[2024-01-24 11:20:49,853] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:20:49,855] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:20:49,855] [INFO] DQC Reference Directory: /var/lib/cwl/stg8a3f45df-64f9-4963-9824-2b9a6d78eeba/dqc_reference
[2024-01-24 11:20:51,093] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:20:51,094] [INFO] Task started: Prodigal
[2024-01-24 11:20:51,094] [INFO] Running command: gunzip -c /var/lib/cwl/stga140eb22-fb4b-4f1e-916b-449baafe6ba0/GCF_016125985.1_ASM1612598v1_genomic.fna.gz | prodigal -d GCF_016125985.1_ASM1612598v1_genomic.fna/cds.fna -a GCF_016125985.1_ASM1612598v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:21:02,023] [INFO] Task succeeded: Prodigal
[2024-01-24 11:21:02,024] [INFO] Task started: HMMsearch
[2024-01-24 11:21:02,024] [INFO] Running command: hmmsearch --tblout GCF_016125985.1_ASM1612598v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8a3f45df-64f9-4963-9824-2b9a6d78eeba/dqc_reference/reference_markers.hmm GCF_016125985.1_ASM1612598v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:21:02,277] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:21:02,279] [INFO] Found 6/6 markers.
[2024-01-24 11:21:02,319] [INFO] Query marker FASTA was written to GCF_016125985.1_ASM1612598v1_genomic.fna/markers.fasta
[2024-01-24 11:21:02,319] [INFO] Task started: Blastn
[2024-01-24 11:21:02,319] [INFO] Running command: blastn -query GCF_016125985.1_ASM1612598v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8a3f45df-64f9-4963-9824-2b9a6d78eeba/dqc_reference/reference_markers.fasta -out GCF_016125985.1_ASM1612598v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:21:03,212] [INFO] Task succeeded: Blastn
[2024-01-24 11:21:03,215] [INFO] Selected 17 target genomes.
[2024-01-24 11:21:03,215] [INFO] Target genome list was writen to GCF_016125985.1_ASM1612598v1_genomic.fna/target_genomes.txt
[2024-01-24 11:21:03,238] [INFO] Task started: fastANI
[2024-01-24 11:21:03,238] [INFO] Running command: fastANI --query /var/lib/cwl/stga140eb22-fb4b-4f1e-916b-449baafe6ba0/GCF_016125985.1_ASM1612598v1_genomic.fna.gz --refList GCF_016125985.1_ASM1612598v1_genomic.fna/target_genomes.txt --output GCF_016125985.1_ASM1612598v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:21:16,306] [INFO] Task succeeded: fastANI
[2024-01-24 11:21:16,306] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8a3f45df-64f9-4963-9824-2b9a6d78eeba/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:21:16,307] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8a3f45df-64f9-4963-9824-2b9a6d78eeba/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:21:16,322] [INFO] Found 17 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:21:16,322] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:21:16,322] [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
Hyphomicrobium sulfonivorans	strain=S1	GCA_016125985.1	121290	121290	type	True	100.0	1175	1177	95	conclusive
Hyphomicrobium sulfonivorans	strain=S1	GCA_013306565.1	121290	121290	type	True	99.9982	1174	1177	95	conclusive
Hyphomicrobium album	strain=XQ2	GCA_009708035.1	2665159	2665159	type	True	79.206	526	1177	95	below_threshold
Hyphomicrobium nitrativorans	strain=NL23	GCA_000503895.1	1427356	1427356	type	True	77.8537	252	1177	95	below_threshold
Hyphomicrobium zavarzinii	strain=ZV-622	GCA_000383415.1	48292	48292	type	True	77.8142	269	1177	95	below_threshold
Hyphomicrobium denitrificans	strain=ATCC 51888	GCA_000143145.1	53399	53399	type	True	77.3637	230	1177	95	below_threshold
Hyphomicrobium facile	strain=DSM 1565	GCA_900116175.1	51670	51670	type	True	77.3486	187	1177	95	below_threshold
Pyruvatibacter mobilis	strain=GYP-11	GCA_009910475.1	1712261	1712261	type	True	77.065	86	1177	95	below_threshold
Aestuariivirga litoralis	strain=KCTC 52945	GCA_003234965.1	2650924	2650924	type	True	76.9367	115	1177	95	below_threshold
Roseibium litorale	strain=4C16A	GCA_014842915.1	2803841	2803841	type	True	76.8601	66	1177	95	below_threshold
Rhodoplanes piscinae	strain=DSM 19946	GCA_003258855.1	444923	444923	type	True	76.5896	147	1177	95	below_threshold
Stappia taiwanensis	strain=CCM 7757	GCA_014635285.1	992267	992267	type	True	76.5268	115	1177	95	below_threshold
Aurantimonas endophytica	strain=KCTC 52296	GCA_024105745.1	1522175	1522175	type	True	76.4931	113	1177	95	below_threshold
Reyranella aquatilis	strain=KCTC 52223	GCA_020880995.1	2035356	2035356	type	True	76.4262	105	1177	95	below_threshold
Shinella daejeonensis	strain=JCM 16236	GCA_024281235.1	659017	659017	type	True	76.2286	105	1177	95	below_threshold
Vineibacter terrae	strain=CC-CFT640	GCA_008039615.1	2586908	2586908	type	True	76.1163	132	1177	95	below_threshold
Rhodobacter calidifons	strain=M37P	GCA_011174775.1	2715277	2715277	type	True	75.9563	53	1177	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:21:16,324] [INFO] DFAST Taxonomy check result was written to GCF_016125985.1_ASM1612598v1_genomic.fna/tc_result.tsv
