[2023-03-15 04:45:50,404] [INFO] DFAST_QC pipeline started.
[2023-03-15 04:45:50,404] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 04:45:50,404] [INFO] DQC Reference Directory: /var/lib/cwl/stg2d9095a7-9443-47da-a767-791b1c0b4952/dqc_reference
[2023-03-15 04:45:51,527] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 04:45:51,527] [INFO] Task started: Prodigal
[2023-03-15 04:45:51,527] [INFO] Running command: cat /var/lib/cwl/stg4f857c93-5dbe-4c0a-9fba-323f19f2ac1c/OceanDNA-b31671.fa | prodigal -d OceanDNA-b31671/cds.fna -a OceanDNA-b31671/protein.faa -g 11 -q > /dev/null
[2023-03-15 04:46:13,304] [INFO] Task succeeded: Prodigal
[2023-03-15 04:46:13,304] [INFO] Task started: HMMsearch
[2023-03-15 04:46:13,304] [INFO] Running command: hmmsearch --tblout OceanDNA-b31671/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2d9095a7-9443-47da-a767-791b1c0b4952/dqc_reference/reference_markers.hmm OceanDNA-b31671/protein.faa > /dev/null
[2023-03-15 04:46:13,518] [INFO] Task succeeded: HMMsearch
[2023-03-15 04:46:13,518] [INFO] Found 6/6 markers.
[2023-03-15 04:46:13,565] [INFO] Query marker FASTA was written to OceanDNA-b31671/markers.fasta
[2023-03-15 04:46:13,565] [INFO] Task started: Blastn
[2023-03-15 04:46:13,566] [INFO] Running command: blastn -query OceanDNA-b31671/markers.fasta -db /var/lib/cwl/stg2d9095a7-9443-47da-a767-791b1c0b4952/dqc_reference/reference_markers.fasta -out OceanDNA-b31671/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 04:46:14,198] [INFO] Task succeeded: Blastn
[2023-03-15 04:46:14,204] [INFO] Selected 28 target genomes.
[2023-03-15 04:46:14,204] [INFO] Target genome list was writen to OceanDNA-b31671/target_genomes.txt
[2023-03-15 04:46:14,223] [INFO] Task started: fastANI
[2023-03-15 04:46:14,223] [INFO] Running command: fastANI --query /var/lib/cwl/stg4f857c93-5dbe-4c0a-9fba-323f19f2ac1c/OceanDNA-b31671.fa --refList OceanDNA-b31671/target_genomes.txt --output OceanDNA-b31671/fastani_result.tsv --threads 1
[2023-03-15 04:46:30,336] [INFO] Task succeeded: fastANI
[2023-03-15 04:46:30,337] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2d9095a7-9443-47da-a767-791b1c0b4952/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 04:46:30,337] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2d9095a7-9443-47da-a767-791b1c0b4952/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 04:46:30,352] [INFO] Found 28 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 04:46:30,352] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 04:46:30,352] [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 sanguineus	strain=DSM 11032	GCA_900143235.1	198312	198312	type	True	78.2514	400	1117	95	below_threshold
Erythrobacter rubeus	strain=KMU-140	GCA_014705715.1	2760803	2760803	type	True	78.247	383	1117	95	below_threshold
Erythrobacter sanguineus	strain=JCM 20691	GCA_002155655.1	198312	198312	type	True	78.2412	401	1117	95	below_threshold
Erythrobacter longus	strain=DSM 6997	GCA_000715015.1	1044	1044	type	True	78.1255	416	1117	95	below_threshold
Erythrobacter litoralis	strain=DSM 8509	GCA_000714795.1	39960	39960	type	True	78.0278	414	1117	95	below_threshold
Erythrobacter colymbi	strain=JCM 18338	GCA_002155685.1	1161202	1161202	type	True	78.0152	370	1117	95	below_threshold
Erythrobacter litoralis	strain=DSM 8509	GCA_001719165.1	39960	39960	type	True	78.0052	416	1117	95	below_threshold
Erythrobacter dokdonensis	strain=DSM 17193	GCA_002155305.1	328225	328225	type	True	77.9963	391	1117	95	below_threshold
Erythrobacter neustonensis	strain=DSM 9434	GCA_001663175.1	1112	1112	type	True	77.9805	358	1117	95	below_threshold
Erythrobacter dokdonensis	strain=DSW-74	GCA_001677335.1	328225	328225	type	True	77.9784	383	1117	95	below_threshold
Qipengyuania polymorpha	strain=1NDH17	GCA_019711435.1	2867234	2867234	type	True	77.9345	268	1117	95	below_threshold
Qipengyuania qiaonensis	strain=6D47A	GCA_019711515.1	2867240	2867240	type	True	77.7678	234	1117	95	below_threshold
Pelagerythrobacter marensis	strain=KCTC 22370	GCA_001028625.1	543877	543877	type	True	77.7641	194	1117	95	below_threshold
Qipengyuania vesicularis	strain=1NDH10	GCA_019711415.1	2867232	2867232	type	True	77.7024	260	1117	95	below_threshold
Erythrobacter ramosus	strain=JCM 10282	GCA_009828055.1	35811	35811	type	True	77.6712	370	1117	95	below_threshold
Pelagerythrobacter marensis	strain=DSM 21428	GCA_001461885.1	543877	543877	type	True	77.6679	203	1117	95	below_threshold
Erythrobacter ramosus	strain=DSM 8510	GCA_014195675.1	35811	35811	type	True	77.6384	371	1117	95	below_threshold
Qipengyuania intermedia	strain=GH38	GCA_019711615.1	2867244	2867244	type	True	77.5798	242	1117	95	below_threshold
Altererythrobacter lutimaris	strain=JGD-16	GCA_013371495.1	2743979	2743979	type	True	77.535	266	1117	95	below_threshold
Aurantiacibacter gangjinensis	strain=CGMCC 1.15024	GCA_001886695.1	502682	502682	type	True	77.5314	205	1117	95	below_threshold
Qipengyuania pelagi	strain=JCM 17468	GCA_009827295.1	994320	994320	type	True	77.5094	234	1117	95	below_threshold
Pelagerythrobacter rhizovicinus	strain=AY-3R	GCA_004135625.1	2268576	2268576	type	True	77.4854	208	1117	95	below_threshold
