[2024-01-24 12:30:33,483] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:30:33,484] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:30:33,485] [INFO] DQC Reference Directory: /var/lib/cwl/stg33466344-11fe-47b2-8e63-36e6b12468e0/dqc_reference
[2024-01-24 12:30:34,734] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:30:34,735] [INFO] Task started: Prodigal
[2024-01-24 12:30:34,735] [INFO] Running command: gunzip -c /var/lib/cwl/stgee68f07e-7b37-425b-a0f7-0087681cb8ad/GCF_000427445.1_ASM42744v1_genomic.fna.gz | prodigal -d GCF_000427445.1_ASM42744v1_genomic.fna/cds.fna -a GCF_000427445.1_ASM42744v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:30:46,652] [INFO] Task succeeded: Prodigal
[2024-01-24 12:30:46,653] [INFO] Task started: HMMsearch
[2024-01-24 12:30:46,653] [INFO] Running command: hmmsearch --tblout GCF_000427445.1_ASM42744v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg33466344-11fe-47b2-8e63-36e6b12468e0/dqc_reference/reference_markers.hmm GCF_000427445.1_ASM42744v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:30:46,973] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:30:46,975] [INFO] Found 6/6 markers.
[2024-01-24 12:30:47,009] [INFO] Query marker FASTA was written to GCF_000427445.1_ASM42744v1_genomic.fna/markers.fasta
[2024-01-24 12:30:47,010] [INFO] Task started: Blastn
[2024-01-24 12:30:47,010] [INFO] Running command: blastn -query GCF_000427445.1_ASM42744v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg33466344-11fe-47b2-8e63-36e6b12468e0/dqc_reference/reference_markers.fasta -out GCF_000427445.1_ASM42744v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:30:47,962] [INFO] Task succeeded: Blastn
[2024-01-24 12:30:47,966] [INFO] Selected 21 target genomes.
[2024-01-24 12:30:47,966] [INFO] Target genome list was writen to GCF_000427445.1_ASM42744v1_genomic.fna/target_genomes.txt
[2024-01-24 12:30:47,973] [INFO] Task started: fastANI
[2024-01-24 12:30:47,974] [INFO] Running command: fastANI --query /var/lib/cwl/stgee68f07e-7b37-425b-a0f7-0087681cb8ad/GCF_000427445.1_ASM42744v1_genomic.fna.gz --refList GCF_000427445.1_ASM42744v1_genomic.fna/target_genomes.txt --output GCF_000427445.1_ASM42744v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:31:06,974] [INFO] Task succeeded: fastANI
[2024-01-24 12:31:06,975] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg33466344-11fe-47b2-8e63-36e6b12468e0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:31:06,975] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg33466344-11fe-47b2-8e63-36e6b12468e0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:31:06,991] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:31:06,991] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:31:06,991] [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
Methylocapsa acidiphila	strain=B2	GCA_000427445.1	133552	133552	type	True	100.0	1367	1367	95	conclusive
Methylocapsa aurea	strain=KYG	GCA_000746085.1	663610	663610	type	True	79.4688	597	1367	95	below_threshold
Methylocella silvestris	strain=BL2	GCA_000021745.1	199596	199596	type	True	78.4094	433	1367	95	below_threshold
Methylocapsa palsarum	strain=NE2	GCA_900114285.1	1612308	1612308	type	True	78.1854	422	1367	95	below_threshold
Methyloferula stellata	strain=AR4T	GCA_000385335.1	876270	876270	type	True	78.1219	312	1367	95	below_threshold
Candidatus Rhodoblastus alkanivorans		GCA_022760755.1	2954117	2954117	type	True	77.84	266	1367	95	below_threshold
Methylosinus trichosporium	strain=OB3b	GCA_002752655.1	426	426	type	True	77.7254	339	1367	95	below_threshold
Methylosinus trichosporium	strain=OB3b	GCA_000178815.2	426	426	type	True	77.7123	334	1367	95	below_threshold
Beijerinckia indica subsp. indica	strain=ATCC 9039	GCA_000019845.1	31994	533	type	True	77.548	243	1367	95	below_threshold
Beijerinckia mobilis	strain=UQM 1969	GCA_000745425.1	231434	231434	type	True	77.4814	218	1367	95	below_threshold
Methylocystis hirsuta	strain=CSC1	GCA_003722355.1	369798	369798	type	True	77.1761	224	1367	95	below_threshold
Methylocystis silviterrae	strain=FS	GCA_013350005.1	2743612	2743612	type	True	77.1493	230	1367	95	below_threshold
Methylocystis rosea	strain=SV97	GCA_000372845.1	173366	173366	type	True	77.117	233	1367	95	below_threshold
Afipia felis	strain=ATCC 53690	GCA_000314735.2	1035	1035	type	True	76.5756	117	1367	95	below_threshold
Bradyrhizobium acaciae	strain=10BB	GCA_020889785.1	2683706	2683706	type	True	76.5413	182	1367	95	below_threshold
Microvirga lenta	strain=SM9	GCA_020532555.1	2881337	2881337	type	True	76.5243	150	1367	95	below_threshold
Variibacter gotjawalensis	strain=DSM 29671	GCA_004216635.1	1333996	1333996	type	True	76.4657	116	1367	95	below_threshold
Variibacter gotjawalensis	strain=CECT 8514	GCA_011761465.1	1333996	1333996	type	True	76.4657	116	1367	95	below_threshold
Variibacter gotjawalensis	strain=GJW-30	GCA_002355335.1	1333996	1333996	type	True	76.4493	117	1367	95	below_threshold
Bradyrhizobium oropedii	strain=Pear76	GCA_020889685.1	1571201	1571201	type	True	76.4327	187	1367	95	below_threshold
Rhodoplanes roseus	strain=DSM 5909	GCA_003258865.1	29409	29409	type	True	76.327	182	1367	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:31:06,993] [INFO] DFAST Taxonomy check result was written to GCF_000427445.1_ASM42744v1_genomic.fna/tc_result.tsv