[2024-01-24 11:21:16,324] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:21:16,324] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:21:16,325] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8a3f45df-64f9-4963-9824-2b9a6d78eeba/dqc_reference/checkm_data
[2024-01-24 11:21:16,325] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:21:16,365] [INFO] Task started: CheckM
[2024-01-24 11:21:16,365] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016125985.1_ASM1612598v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016125985.1_ASM1612598v1_genomic.fna/checkm_input GCF_016125985.1_ASM1612598v1_genomic.fna/checkm_result
[2024-01-24 11:21:51,813] [INFO] Task succeeded: CheckM
[2024-01-24 11:21:51,814] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:21:51,837] [INFO] ===== Completeness check finished =====
[2024-01-24 11:21:51,837] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:21:51,838] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016125985.1_ASM1612598v1_genomic.fna/markers.fasta)
[2024-01-24 11:21:51,838] [INFO] Task started: Blastn
[2024-01-24 11:21:51,839] [INFO] Running command: blastn -query GCF_016125985.1_ASM1612598v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8a3f45df-64f9-4963-9824-2b9a6d78eeba/dqc_reference/reference_markers_gtdb.fasta -out GCF_016125985.1_ASM1612598v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:21:53,538] [INFO] Task succeeded: Blastn
[2024-01-24 11:21:53,543] [INFO] Selected 13 target genomes.
[2024-01-24 11:21:53,543] [INFO] Target genome list was writen to GCF_016125985.1_ASM1612598v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:21:53,570] [INFO] Task started: fastANI
[2024-01-24 11:21:53,570] [INFO] Running command: fastANI --query /var/lib/cwl/stga140eb22-fb4b-4f1e-916b-449baafe6ba0/GCF_016125985.1_ASM1612598v1_genomic.fna.gz --refList GCF_016125985.1_ASM1612598v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016125985.1_ASM1612598v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:22:04,376] [INFO] Task succeeded: fastANI
[2024-01-24 11:22:04,398] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:22:04,398] [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_013306565.1	s__Hyphomicrobium_A sulfonivorans	99.9982	1173	1177	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Hyphomicrobiaceae;g__Hyphomicrobium_A	95.0	98.55	97.10	0.95	0.91	3	conclusive
GCF_009708035.1	s__Hyphomicrobium_A sp009708035	79.206	526	1177	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Hyphomicrobiaceae;g__Hyphomicrobium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009026145.1	s__Hyphomicrobium_A sp009026145	79.1513	516	1177	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Hyphomicrobiaceae;g__Hyphomicrobium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900117445.1	s__Hyphomicrobium_A sp900117445	79.0931	509	1177	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Hyphomicrobiaceae;g__Hyphomicrobium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000383415.1	s__Hyphomicrobium zavarzinii	77.7897	271	1177	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Hyphomicrobiaceae;g__Hyphomicrobium	95.0	98.69	98.69	0.95	0.95	2	-
GCA_902826555.1	s__Hyphomicrobium sp902826555	77.7486	223	1177	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Hyphomicrobiaceae;g__Hyphomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000253295.1	s__Hyphomicrobium sp000253295	77.4548	194	1177	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Hyphomicrobiaceae;g__Hyphomicrobium	95.0	99.46	99.46	0.96	0.96	2	-
GCA_017304275.1	s__Hyphomicrobium sp017304275	77.4288	180	1177	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Hyphomicrobiaceae;g__Hyphomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900116175.1	s__Hyphomicrobium facile	77.371	186	1177	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Hyphomicrobiaceae;g__Hyphomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003963125.1	s__AWTP1-13 sp003963125	77.3109	197	1177	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Hyphomicrobiaceae;g__AWTP1-13	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009720755.1	s__Rhodoplanes serenus	76.5235	166	1177	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Rhodoplanes	95.0	97.72	97.48	0.91	0.88	4	-
GCA_003242645.1	s__ZC4RG25 sp003242645	76.4514	115	1177	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Hyphomicrobiaceae;g__ZC4RG25	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:22:04,400] [INFO] GTDB search result was written to GCF_016125985.1_ASM1612598v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:22:04,401] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:22:04,404] [INFO] DFAST_QC result json was written to GCF_016125985.1_ASM1612598v1_genomic.fna/dqc_result.json
[2024-01-24 11:22:04,405] [INFO] DFAST_QC completed!
[2024-01-24 11:22:04,405] [INFO] Total running time: 0h1m15s