[2024-01-24 12:45:18,295] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:45:18,298] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:45:18,298] [INFO] DQC Reference Directory: /var/lib/cwl/stg184e8799-ca82-4716-80b8-166535306775/dqc_reference
[2024-01-24 12:45:19,508] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:45:19,509] [INFO] Task started: Prodigal
[2024-01-24 12:45:19,509] [INFO] Running command: gunzip -c /var/lib/cwl/stg8ccc031f-1de0-4ba0-bbff-79d242a81dc8/GCF_014643715.1_ASM1464371v1_genomic.fna.gz | prodigal -d GCF_014643715.1_ASM1464371v1_genomic.fna/cds.fna -a GCF_014643715.1_ASM1464371v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:45:30,421] [INFO] Task succeeded: Prodigal
[2024-01-24 12:45:30,422] [INFO] Task started: HMMsearch
[2024-01-24 12:45:30,422] [INFO] Running command: hmmsearch --tblout GCF_014643715.1_ASM1464371v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg184e8799-ca82-4716-80b8-166535306775/dqc_reference/reference_markers.hmm GCF_014643715.1_ASM1464371v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:45:30,669] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:45:30,671] [INFO] Found 6/6 markers.
[2024-01-24 12:45:30,711] [INFO] Query marker FASTA was written to GCF_014643715.1_ASM1464371v1_genomic.fna/markers.fasta
[2024-01-24 12:45:30,712] [INFO] Task started: Blastn
[2024-01-24 12:45:30,712] [INFO] Running command: blastn -query GCF_014643715.1_ASM1464371v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg184e8799-ca82-4716-80b8-166535306775/dqc_reference/reference_markers.fasta -out GCF_014643715.1_ASM1464371v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:45:31,430] [INFO] Task succeeded: Blastn
[2024-01-24 12:45:31,435] [INFO] Selected 16 target genomes.
[2024-01-24 12:45:31,435] [INFO] Target genome list was writen to GCF_014643715.1_ASM1464371v1_genomic.fna/target_genomes.txt
[2024-01-24 12:45:31,446] [INFO] Task started: fastANI
[2024-01-24 12:45:31,446] [INFO] Running command: fastANI --query /var/lib/cwl/stg8ccc031f-1de0-4ba0-bbff-79d242a81dc8/GCF_014643715.1_ASM1464371v1_genomic.fna.gz --refList GCF_014643715.1_ASM1464371v1_genomic.fna/target_genomes.txt --output GCF_014643715.1_ASM1464371v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:45:46,152] [INFO] Task succeeded: fastANI
[2024-01-24 12:45:46,152] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg184e8799-ca82-4716-80b8-166535306775/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:45:46,153] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg184e8799-ca82-4716-80b8-166535306775/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:45:46,167] [INFO] Found 15 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:45:46,167] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:45:46,167] [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
Elstera cyanobacteriorum	strain=CGMCC 1.15802	GCA_014643715.1	2022747	2022747	type	True	100.0	1308	1309	95	conclusive
Elstera cyanobacteriorum	strain=TH019	GCA_002251735.1	2022747	2022747	type	True	99.9925	1288	1309	95	conclusive
Elstera litoralis	strain=Dia-1	GCA_000963705.1	552518	552518	type	True	81.4692	606	1309	95	below_threshold
Niveispirillum irakense	strain=DSM 11586	GCA_000429645.1	34011	34011	type	True	76.4836	136	1309	95	below_threshold
Azospirillum argentinense	strain=Az39	GCA_000632475.2	2970906	2970906	type	True	76.1495	214	1309	95	below_threshold
Nitrospirillum iridis	strain=DSM 22198	GCA_014205765.1	765888	765888	type	True	76.1259	130	1309	95	below_threshold
Azospirillum melinis	strain=TMCY 0552	GCA_017876055.1	328839	328839	type	True	76.0946	229	1309	95	below_threshold
Azospirillum melinis	strain=TMCY0552	GCA_013340935.1	328839	328839	type	True	76.0895	229	1309	95	below_threshold
Azospirillum doebereinerae	strain=GSF71	GCA_003989665.1	92933	92933	type	True	76.0448	213	1309	95	below_threshold
Pararhodospirillum photometricum	strain=DSM 122	GCA_000284415.2	1084	1084	type	True	75.9836	68	1309	95	below_threshold
Inquilinus limosus	strain=DSM 16000	GCA_000423185.1	171674	171674	type	True	75.9733	173	1309	95	below_threshold
Azospirillum agricola	strain=CC-HIH038	GCA_017876095.1	1720247	1720247	type	True	75.8617	221	1309	95	below_threshold
Skermanella stibiiresistens	strain=SB22	GCA_000576635.1	913326	913326	type	True	75.8383	148	1309	95	below_threshold
Methylobacterium radiodurans	strain=17Sr1-43	GCA_003173735.1	2202828	2202828	type	True	75.5928	85	1309	95	below_threshold
Roseospira goensis	strain=JA135	GCA_014197795.1	391922	391922	type	True	75.445	112	1309	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:45:46,169] [INFO] DFAST Taxonomy check result was written to GCF_014643715.1_ASM1464371v1_genomic.fna/tc_result.tsv
[2024-01-24 12:45:46,170] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:45:46,170] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:45:46,170] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg184e8799-ca82-4716-80b8-166535306775/dqc_reference/checkm_data
