[2024-01-24 13:24:48,127] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:24:48,129] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:24:48,129] [INFO] DQC Reference Directory: /var/lib/cwl/stg296a817b-6a54-47f5-a95e-f1fe710fe380/dqc_reference
[2024-01-24 13:24:49,575] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:24:49,576] [INFO] Task started: Prodigal
[2024-01-24 13:24:49,576] [INFO] Running command: gunzip -c /var/lib/cwl/stg8888d404-1339-4bb8-b193-1793a6cc8cc6/GCF_009807005.1_ASM980700v1_genomic.fna.gz | prodigal -d GCF_009807005.1_ASM980700v1_genomic.fna/cds.fna -a GCF_009807005.1_ASM980700v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:25:01,609] [INFO] Task succeeded: Prodigal
[2024-01-24 13:25:01,610] [INFO] Task started: HMMsearch
[2024-01-24 13:25:01,610] [INFO] Running command: hmmsearch --tblout GCF_009807005.1_ASM980700v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg296a817b-6a54-47f5-a95e-f1fe710fe380/dqc_reference/reference_markers.hmm GCF_009807005.1_ASM980700v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:25:01,897] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:25:01,898] [INFO] Found 6/6 markers.
[2024-01-24 13:25:01,941] [INFO] Query marker FASTA was written to GCF_009807005.1_ASM980700v1_genomic.fna/markers.fasta
[2024-01-24 13:25:01,942] [INFO] Task started: Blastn
[2024-01-24 13:25:01,942] [INFO] Running command: blastn -query GCF_009807005.1_ASM980700v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg296a817b-6a54-47f5-a95e-f1fe710fe380/dqc_reference/reference_markers.fasta -out GCF_009807005.1_ASM980700v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:25:02,823] [INFO] Task succeeded: Blastn
[2024-01-24 13:25:02,828] [INFO] Selected 15 target genomes.
[2024-01-24 13:25:02,829] [INFO] Target genome list was writen to GCF_009807005.1_ASM980700v1_genomic.fna/target_genomes.txt
[2024-01-24 13:25:02,837] [INFO] Task started: fastANI
[2024-01-24 13:25:02,838] [INFO] Running command: fastANI --query /var/lib/cwl/stg8888d404-1339-4bb8-b193-1793a6cc8cc6/GCF_009807005.1_ASM980700v1_genomic.fna.gz --refList GCF_009807005.1_ASM980700v1_genomic.fna/target_genomes.txt --output GCF_009807005.1_ASM980700v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:25:11,950] [INFO] Task succeeded: fastANI
[2024-01-24 13:25:11,951] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg296a817b-6a54-47f5-a95e-f1fe710fe380/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:25:11,952] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg296a817b-6a54-47f5-a95e-f1fe710fe380/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:25:11,965] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:25:11,965] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:25:11,965] [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
Aurantiacibacter rhizosphaerae	strain=GH3-10	GCA_009807005.1	2691582	2691582	type	True	100.0	1136	1136	95	conclusive
Aurantiacibacter odishensis	strain=KCTC 23981	GCA_003605195.1	1155476	1155476	type	True	81.8817	697	1136	95	below_threshold
Aurantiacibacter zhengii	strain=V18	GCA_003584125.1	2307003	2307003	type	True	81.8111	664	1136	95	below_threshold
Aurantiacibacter gangjinensis	strain=K7-2	GCA_001010925.1	502682	502682	type	True	79.8218	513	1136	95	below_threshold
Aurantiacibacter gangjinensis	strain=CGMCC 1.15024	GCA_001886695.1	502682	502682	type	True	79.8071	506	1136	95	below_threshold
Alteraurantiacibacter aestuarii	strain=JCM 16339	GCA_009827405.1	650004	650004	type	True	79.6841	367	1136	95	below_threshold
Qipengyuania aurantiaca	strain=1NDH13	GCA_019711375.1	2867233	2867233	type	True	79.2818	327	1136	95	below_threshold
Qipengyuania qiaonensis	strain=6D47A	GCA_019711515.1	2867240	2867240	type	True	78.968	276	1136	95	below_threshold
Aurantiacibacter marinus	strain=HWDM-33	GCA_001013305.1	874156	874156	type	True	78.851	430	1136	95	below_threshold
Aurantiacibacter marinus	strain=KCTC 23554	GCA_001021555.1	874156	874156	type	True	78.8464	427	1136	95	below_threshold
Aurantiacibacter sediminis	strain=JGD-13	GCA_016019885.1	2793064	2793064	type	True	78.801	430	1136	95	below_threshold
Croceibacterium atlanticum	strain=26DY36	GCA_001008165.2	1267766	1267766	type	True	78.613	390	1136	95	below_threshold
Croceibacterium atlanticum	strain=DSM 100738	GCA_014199315.1	1267766	1267766	type	True	78.6068	394	1136	95	below_threshold
Qipengyuania huizhouensis	strain=YG19	GCA_019711635.1	2867245	2867245	type	True	78.1817	250	1136	95	below_threshold
