b607-dc792780790f/dqc_reference
[2023-03-17 05:59:12,175] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 05:59:12,175] [INFO] Task started: Prodigal
[2023-03-17 05:59:12,176] [INFO] Running command: cat /var/lib/cwl/stgbf32987e-62fe-48b4-89bf-5fb57e50144b/OceanDNA-b26928.fa | prodigal -d OceanDNA-b26928/cds.fna -a OceanDNA-b26928/protein.faa -g 11 -q > /dev/null
[2023-03-17 05:59:36,989] [INFO] Task succeeded: Prodigal
[2023-03-17 05:59:36,990] [INFO] Task started: HMMsearch
[2023-03-17 05:59:36,990] [INFO] Running command: hmmsearch --tblout OceanDNA-b26928/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8d2ede56-482a-4d56-b607-dc792780790f/dqc_reference/reference_markers.hmm OceanDNA-b26928/protein.faa > /dev/null
[2023-03-17 05:59:37,206] [INFO] Task succeeded: HMMsearch
[2023-03-17 05:59:37,207] [INFO] Found 6/6 markers.
[2023-03-17 05:59:37,232] [INFO] Query marker FASTA was written to OceanDNA-b26928/markers.fasta
[2023-03-17 05:59:37,232] [INFO] Task started: Blastn
[2023-03-17 05:59:37,232] [INFO] Running command: blastn -query OceanDNA-b26928/markers.fasta -db /var/lib/cwl/stg8d2ede56-482a-4d56-b607-dc792780790f/dqc_reference/reference_markers.fasta -out OceanDNA-b26928/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 05:59:38,112] [INFO] Task succeeded: Blastn
[2023-03-17 05:59:38,112] [INFO] Selected 24 target genomes.
[2023-03-17 05:59:38,113] [INFO] Target genome list was writen to OceanDNA-b26928/target_genomes.txt
[2023-03-17 05:59:38,123] [INFO] Task started: fastANI
[2023-03-17 05:59:38,123] [INFO] Running command: fastANI --query /var/lib/cwl/stgbf32987e-62fe-48b4-89bf-5fb57e50144b/OceanDNA-b26928.fa --refList OceanDNA-b26928/target_genomes.txt --output OceanDNA-b26928/fastani_result.tsv --threads 1
[2023-03-17 05:59:57,626] [INFO] Task succeeded: fastANI
[2023-03-17 05:59:57,626] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8d2ede56-482a-4d56-b607-dc792780790f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 05:59:57,626] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8d2ede56-482a-4d56-b607-dc792780790f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 05:59:57,639] [INFO] Found 24 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 05:59:57,640] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 05:59:57,640] [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
Stappia stellulata	strain=DSM 5886	GCA_000423705.1	71235	71235	type	True	79.7318	675	1338	95	below_threshold
Stappia taiwanensis	strain=CCM 7757	GCA_014635285.1	992267	992267	type	True	79.5662	658	1338	95	below_threshold
Stappia taiwanensis	strain=DSM 23284	GCA_013868145.1	992267	992267	type	True	79.4878	663	1338	95	below_threshold
Stappia albiluteola	strain=F7233	GCA_014050225.1	2758565	2758565	type	True	78.4832	482	1338	95	below_threshold
Pannonibacter phragmitetus	strain=DSM 14782	GCA_000382365.1	121719	121719	suspected-type	True	78.1654	396	1338	95	below_threshold
Pannonibacter phragmitetus	strain=NCTC13350	GCA_900454465.1	121719	121719	suspected-type	True	78.1556	400	1338	95	below_threshold
Pannonibacter indicus	strain=DSM 23407	GCA_001517385.1	466044	466044	type	True	78.0434	406	1338	95	below_threshold
Pannonibacter indicus	strain=DSM 23407	GCA_001418225.1	466044	466044	type	True	78.0347	407	1338	95	below_threshold
Pannonibacter carbonis	strain=Q4.6	GCA_003012935.1	2067569	2067569	type	True	77.9775	407	1338	95	below_threshold
Breoghania corrubedonensis	strain=DSM 23382	GCA_003053845.1	665038	665038	type	True	77.7807	374	1338	95	below_threshold
Ciceribacter ferrooxidans	strain=F8825	GCA_004137355.1	2509717	2509717	type	True	77.2212	224	1338	95	below_threshold
Jiella pacifica	strain=40Bstr34	GCA_010500815.1	2696469	2696469	type	True	77.1519	275	1338	95	below_threshold
Shinella oryzae	strain=Z-25	GCA_023038235.1	2871820	2871820	type	True	77.1497	233	1338	95	below_threshold
Blastochloris sulfoviridis	strain=DSM 729	GCA_008630065.1	50712	50712	type	True	77.147	247	1338	95	below_threshold
Shinella sumterensis	strain=MEC087	GCA_004514425.2	1967501	1967501	type	True	77.0971	257	1338	95	below_threshold
Xanthobacter dioxanivorans	strain=YN2	GCA_016807805.1	2528964	2528964	type	True	76.9877	270	1338	95	below_threshold
Pseudaminobacter soli	strain=HC19	GCA_014595955.1	2831468	2831468	type	True	76.948	235	1338	95	below_threshold
Pseudaminobacter soli	strain=19-2017	GCA_018310375.1	2831468	2831468	type	True	76.9382	236	1338	95	below_threshold
Rhizobium sophoriradicis	strain=CCBAU 03470	GCA_003939025.1	1535245	1535245	type	True	76.8937	217	1338	95	below_threshold
Rhizobium esperanzae	strain=CNPSo 668	GCA_002204185.1	1967781	1967781	suspected-type	True	76.6453	203	1338	95	below_threshold
Rhodoligotrophos defluvii	strain=lm1	GCA_005281615.1	2561934	2561934	type	True	76.5796	146	1338	95	below_threshold
