[2023-06-16 19:04:14,015] [INFO] DFAST_QC pipeline started.
[2023-06-16 19:04:14,018] [INFO] DFAST_QC version: 0.5.7
[2023-06-16 19:04:14,018] [INFO] DQC Reference Directory: /var/lib/cwl/stg0b1faeea-42b9-49fe-a538-0bbd03c32db1/dqc_reference
[2023-06-16 19:04:15,181] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-16 19:04:15,182] [INFO] Task started: Prodigal
[2023-06-16 19:04:15,182] [INFO] Running command: gunzip -c /var/lib/cwl/stge64acf47-bc65-4942-b05d-b13caaa26b83/GCA_003504375.1_ASM350437v1_genomic.fna.gz | prodigal -d GCA_003504375.1_ASM350437v1_genomic.fna/cds.fna -a GCA_003504375.1_ASM350437v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-16 19:04:19,362] [INFO] Task succeeded: Prodigal
[2023-06-16 19:04:19,362] [INFO] Task started: HMMsearch
[2023-06-16 19:04:19,362] [INFO] Running command: hmmsearch --tblout GCA_003504375.1_ASM350437v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0b1faeea-42b9-49fe-a538-0bbd03c32db1/dqc_reference/reference_markers.hmm GCA_003504375.1_ASM350437v1_genomic.fna/protein.faa > /dev/null
[2023-06-16 19:04:19,516] [INFO] Task succeeded: HMMsearch
[2023-06-16 19:04:19,517] [WARNING] Found 4/6 markers. [/var/lib/cwl/stge64acf47-bc65-4942-b05d-b13caaa26b83/GCA_003504375.1_ASM350437v1_genomic.fna.gz]
[2023-06-16 19:04:19,540] [INFO] Query marker FASTA was written to GCA_003504375.1_ASM350437v1_genomic.fna/markers.fasta
[2023-06-16 19:04:19,540] [INFO] Task started: Blastn
[2023-06-16 19:04:19,541] [INFO] Running command: blastn -query GCA_003504375.1_ASM350437v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0b1faeea-42b9-49fe-a538-0bbd03c32db1/dqc_reference/reference_markers.fasta -out GCA_003504375.1_ASM350437v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-16 19:04:20,150] [INFO] Task succeeded: Blastn
[2023-06-16 19:04:20,153] [INFO] Selected 16 target genomes.
[2023-06-16 19:04:20,154] [INFO] Target genome list was writen to GCA_003504375.1_ASM350437v1_genomic.fna/target_genomes.txt
[2023-06-16 19:04:20,166] [INFO] Task started: fastANI
[2023-06-16 19:04:20,166] [INFO] Running command: fastANI --query /var/lib/cwl/stge64acf47-bc65-4942-b05d-b13caaa26b83/GCA_003504375.1_ASM350437v1_genomic.fna.gz --refList GCA_003504375.1_ASM350437v1_genomic.fna/target_genomes.txt --output GCA_003504375.1_ASM350437v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-16 19:04:28,876] [INFO] Task succeeded: fastANI
[2023-06-16 19:04:28,877] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0b1faeea-42b9-49fe-a538-0bbd03c32db1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-16 19:04:28,877] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0b1faeea-42b9-49fe-a538-0bbd03c32db1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-16 19:04:28,890] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2023-06-16 19:04:28,890] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-16 19:04:28,891] [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
Qipengyuania flava	strain=DSM 16421	GCA_011762005.1	192812	192812	type	True	84.6508	430	491	95	below_threshold
Qipengyuania proteolytica	strain=6B39	GCA_019711565.1	2867239	2867239	type	True	81.7879	371	491	95	below_threshold
Qipengyuania qiaonensis	strain=6D47A	GCA_019711515.1	2867240	2867240	type	True	81.7207	376	491	95	below_threshold
Qipengyuania xiamenensis	strain=1XM1-15A	GCA_019711495.1	2867237	2867237	type	True	81.2209	327	491	95	below_threshold
Qipengyuania aurantiaca	strain=1NDH13	GCA_019711375.1	2867233	2867233	type	True	81.2041	343	491	95	below_threshold
Qipengyuania gaetbuli	strain=DSM 16225	GCA_009827315.1	266952	266952	type	True	81.1451	360	491	95	below_threshold
Qipengyuania sphaerica	strain=GH29	GCA_019711595.1	2867243	2867243	type	True	81.1071	325	491	95	below_threshold
Qipengyuania aerophila	strain=GH25	GCA_019711555.1	2867242	2867242	type	True	81.1	336	491	95	below_threshold
Qipengyuania pacifica	strain=NZ-96	GCA_019857205.1	2860199	2860199	type	True	81.0211	333	491	95	below_threshold
Qipengyuania gelatinilytica	strain=1NDH1	GCA_019711315.1	2867231	2867231	type	True	80.9411	338	491	95	below_threshold
Qipengyuania xiapuensis	strain=1NDW9	GCA_019711395.1	2867236	2867236	type	True	80.906	347	491	95	below_threshold
Qipengyuania huizhouensis	strain=YG19	GCA_019711635.1	2867245	2867245	type	True	80.0955	289	491	95	below_threshold
Qipengyuania pelagi	strain=JCM 17468	GCA_009827295.1	994320	994320	type	True	80.0477	334	491	95	below_threshold
Pelagerythrobacter rhizovicinus	strain=AY-3R	GCA_004135625.1	2268576	2268576	type	True	79.3756	288	491	95	below_threshold
Novosphingobium arvoryzae	strain=KCTC 32422	GCA_014652615.1	1256514	1256514	type	True	78.5208	218	491	95	below_threshold