Qipengyuania sphaerica	strain=GH29	GCA_019711595.1	2867243	2867243	type	True	78.1794	298	1136	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:25:11,967] [INFO] DFAST Taxonomy check result was written to GCF_009807005.1_ASM980700v1_genomic.fna/tc_result.tsv
[2024-01-24 13:25:11,968] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:25:11,968] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:25:11,968] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg296a817b-6a54-47f5-a95e-f1fe710fe380/dqc_reference/checkm_data
[2024-01-24 13:25:11,970] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:25:12,005] [INFO] Task started: CheckM
[2024-01-24 13:25:12,005] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009807005.1_ASM980700v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009807005.1_ASM980700v1_genomic.fna/checkm_input GCF_009807005.1_ASM980700v1_genomic.fna/checkm_result
[2024-01-24 13:25:47,287] [INFO] Task succeeded: CheckM
[2024-01-24 13:25:47,289] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:25:47,305] [INFO] ===== Completeness check finished =====
[2024-01-24 13:25:47,306] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:25:47,306] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009807005.1_ASM980700v1_genomic.fna/markers.fasta)
[2024-01-24 13:25:47,306] [INFO] Task started: Blastn
[2024-01-24 13:25:47,307] [INFO] Running command: blastn -query GCF_009807005.1_ASM980700v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg296a817b-6a54-47f5-a95e-f1fe710fe380/dqc_reference/reference_markers_gtdb.fasta -out GCF_009807005.1_ASM980700v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:25:48,845] [INFO] Task succeeded: Blastn
[2024-01-24 13:25:48,849] [INFO] Selected 13 target genomes.
[2024-01-24 13:25:48,850] [INFO] Target genome list was writen to GCF_009807005.1_ASM980700v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:25:48,864] [INFO] Task started: fastANI
[2024-01-24 13:25:48,864] [INFO] Running command: fastANI --query /var/lib/cwl/stg8888d404-1339-4bb8-b193-1793a6cc8cc6/GCF_009807005.1_ASM980700v1_genomic.fna.gz --refList GCF_009807005.1_ASM980700v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009807005.1_ASM980700v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:25:57,796] [INFO] Task succeeded: fastANI
[2024-01-24 13:25:57,807] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:25:57,807] [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_009807005.1	s__Alteraurantiacibacter rhizosphaerae	100.0	1136	1136	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003605195.1	s__Alteraurantiacibacter odishensis	81.893	695	1136	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003584125.1	s__Alteraurantiacibacter zhengii	81.789	666	1136	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001886695.1	s__Alteraurantiacibacter gangjinensis	79.8071	506	1136	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_009827405.1	s__Alteraurantiacibacter aestuarii	79.6841	367	1136	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902498745.1	s__Alteraurantiacibacter sp902498745	79.3189	469	1136	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001687545.1	s__Paraurantiacibacter namhicola	79.105	408	1136	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Paraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009827655.1	s__Alteraurantiacibacter buctensis	79.0279	468	1136	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003815535.1	s__Alteraurantiacibacter spongiae	78.9696	437	1136	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001021555.1	s__Alteraurantiacibacter marinus	78.8363	428	1136	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCA_002337385.1	s__Alteraurantiacibacter sp002337385	78.8109	382	1136	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016019885.1	s__Alteraurantiacibacter sp016019885	78.801	430	1136	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005434915.1	s__Alteraurantiacibacter suaedae	78.574	415	1136	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:25:57,809] [INFO] GTDB search result was written to GCF_009807005.1_ASM980700v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:25:57,810] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:25:57,813] [INFO] DFAST_QC result json was written to GCF_009807005.1_ASM980700v1_genomic.fna/dqc_result.json
[2024-01-24 13:25:57,814] [INFO] DFAST_QC completed!
[2024-01-24 13:25:57,814] [INFO] Total running time: 0h1m10s