[2024-01-24 13:40:33,331] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:33,333] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:33,334] [INFO] DQC Reference Directory: /var/lib/cwl/stg1955509e-ae52-467e-ad78-472903526987/dqc_reference
[2024-01-24 13:40:34,682] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:34,684] [INFO] Task started: Prodigal
[2024-01-24 13:40:34,685] [INFO] Running command: gunzip -c /var/lib/cwl/stgdd3350a3-6011-4700-a598-30892001b694/GCF_019711555.1_ASM1971155v1_genomic.fna.gz | prodigal -d GCF_019711555.1_ASM1971155v1_genomic.fna/cds.fna -a GCF_019711555.1_ASM1971155v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:40:44,842] [INFO] Task succeeded: Prodigal
[2024-01-24 13:40:44,843] [INFO] Task started: HMMsearch
[2024-01-24 13:40:44,843] [INFO] Running command: hmmsearch --tblout GCF_019711555.1_ASM1971155v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1955509e-ae52-467e-ad78-472903526987/dqc_reference/reference_markers.hmm GCF_019711555.1_ASM1971155v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:40:45,155] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:40:45,156] [INFO] Found 6/6 markers.
[2024-01-24 13:40:45,189] [INFO] Query marker FASTA was written to GCF_019711555.1_ASM1971155v1_genomic.fna/markers.fasta
[2024-01-24 13:40:45,190] [INFO] Task started: Blastn
[2024-01-24 13:40:45,190] [INFO] Running command: blastn -query GCF_019711555.1_ASM1971155v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1955509e-ae52-467e-ad78-472903526987/dqc_reference/reference_markers.fasta -out GCF_019711555.1_ASM1971155v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:40:46,148] [INFO] Task succeeded: Blastn
[2024-01-24 13:40:46,158] [INFO] Selected 10 target genomes.
[2024-01-24 13:40:46,158] [INFO] Target genome list was writen to GCF_019711555.1_ASM1971155v1_genomic.fna/target_genomes.txt
[2024-01-24 13:40:46,164] [INFO] Task started: fastANI
[2024-01-24 13:40:46,164] [INFO] Running command: fastANI --query /var/lib/cwl/stgdd3350a3-6011-4700-a598-30892001b694/GCF_019711555.1_ASM1971155v1_genomic.fna.gz --refList GCF_019711555.1_ASM1971155v1_genomic.fna/target_genomes.txt --output GCF_019711555.1_ASM1971155v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:40:53,131] [INFO] Task succeeded: fastANI
[2024-01-24 13:40:53,131] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1955509e-ae52-467e-ad78-472903526987/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:40:53,132] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1955509e-ae52-467e-ad78-472903526987/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:40:53,141] [INFO] Found 10 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:40:53,141] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 13:40:53,142] [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 aerophila	strain=GH25	GCA_019711555.1	2867242	2867242	type	True	100.0	1052	1052	95	inconclusive
Qipengyuania pacifica	strain=NZ-96	GCA_019857205.1	2860199	2860199	type	True	96.9878	903	1052	95	inconclusive
Qipengyuania qiaonensis	strain=6D47A	GCA_019711515.1	2867240	2867240	type	True	81.7587	633	1052	95	below_threshold
Qipengyuania flava	strain=DSM 16421	GCA_011762005.1	192812	192812	type	True	80.6709	560	1052	95	below_threshold
Qipengyuania proteolytica	strain=6B39	GCA_019711565.1	2867239	2867239	type	True	80.5258	534	1052	95	below_threshold
Qipengyuania aestuarii	strain=GH1	GCA_019711535.1	2867241	2867241	type	True	80.1279	421	1052	95	below_threshold
Qipengyuania soli	strain=6D36	GCA_015529805.1	2782568	2782568	type	True	79.6873	457	1052	95	below_threshold
Qipengyuania xiapuensis	strain=1NDW9	GCA_019711395.1	2867236	2867236	type	True	79.5917	432	1052	95	below_threshold
Qipengyuania seohaensis	strain=SW-135	GCA_002795865.1	266951	266951	type	True	79.3707	438	1052	95	below_threshold
Qipengyuania pelagi	strain=JCM 17468	GCA_009827295.1	994320	994320	type	True	79.3024	430	1052	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:40:53,143] [INFO] DFAST Taxonomy check result was written to GCF_019711555.1_ASM1971155v1_genomic.fna/tc_result.tsv
