[2024-01-24 12:22:48,420] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:22:48,424] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:22:48,424] [INFO] DQC Reference Directory: /var/lib/cwl/stg416b4879-7d17-4e5a-b32d-4372ecd14782/dqc_reference
[2024-01-24 12:22:49,688] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:22:49,688] [INFO] Task started: Prodigal
[2024-01-24 12:22:49,689] [INFO] Running command: gunzip -c /var/lib/cwl/stgfd49f1a5-a603-4462-aadf-8f99f68af6dc/GCF_019711515.1_ASM1971151v1_genomic.fna.gz | prodigal -d GCF_019711515.1_ASM1971151v1_genomic.fna/cds.fna -a GCF_019711515.1_ASM1971151v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:23:00,176] [INFO] Task succeeded: Prodigal
[2024-01-24 12:23:00,177] [INFO] Task started: HMMsearch
[2024-01-24 12:23:00,177] [INFO] Running command: hmmsearch --tblout GCF_019711515.1_ASM1971151v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg416b4879-7d17-4e5a-b32d-4372ecd14782/dqc_reference/reference_markers.hmm GCF_019711515.1_ASM1971151v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:23:00,464] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:23:00,465] [INFO] Found 6/6 markers.
[2024-01-24 12:23:00,503] [INFO] Query marker FASTA was written to GCF_019711515.1_ASM1971151v1_genomic.fna/markers.fasta
[2024-01-24 12:23:00,504] [INFO] Task started: Blastn
[2024-01-24 12:23:00,504] [INFO] Running command: blastn -query GCF_019711515.1_ASM1971151v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg416b4879-7d17-4e5a-b32d-4372ecd14782/dqc_reference/reference_markers.fasta -out GCF_019711515.1_ASM1971151v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:23:01,505] [INFO] Task succeeded: Blastn
[2024-01-24 12:23:01,510] [INFO] Selected 12 target genomes.
[2024-01-24 12:23:01,510] [INFO] Target genome list was writen to GCF_019711515.1_ASM1971151v1_genomic.fna/target_genomes.txt
[2024-01-24 12:23:01,521] [INFO] Task started: fastANI
[2024-01-24 12:23:01,521] [INFO] Running command: fastANI --query /var/lib/cwl/stgfd49f1a5-a603-4462-aadf-8f99f68af6dc/GCF_019711515.1_ASM1971151v1_genomic.fna.gz --refList GCF_019711515.1_ASM1971151v1_genomic.fna/target_genomes.txt --output GCF_019711515.1_ASM1971151v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:23:09,623] [INFO] Task succeeded: fastANI
[2024-01-24 12:23:09,624] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg416b4879-7d17-4e5a-b32d-4372ecd14782/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:23:09,624] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg416b4879-7d17-4e5a-b32d-4372ecd14782/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:23:09,634] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:23:09,634] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:23:09,635] [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 qiaonensis	strain=6D47A	GCA_019711515.1	2867240	2867240	type	True	100.0	1112	1113	95	conclusive
Qipengyuania aerophila	strain=GH25	GCA_019711555.1	2867242	2867242	type	True	81.843	624	1113	95	below_threshold
Qipengyuania flava	strain=DSM 16421	GCA_011762005.1	192812	192812	type	True	81.7572	600	1113	95	below_threshold
Qipengyuania proteolytica	strain=6B39	GCA_019711565.1	2867239	2867239	type	True	81.5272	603	1113	95	below_threshold
Qipengyuania pacifica	strain=NZ-96	GCA_019857205.1	2860199	2860199	type	True	81.4436	654	1113	95	below_threshold
Qipengyuania gaetbuli	strain=DSM 16225	GCA_009827315.1	266952	266952	type	True	80.4546	522	1113	95	below_threshold
Qipengyuania xiapuensis	strain=1NDW9	GCA_019711395.1	2867236	2867236	type	True	80.4106	490	1113	95	below_threshold
Qipengyuania soli	strain=6D36	GCA_015529805.1	2782568	2782568	type	True	80.1573	528	1113	95	below_threshold
Qipengyuania vesicularis	strain=1NDH10	GCA_019711415.1	2867232	2867232	type	True	80.0502	473	1113	95	below_threshold
Qipengyuania pelagi	strain=JCM 17468	GCA_009827295.1	994320	994320	type	True	79.7679	461	1113	95	below_threshold
Qipengyuania aestuarii	strain=GH1	GCA_019711535.1	2867241	2867241	type	True	79.6579	408	1113	95	below_threshold