[2024-01-24 12:31:06,994] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:31:06,994] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:31:06,995] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg33466344-11fe-47b2-8e63-36e6b12468e0/dqc_reference/checkm_data
[2024-01-24 12:31:06,996] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:31:07,038] [INFO] Task started: CheckM
[2024-01-24 12:31:07,038] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000427445.1_ASM42744v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000427445.1_ASM42744v1_genomic.fna/checkm_input GCF_000427445.1_ASM42744v1_genomic.fna/checkm_result
[2024-01-24 12:31:44,643] [INFO] Task succeeded: CheckM
[2024-01-24 12:31:44,645] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:31:44,663] [INFO] ===== Completeness check finished =====
[2024-01-24 12:31:44,664] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:31:44,664] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000427445.1_ASM42744v1_genomic.fna/markers.fasta)
[2024-01-24 12:31:44,665] [INFO] Task started: Blastn
[2024-01-24 12:31:44,665] [INFO] Running command: blastn -query GCF_000427445.1_ASM42744v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg33466344-11fe-47b2-8e63-36e6b12468e0/dqc_reference/reference_markers_gtdb.fasta -out GCF_000427445.1_ASM42744v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:31:46,338] [INFO] Task succeeded: Blastn
[2024-01-24 12:31:46,343] [INFO] Selected 16 target genomes.
[2024-01-24 12:31:46,343] [INFO] Target genome list was writen to GCF_000427445.1_ASM42744v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:31:46,373] [INFO] Task started: fastANI
[2024-01-24 12:31:46,374] [INFO] Running command: fastANI --query /var/lib/cwl/stgee68f07e-7b37-425b-a0f7-0087681cb8ad/GCF_000427445.1_ASM42744v1_genomic.fna.gz --refList GCF_000427445.1_ASM42744v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000427445.1_ASM42744v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:31:59,122] [INFO] Task succeeded: fastANI
[2024-01-24 12:31:59,142] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:31:59,143] [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_000427445.1	s__Methylocella acidiphila	100.0	1366	1367	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylocella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000746085.1	s__Methylocella aurea	79.466	597	1367	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylocella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_901905185.1	s__Methylocella tundrae	78.621	423	1367	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylocella	95.0	97.31	97.31	0.88	0.88	2	-
GCF_000021745.1	s__Methylocella silvestris	78.4772	430	1367	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylocella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002891535.1	s__Methylocella silvestris_A	78.3017	430	1367	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylocella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114285.1	s__Methylocella palsarum	78.1854	422	1367	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylocella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004564215.1	s__Methylocella sp004564215	77.6396	308	1367	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylocella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_006514895.1	s__Methylocella sp006514895	77.5411	282	1367	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylocella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000019845.1	s__Beijerinckia indica	77.5063	242	1367	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Beijerinckia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002890675.1	s__Methylocella sp002890675	77.2955	274	1367	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylocella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000304315.1	s__Methylocystis sp000304315	77.1703	250	1367	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylocystis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015655535.1	s__Methyloferula sp015655535	77.0607	233	1367	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methyloferula	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016869435.1	s__Methylocystis sp016869435	77.0174	201	1367	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylocystis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002355335.1	s__Variibacter gotjawalensis	76.4491	117	1367	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Variibacter	95.0	100.00	100.00	1.00	1.00	3	-
GCA_009772935.1	s__Reyranella sp009772935	75.868	115	1367	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018971215.1	s__REEB95 sp018971215	75.6694	86	1367	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__ATCC43930;f__Stellaceae;g__REEB95	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:31:59,145] [INFO] GTDB search result was written to GCF_000427445.1_ASM42744v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:31:59,146] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:31:59,151] [INFO] DFAST_QC result json was written to GCF_000427445.1_ASM42744v1_genomic.fna/dqc_result.json
[2024-01-24 12:31:59,151] [INFO] DFAST_QC completed!
[2024-01-24 12:31:59,151] [INFO] Total running time: 0h1m26s