Novosphingobium aquimarinum	strain=M24A2M	GCA_009746585.1	2682494	2682494	type	True	77.9915	204	491	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-16 19:04:28,893] [INFO] DFAST Taxonomy check result was written to GCA_003504375.1_ASM350437v1_genomic.fna/tc_result.tsv
[2023-06-16 19:04:28,894] [INFO] ===== Taxonomy check completed =====
[2023-06-16 19:04:28,894] [INFO] ===== Start completeness check using CheckM =====
[2023-06-16 19:04:28,894] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0b1faeea-42b9-49fe-a538-0bbd03c32db1/dqc_reference/checkm_data
[2023-06-16 19:04:28,895] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-16 19:04:28,917] [INFO] Task started: CheckM
[2023-06-16 19:04:28,917] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_003504375.1_ASM350437v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_003504375.1_ASM350437v1_genomic.fna/checkm_input GCA_003504375.1_ASM350437v1_genomic.fna/checkm_result
[2023-06-16 19:04:44,805] [INFO] Task succeeded: CheckM
[2023-06-16 19:04:44,806] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 58.97%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-16 19:04:44,823] [INFO] ===== Completeness check finished =====
[2023-06-16 19:04:44,823] [INFO] ===== Start GTDB Search =====
[2023-06-16 19:04:44,824] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_003504375.1_ASM350437v1_genomic.fna/markers.fasta)
[2023-06-16 19:04:44,824] [INFO] Task started: Blastn
[2023-06-16 19:04:44,824] [INFO] Running command: blastn -query GCA_003504375.1_ASM350437v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0b1faeea-42b9-49fe-a538-0bbd03c32db1/dqc_reference/reference_markers_gtdb.fasta -out GCA_003504375.1_ASM350437v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-16 19:04:45,699] [INFO] Task succeeded: Blastn
[2023-06-16 19:04:45,703] [INFO] Selected 13 target genomes.
[2023-06-16 19:04:45,703] [INFO] Target genome list was writen to GCA_003504375.1_ASM350437v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-16 19:04:45,724] [INFO] Task started: fastANI
[2023-06-16 19:04:45,725] [INFO] Running command: fastANI --query /var/lib/cwl/stge64acf47-bc65-4942-b05d-b13caaa26b83/GCA_003504375.1_ASM350437v1_genomic.fna.gz --refList GCA_003504375.1_ASM350437v1_genomic.fna/target_genomes_gtdb.txt --output GCA_003504375.1_ASM350437v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-16 19:04:52,907] [INFO] Task succeeded: fastANI
[2023-06-16 19:04:52,919] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-16 19:04:52,919] [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_009828015.1	s__Qipengyuania citrea	98.4945	468	491	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	97.91	97.49	0.87	0.80	20	conclusive
GCA_016764075.1	s__Qipengyuania sp016764075	85.6049	346	491	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011762005.1	s__Qipengyuania flava	84.6508	430	491	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	97.04	96.57	0.91	0.85	10	-
GCF_001542855.1	s__Qipengyuania sp001542855	83.081	403	491	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	97.07	97.03	0.89	0.88	4	-
GCF_003355455.1	s__Qipengyuania aurea	82.2006	387	491	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	97.67	97.64	0.83	0.82	3	-
GCF_015767595.1	s__Qipengyuania sp002895025	81.1105	344	491	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	97.29	96.55	0.87	0.78	16	-
GCF_015529805.1	s__Qipengyuania soli	80.7655	332	491	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000756795.1	s__Qipengyuania vulgaris_A	80.5012	328	491	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013260645.1	s__Qipengyuania mangrovi	80.355	319	491	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013001165.1	s__Qipengyuania sp013001165	80.3397	285	491	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003248395.1	s__Qipengyuania sp003248395	79.8013	280	491	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018819685.1	s__Qipengyuania sp018819685	79.3806	241	491	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	99.48	99.48	0.85	0.85	2	-
GCF_004135625.1	s__Pelagerythrobacter rhizovicinus	79.3694	289	491	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pelagerythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-16 19:04:52,922] [INFO] GTDB search result was written to GCA_003504375.1_ASM350437v1_genomic.fna/result_gtdb.tsv
[2023-06-16 19:04:52,923] [INFO] ===== GTDB Search completed =====
[2023-06-16 19:04:52,929] [INFO] DFAST_QC result json was written to GCA_003504375.1_ASM350437v1_genomic.fna/dqc_result.json
[2023-06-16 19:04:52,929] [INFO] DFAST_QC completed!
[2023-06-16 19:04:52,929] [INFO] Total running time: 0h0m39s