Methylobacterium goesingense	strain=DSM 21331	GCA_022179225.1	243690	243690	type	True	76.4829	192	1338	95	below_threshold
Reyranella aquatilis	strain=KCTC 52223	GCA_020880995.1	2035356	2035356	type	True	76.3439	164	1338	95	below_threshold
Frigidibacter albus	strain=SP32	GCA_009881095.1	1465486	1465486	type	True	76.3155	154	1338	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 05:59:57,640] [INFO] DFAST Taxonomy check result was written to OceanDNA-b26928/tc_result.tsv
[2023-03-17 05:59:57,640] [INFO] ===== Taxonomy check completed =====
[2023-03-17 05:59:57,640] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 05:59:57,640] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8d2ede56-482a-4d56-b607-dc792780790f/dqc_reference/checkm_data
[2023-03-17 05:59:57,641] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 05:59:57,679] [INFO] Task started: CheckM
[2023-03-17 05:59:57,679] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b26928/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b26928/checkm_input OceanDNA-b26928/checkm_result
[2023-03-17 06:01:04,578] [INFO] Task succeeded: CheckM
[2023-03-17 06:01:04,579] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 06:01:04,582] [INFO] ===== Completeness check finished =====
[2023-03-17 06:01:04,582] [INFO] ===== Start GTDB Search =====
[2023-03-17 06:01:04,582] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b26928/markers.fasta)
[2023-03-17 06:01:04,582] [INFO] Task started: Blastn
[2023-03-17 06:01:04,582] [INFO] Running command: blastn -query OceanDNA-b26928/markers.fasta -db /var/lib/cwl/stg8d2ede56-482a-4d56-b607-dc792780790f/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b26928/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 06:01:06,160] [INFO] Task succeeded: Blastn
[2023-03-17 06:01:06,161] [INFO] Selected 13 target genomes.
[2023-03-17 06:01:06,161] [INFO] Target genome list was writen to OceanDNA-b26928/target_genomes_gtdb.txt
[2023-03-17 06:01:06,325] [INFO] Task started: fastANI
[2023-03-17 06:01:06,325] [INFO] Running command: fastANI --query /var/lib/cwl/stgbf32987e-62fe-48b4-89bf-5fb57e50144b/OceanDNA-b26928.fa --refList OceanDNA-b26928/target_genomes_gtdb.txt --output OceanDNA-b26928/fastani_result_gtdb.tsv --threads 1
[2023-03-17 06:01:18,114] [INFO] Task succeeded: fastANI
[2023-03-17 06:01:18,122] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 06:01:18,122] [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_002722295.1	s__Stappia sp002722295	99.8596	1249	1338	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Stappia	95.0	99.88	99.88	0.88	0.88	2	conclusive
GCF_009789575.1	s__Stappia indica_A	81.0935	887	1338	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Stappia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001696535.1	s__Stappia indica	81.0435	846	1338	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Stappia	95.0	97.23	96.79	0.94	0.94	3	-
GCF_003610575.1	s__Stappia sp003610575	80.9156	835	1338	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Stappia	95.0	98.18	98.18	0.97	0.97	2	-
GCF_900185725.1	s__Stappia sp900185725	80.8632	819	1338	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Stappia	95.0	98.18	97.99	0.94	0.94	3	-
GCA_002709505.1	s__Stappia sp002709505	80.2568	620	1338	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Stappia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000423705.1	s__Stappia stellulata	79.7121	678	1338	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Stappia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016774605.1	s__Stappia sp016774605	79.6805	565	1338	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Stappia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014635285.1	s__Stappia taiwanensis	79.572	656	1338	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Stappia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900105595.1	s__Stappia sp900105595	79.5607	667	1338	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Stappia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009915765.1	s__Pannonibacter sp009915765	78.7104	465	1338	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Pannonibacter	95.0	98.76	98.76	0.96	0.96	2	-
GCF_008630065.1	s__Blastochloris sulfoviridis	77.1474	247	1338	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Blastochloris	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002700095.1	s__Jiella sp002700095	77.0096	276	1338	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Jiella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 06:01:18,122] [INFO] GTDB search result was written to OceanDNA-b26928/result_gtdb.tsv
[2023-03-17 06:01:18,123] [INFO] ===== GTDB Search completed =====
[2023-03-17 06:01:18,125] [INFO] DFAST_QC result json was written to OceanDNA-b26928/dqc_result.json
[2023-03-17 06:01:18,125] [INFO] DFAST_QC completed!
[2023-03-17 06:01:18,125] [INFO] Total running time: 0h2m7s