[2024-01-24 13:40:53,144] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:40:53,144] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:40:53,144] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1955509e-ae52-467e-ad78-472903526987/dqc_reference/checkm_data
[2024-01-24 13:40:53,145] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:40:53,179] [INFO] Task started: CheckM
[2024-01-24 13:40:53,179] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019711555.1_ASM1971155v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019711555.1_ASM1971155v1_genomic.fna/checkm_input GCF_019711555.1_ASM1971155v1_genomic.fna/checkm_result
[2024-01-24 13:41:27,960] [INFO] Task succeeded: CheckM
[2024-01-24 13:41:27,961] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:41:27,987] [INFO] ===== Completeness check finished =====
[2024-01-24 13:41:27,987] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:41:27,987] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019711555.1_ASM1971155v1_genomic.fna/markers.fasta)
[2024-01-24 13:41:27,988] [INFO] Task started: Blastn
[2024-01-24 13:41:27,988] [INFO] Running command: blastn -query GCF_019711555.1_ASM1971155v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1955509e-ae52-467e-ad78-472903526987/dqc_reference/reference_markers_gtdb.fasta -out GCF_019711555.1_ASM1971155v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:29,786] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:29,792] [INFO] Selected 14 target genomes.
[2024-01-24 13:41:29,792] [INFO] Target genome list was writen to GCF_019711555.1_ASM1971155v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:41:29,807] [INFO] Task started: fastANI
[2024-01-24 13:41:29,807] [INFO] Running command: fastANI --query /var/lib/cwl/stgdd3350a3-6011-4700-a598-30892001b694/GCF_019711555.1_ASM1971155v1_genomic.fna.gz --refList GCF_019711555.1_ASM1971155v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019711555.1_ASM1971155v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:41:39,333] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:39,347] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:41:39,348] [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_015767595.1	s__Qipengyuania sp002895025	97.1315	917	1052	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	97.29	96.55	0.87	0.78	16	conclusive
GCF_001542855.1	s__Qipengyuania sp001542855	81.3677	596	1052	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	97.07	97.03	0.89	0.88	4	-
GCF_009828015.1	s__Qipengyuania citrea	81.277	568	1052	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	97.91	97.49	0.87	0.80	20	-
GCA_016764075.1	s__Qipengyuania sp016764075	80.9794	451	1052	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	80.6599	561	1052	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	97.04	96.57	0.91	0.85	10	-
GCF_003355455.1	s__Qipengyuania aurea	80.4876	557	1052	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	97.67	97.64	0.83	0.82	3	-
GCA_003248395.1	s__Qipengyuania sp003248395	79.9731	401	1052	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009827315.1	s__Qipengyuania gaetbuli	79.8313	458	1052	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015529805.1	s__Qipengyuania soli	79.6817	458	1052	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009827445.1	s__Qipengyuania aquimaris	79.3682	428	1052	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002795865.1	s__Qipengyuania seohaensis	79.3651	439	1052	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009827295.1	s__Qipengyuania pelagi	79.2915	431	1052	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002695185.1	s__Qipengyuania sp002695185	79.0755	378	1052	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	96.33	96.22	0.77	0.72	4	-
GCA_009993605.1	s__Qipengyuania sp009993605	78.7229	414	1052	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:41:39,350] [INFO] GTDB search result was written to GCF_019711555.1_ASM1971155v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:41:39,351] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:41:39,356] [INFO] DFAST_QC result json was written to GCF_019711555.1_ASM1971155v1_genomic.fna/dqc_result.json
[2024-01-24 13:41:39,356] [INFO] DFAST_QC completed!
[2024-01-24 13:41:39,356] [INFO] Total running time: 0h1m6s