[2024-01-24 12:44:10,455] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:44:10,465] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:44:10,465] [INFO] DQC Reference Directory: /var/lib/cwl/stgeaa1c03a-c9f1-4c22-9785-d7d83aef099d/dqc_reference
[2024-01-24 12:44:11,837] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:44:11,838] [INFO] Task started: Prodigal
[2024-01-24 12:44:11,839] [INFO] Running command: gunzip -c /var/lib/cwl/stgfd8b9456-b3b4-4ea0-a19e-fb67116ada91/GCF_013839445.1_ASM1383944v1_genomic.fna.gz | prodigal -d GCF_013839445.1_ASM1383944v1_genomic.fna/cds.fna -a GCF_013839445.1_ASM1383944v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:44:24,947] [INFO] Task succeeded: Prodigal
[2024-01-24 12:44:24,947] [INFO] Task started: HMMsearch
[2024-01-24 12:44:24,948] [INFO] Running command: hmmsearch --tblout GCF_013839445.1_ASM1383944v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgeaa1c03a-c9f1-4c22-9785-d7d83aef099d/dqc_reference/reference_markers.hmm GCF_013839445.1_ASM1383944v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:44:25,297] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:44:25,298] [INFO] Found 6/6 markers.
[2024-01-24 12:44:25,342] [INFO] Query marker FASTA was written to GCF_013839445.1_ASM1383944v1_genomic.fna/markers.fasta
[2024-01-24 12:44:25,343] [INFO] Task started: Blastn
[2024-01-24 12:44:25,343] [INFO] Running command: blastn -query GCF_013839445.1_ASM1383944v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgeaa1c03a-c9f1-4c22-9785-d7d83aef099d/dqc_reference/reference_markers.fasta -out GCF_013839445.1_ASM1383944v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:44:26,389] [INFO] Task succeeded: Blastn
[2024-01-24 12:44:26,394] [INFO] Selected 14 target genomes.
[2024-01-24 12:44:26,394] [INFO] Target genome list was writen to GCF_013839445.1_ASM1383944v1_genomic.fna/target_genomes.txt
[2024-01-24 12:44:26,400] [INFO] Task started: fastANI
[2024-01-24 12:44:26,401] [INFO] Running command: fastANI --query /var/lib/cwl/stgfd8b9456-b3b4-4ea0-a19e-fb67116ada91/GCF_013839445.1_ASM1383944v1_genomic.fna.gz --refList GCF_013839445.1_ASM1383944v1_genomic.fna/target_genomes.txt --output GCF_013839445.1_ASM1383944v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:44:41,665] [INFO] Task succeeded: fastANI
[2024-01-24 12:44:41,665] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgeaa1c03a-c9f1-4c22-9785-d7d83aef099d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:44:41,666] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgeaa1c03a-c9f1-4c22-9785-d7d83aef099d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:44:41,679] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:44:41,679] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:44:41,680] [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
Chthonobacter albigriseus	strain=KCTC 42450	GCA_013839445.1	1683161	1683161	type	True	100.0	1535	1538	95	conclusive
Oharaeibacter diazotrophicus	strain=SM30	GCA_011317485.1	1920512	1920512	type	True	81.2997	705	1538	95	below_threshold
Oharaeibacter diazotrophicus	strain=DSM 102969	GCA_004362745.1	1920512	1920512	type	True	81.1145	848	1538	95	below_threshold
Methylobrevis albus	strain=L22	GCA_015904235.1	2793297	2793297	type	True	79.4582	664	1538	95	below_threshold
Methylobrevis pamukkalensis	strain=PK2	GCA_001720135.1	1439726	1439726	type	True	79.3033	570	1538	95	below_threshold
Pleomorphomonas koreensis	strain=DSM 23070	GCA_000425185.1	257440	257440	type	True	79.18	557	1538	95	below_threshold
Pleomorphomonas carboxyditropha	strain=SVCO-16	GCA_002770725.1	2023338	2023338	type	True	79.1431	556	1538	95	below_threshold
Microvirga lenta	strain=SM9	GCA_020532555.1	2881337	2881337	type	True	77.5555	300	1538	95	below_threshold
Jiella sonneratiae	strain=MQZ13P-4	GCA_017353515.1	2816856	2816856	type	True	77.4301	421	1538	95	below_threshold
Methylobacterium oryzihabitans	strain=TER-1	GCA_004004555.2	2499852	2499852	type	True	77.4044	443	1538	95	below_threshold
Xanthobacter dioxanivorans	strain=YN2	GCA_016807805.1	2528964	2528964	type	True	77.3901	367	1538	95	below_threshold
Bradyrhizobium centrolobii	strain=BR 10245	GCA_001641635.1	1505087	1505087	type	True	77.3869	322	1538	95	below_threshold
Methylobacterium gregans	strain=NBRC 103626	GCA_022179245.1	374424	374424	type	True	77.3039	334	1538	95	below_threshold
Xanthobacter oligotrophicus	strain=29k	GCA_008364685.1	2607286	2607286	type	True	77.2041	334	1538	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:44:41,682] [INFO] DFAST Taxonomy check result was written to GCF_013839445.1_ASM1383944v1_genomic.fna/tc_result.tsv