Qipengyuania pacifica	strain=NZ-96	GCA_019857205.1	2860199	2860199	type	True	77.4816	190	1117	95	below_threshold
Qipengyuania aerophila	strain=GH25	GCA_019711555.1	2867242	2867242	type	True	77.4518	194	1117	95	below_threshold
Pelagerythrobacter aerophilus	strain=Ery1	GCA_003581645.1	2306995	2306995	type	True	77.3142	214	1117	95	below_threshold
Allopontixanthobacter confluentis	strain=KCTC 52259	GCA_009827615.1	1849021	1849021	type	True	77.1679	171	1117	95	below_threshold
Aurantiacibacter atlanticus	strain=s21-N3	GCA_001077815.2	1648404	1648404	type	True	77.0693	157	1117	95	below_threshold
Sphingomonas laterariae	strain=LNB2	GCA_900188165.1	861865	861865	type	True	76.7854	111	1117	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 04:46:30,356] [INFO] DFAST Taxonomy check result was written to OceanDNA-b31671/tc_result.tsv
[2023-03-15 04:46:30,356] [INFO] ===== Taxonomy check completed =====
[2023-03-15 04:46:30,356] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 04:46:30,356] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2d9095a7-9443-47da-a767-791b1c0b4952/dqc_reference/checkm_data
[2023-03-15 04:46:30,357] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 04:46:30,363] [INFO] Task started: CheckM
[2023-03-15 04:46:30,363] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b31671/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b31671/checkm_input OceanDNA-b31671/checkm_result
[2023-03-15 04:47:28,111] [INFO] Task succeeded: CheckM
[2023-03-15 04:47:28,112] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 04:47:28,165] [INFO] ===== Completeness check finished =====
[2023-03-15 04:47:28,165] [INFO] ===== Start GTDB Search =====
[2023-03-15 04:47:28,166] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b31671/markers.fasta)
[2023-03-15 04:47:28,167] [INFO] Task started: Blastn
[2023-03-15 04:47:28,167] [INFO] Running command: blastn -query OceanDNA-b31671/markers.fasta -db /var/lib/cwl/stg2d9095a7-9443-47da-a767-791b1c0b4952/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b31671/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 04:47:29,076] [INFO] Task succeeded: Blastn
[2023-03-15 04:47:29,085] [INFO] Selected 19 target genomes.
[2023-03-15 04:47:29,085] [INFO] Target genome list was writen to OceanDNA-b31671/target_genomes_gtdb.txt
[2023-03-15 04:47:29,105] [INFO] Task started: fastANI
[2023-03-15 04:47:29,105] [INFO] Running command: fastANI --query /var/lib/cwl/stg4f857c93-5dbe-4c0a-9fba-323f19f2ac1c/OceanDNA-b31671.fa --refList OceanDNA-b31671/target_genomes_gtdb.txt --output OceanDNA-b31671/fastani_result_gtdb.tsv --threads 1
[2023-03-15 04:47:40,201] [INFO] Task succeeded: fastANI
[2023-03-15 04:47:40,212] [INFO] Found 19 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 04:47:40,213] [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_000152865.1	s__Erythrobacter sp000152865	79.6631	628	1117	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	79.4691	616	1117	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	79.1911	543	1117	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	78.9465	348	1117	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	78.7434	438	1117	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	78.5784	284	1117	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	78.2077	407	1117	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000715015.1	s__Erythrobacter longus	78.1299	417	1117	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	78.11	348	1117	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011054555.1	s__Erythrobacter sp011054555	78.0178	281	1117	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001719165.1	s__Erythrobacter litoralis	78.0065	417	1117	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001663175.1	s__Erythrobacter neustonensis	77.9707	359	1117	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016125555.1	s__Erythrobacter sp016125555	77.9189	357	1117	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900105095.1	s__Erythrobacter sp900105095	77.792	397	1117	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	99.99	99.99	1.00	1.00	2	-
GCF_002215495.1	s__Erythrobacter sp002215495	77.7463	357	1117	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018830415.1	s__Erythrobacter sp018830415	77.7403	254	1117	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013911835.1	s__Erythrobacter sp013911835	77.7235	266	1117	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	77.6478	343	1117	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001557115.1	s__Erythrobacter sp001557115	77.6426	328	1117	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	99.84	99.84	0.90	0.90	2	-
--------------------------------------------------------------------------------
[2023-03-15 04:47:40,215] [INFO] GTDB search result was written to OceanDNA-b31671/result_gtdb.tsv
[2023-03-15 04:47:40,217] [INFO] ===== GTDB Search completed =====
[2023-03-15 04:47:40,223] [INFO] DFAST_QC result json was written to OceanDNA-b31671/dqc_result.json
[2023-03-15 04:47:40,223] [INFO] DFAST_QC completed!
[2023-03-15 04:47:40,223] [INFO] Total running time: 0h1m50s