Qipengyuania aquimaris	strain=JCM 12189	GCA_009827445.1	255984	255984	suspected-type	True	79.5769	472	1113	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:23:09,636] [INFO] DFAST Taxonomy check result was written to GCF_019711515.1_ASM1971151v1_genomic.fna/tc_result.tsv
[2024-01-24 12:23:09,637] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:23:09,637] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:23:09,637] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg416b4879-7d17-4e5a-b32d-4372ecd14782/dqc_reference/checkm_data
[2024-01-24 12:23:09,638] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:23:09,680] [INFO] Task started: CheckM
[2024-01-24 12:23:09,680] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019711515.1_ASM1971151v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019711515.1_ASM1971151v1_genomic.fna/checkm_input GCF_019711515.1_ASM1971151v1_genomic.fna/checkm_result
[2024-01-24 12:23:43,862] [INFO] Task succeeded: CheckM
[2024-01-24 12:23:43,863] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:23:43,888] [INFO] ===== Completeness check finished =====
[2024-01-24 12:23:43,889] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:23:43,889] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019711515.1_ASM1971151v1_genomic.fna/markers.fasta)
[2024-01-24 12:23:43,890] [INFO] Task started: Blastn
[2024-01-24 12:23:43,890] [INFO] Running command: blastn -query GCF_019711515.1_ASM1971151v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg416b4879-7d17-4e5a-b32d-4372ecd14782/dqc_reference/reference_markers_gtdb.fasta -out GCF_019711515.1_ASM1971151v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:23:45,610] [INFO] Task succeeded: Blastn
[2024-01-24 12:23:45,615] [INFO] Selected 12 target genomes.
[2024-01-24 12:23:45,615] [INFO] Target genome list was writen to GCF_019711515.1_ASM1971151v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:23:45,627] [INFO] Task started: fastANI
[2024-01-24 12:23:45,628] [INFO] Running command: fastANI --query /var/lib/cwl/stgfd49f1a5-a603-4462-aadf-8f99f68af6dc/GCF_019711515.1_ASM1971151v1_genomic.fna.gz --refList GCF_019711515.1_ASM1971151v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019711515.1_ASM1971151v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:23:53,788] [INFO] Task succeeded: fastANI
[2024-01-24 12:23:53,798] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:23:53,799] [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_001542855.1	s__Qipengyuania sp001542855	82.3013	671	1113	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	97.07	97.03	0.89	0.88	4	-
GCA_016764075.1	s__Qipengyuania sp016764075	82.1746	481	1113	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009828015.1	s__Qipengyuania citrea	81.8612	603	1113	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	97.91	97.49	0.87	0.80	20	-
GCF_011762005.1	s__Qipengyuania flava	81.7572	600	1113	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	81.6997	614	1113	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	81.6058	657	1113	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	97.29	96.55	0.87	0.78	16	-
GCF_009827315.1	s__Qipengyuania gaetbuli	80.4546	522	1113	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	80.1785	526	1113	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	80.0816	513	1113	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	79.7793	460	1113	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	79.7734	399	1113	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	79.5769	472	1113	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 12:23:53,800] [INFO] GTDB search result was written to GCF_019711515.1_ASM1971151v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:23:53,801] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:23:53,805] [INFO] DFAST_QC result json was written to GCF_019711515.1_ASM1971151v1_genomic.fna/dqc_result.json
[2024-01-24 12:23:53,806] [INFO] DFAST_QC completed!
[2024-01-24 12:23:53,806] [INFO] Total running time: 0h1m5s