[2024-01-24 12:44:41,682] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:44:41,682] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:44:41,683] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgeaa1c03a-c9f1-4c22-9785-d7d83aef099d/dqc_reference/checkm_data
[2024-01-24 12:44:41,684] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:44:41,734] [INFO] Task started: CheckM
[2024-01-24 12:44:41,734] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013839445.1_ASM1383944v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013839445.1_ASM1383944v1_genomic.fna/checkm_input GCF_013839445.1_ASM1383944v1_genomic.fna/checkm_result
[2024-01-24 12:45:25,914] [INFO] Task succeeded: CheckM
[2024-01-24 12:45:25,915] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:45:25,940] [INFO] ===== Completeness check finished =====
[2024-01-24 12:45:25,940] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:45:25,941] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013839445.1_ASM1383944v1_genomic.fna/markers.fasta)
[2024-01-24 12:45:25,941] [INFO] Task started: Blastn
[2024-01-24 12:45:25,941] [INFO] Running command: blastn -query GCF_013839445.1_ASM1383944v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgeaa1c03a-c9f1-4c22-9785-d7d83aef099d/dqc_reference/reference_markers_gtdb.fasta -out GCF_013839445.1_ASM1383944v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:45:27,995] [INFO] Task succeeded: Blastn
[2024-01-24 12:45:27,999] [INFO] Selected 9 target genomes.
[2024-01-24 12:45:27,999] [INFO] Target genome list was writen to GCF_013839445.1_ASM1383944v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:45:28,008] [INFO] Task started: fastANI
[2024-01-24 12:45:28,009] [INFO] Running command: fastANI --query /var/lib/cwl/stgfd8b9456-b3b4-4ea0-a19e-fb67116ada91/GCF_013839445.1_ASM1383944v1_genomic.fna.gz --refList GCF_013839445.1_ASM1383944v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013839445.1_ASM1383944v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:45:37,728] [INFO] Task succeeded: fastANI
[2024-01-24 12:45:37,743] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:45:37,743] [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_013839445.1	s__Chthonobacter albigriseus	100.0	1535	1538	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Pleomorphomonadaceae;g__Chthonobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_013839525.1	s__Mongoliimonas rhizosphaerae	81.1512	893	1538	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Pleomorphomonadaceae;g__Mongoliimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004362745.1	s__Oharaeibacter diazotrophicus	81.1246	851	1538	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Pleomorphomonadaceae;g__Oharaeibacter	95.0	99.98	99.97	1.00	1.00	3	-
GCF_001927285.1	s__Mongoliimonas terrestris	80.9016	908	1538	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Pleomorphomonadaceae;g__Mongoliimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015904235.1	s__L22 sp015904235	79.438	665	1538	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Pleomorphomonadaceae;g__L22	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001720135.1	s__Methylobrevis pamukkalensis	79.2989	570	1538	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Pleomorphomonadaceae;g__Methylobrevis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000425185.1	s__Pleomorphomonas koreensis	79.1966	555	1538	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Pleomorphomonadaceae;g__Pleomorphomonas	95.0	95.03	95.03	0.88	0.88	2	-
GCA_018262575.1	s__Pleomorphomonas sp018262575	77.9672	381	1538	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Pleomorphomonadaceae;g__Pleomorphomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001713455.1	s__Bosea sp001713455	77.2689	370	1538	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea	95.0	97.00	96.54	0.90	0.82	3	-
--------------------------------------------------------------------------------
[2024-01-24 12:45:37,745] [INFO] GTDB search result was written to GCF_013839445.1_ASM1383944v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:45:37,746] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:45:37,751] [INFO] DFAST_QC result json was written to GCF_013839445.1_ASM1383944v1_genomic.fna/dqc_result.json
[2024-01-24 12:45:37,751] [INFO] DFAST_QC completed!
[2024-01-24 12:45:37,751] [INFO] Total running time: 0h1m27s