[2024-01-24 12:45:46,172] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:45:46,214] [INFO] Task started: CheckM
[2024-01-24 12:45:46,214] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014643715.1_ASM1464371v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014643715.1_ASM1464371v1_genomic.fna/checkm_input GCF_014643715.1_ASM1464371v1_genomic.fna/checkm_result
[2024-01-24 12:46:21,390] [INFO] Task succeeded: CheckM
[2024-01-24 12:46:21,391] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:46:21,411] [INFO] ===== Completeness check finished =====
[2024-01-24 12:46:21,412] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:46:21,412] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014643715.1_ASM1464371v1_genomic.fna/markers.fasta)
[2024-01-24 12:46:21,413] [INFO] Task started: Blastn
[2024-01-24 12:46:21,413] [INFO] Running command: blastn -query GCF_014643715.1_ASM1464371v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg184e8799-ca82-4716-80b8-166535306775/dqc_reference/reference_markers_gtdb.fasta -out GCF_014643715.1_ASM1464371v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:46:22,586] [INFO] Task succeeded: Blastn
[2024-01-24 12:46:22,590] [INFO] Selected 17 target genomes.
[2024-01-24 12:46:22,590] [INFO] Target genome list was writen to GCF_014643715.1_ASM1464371v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:46:22,617] [INFO] Task started: fastANI
[2024-01-24 12:46:22,618] [INFO] Running command: fastANI --query /var/lib/cwl/stg8ccc031f-1de0-4ba0-bbff-79d242a81dc8/GCF_014643715.1_ASM1464371v1_genomic.fna.gz --refList GCF_014643715.1_ASM1464371v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014643715.1_ASM1464371v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:46:35,640] [INFO] Task succeeded: fastANI
[2024-01-24 12:46:35,657] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:46:35,657] [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_002251735.1	s__Elstera cyanobacteriorum	99.9925	1288	1309	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Elsterales;f__Elsteraceae;g__Elstera	95.0	100.00	100.00	0.99	0.99	2	conclusive
GCF_000963705.1	s__Elstera litoralis	81.4462	609	1309	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Elsterales;f__Elsteraceae;g__Elstera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013298565.1	s__Elstera sp013298565	79.5921	573	1309	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Elsterales;f__Elsteraceae;g__Elstera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000299935.1	s__Oceanibaculum indicum	76.6754	150	1309	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Oceanibaculales;f__Oceanibaculaceae;g__Oceanibaculum	95.0	97.37	97.37	0.93	0.93	2	-
GCF_007828045.1	s__Nitrospirillum amazonense_C	76.1086	141	1309	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Nitrospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007827955.1	s__Nitrospirillum amazonense_B	76.1067	135	1309	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Nitrospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000442515.1	s__Phaeospirillum fulvum_B	76.0925	111	1309	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Phaeospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013340935.1	s__Azospirillum melinis	76.0538	234	1309	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	97.17	95.47	0.91	0.85	4	-
GCF_000284415.1	s__Pararhodospirillum photometricum	75.9836	68	1309	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__Pararhodospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016869645.1	s__SHVW01 sp016869645	75.9147	105	1309	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__SHVW01;f__SHVW01;g__SHVW01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005938675.2	s__Inquilinus sp005938675	75.8817	173	1309	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__DSM-16000;f__Inquilinaceae;g__Inquilinus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903941095.1	s__Magnetospirillum sp903941095	75.853	95	1309	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Magnetospirillum	95.0	99.83	99.83	0.93	0.93	2	-
GCF_000576635.1	s__Skermanella stibiiresistens	75.8292	149	1309	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Skermanella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002694385.1	s__Sneathiella sp002694385	75.5372	58	1309	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sneathiellales;f__Sneathiellaceae;g__Sneathiella	95.0	95.34	95.31	0.92	0.91	3	-
GCF_014197795.1	s__Rhodospira goensis	75.4471	112	1309	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__Rhodospira	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:46:35,659] [INFO] GTDB search result was written to GCF_014643715.1_ASM1464371v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:46:35,659] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:46:35,663] [INFO] DFAST_QC result json was written to GCF_014643715.1_ASM1464371v1_genomic.fna/dqc_result.json
[2024-01-24 12:46:35,663] [INFO] DFAST_QC completed!
[2024-01-24 12:46:35,663] [INFO] Total running time: 0h1m17s