[2024-01-24 11:21:07,411] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:21:07,413] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:21:07,413] [INFO] DQC Reference Directory: /var/lib/cwl/stg4e5c4250-5412-419b-a76b-4b518ee4bbbd/dqc_reference
[2024-01-24 11:21:11,962] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:21:11,963] [INFO] Task started: Prodigal
[2024-01-24 11:21:11,964] [INFO] Running command: gunzip -c /var/lib/cwl/stgd55152d3-9a3a-4497-b3eb-4c1dd0511acd/GCF_003722355.1_ASM372235v1_genomic.fna.gz | prodigal -d GCF_003722355.1_ASM372235v1_genomic.fna/cds.fna -a GCF_003722355.1_ASM372235v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:21:23,832] [INFO] Task succeeded: Prodigal
[2024-01-24 11:21:23,832] [INFO] Task started: HMMsearch
[2024-01-24 11:21:23,832] [INFO] Running command: hmmsearch --tblout GCF_003722355.1_ASM372235v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4e5c4250-5412-419b-a76b-4b518ee4bbbd/dqc_reference/reference_markers.hmm GCF_003722355.1_ASM372235v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:21:24,085] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:21:24,087] [INFO] Found 6/6 markers.
[2024-01-24 11:21:24,127] [INFO] Query marker FASTA was written to GCF_003722355.1_ASM372235v1_genomic.fna/markers.fasta
[2024-01-24 11:21:24,128] [INFO] Task started: Blastn
[2024-01-24 11:21:24,128] [INFO] Running command: blastn -query GCF_003722355.1_ASM372235v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4e5c4250-5412-419b-a76b-4b518ee4bbbd/dqc_reference/reference_markers.fasta -out GCF_003722355.1_ASM372235v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:21:24,919] [INFO] Task succeeded: Blastn
[2024-01-24 11:21:24,923] [INFO] Selected 14 target genomes.
[2024-01-24 11:21:24,924] [INFO] Target genome list was writen to GCF_003722355.1_ASM372235v1_genomic.fna/target_genomes.txt
[2024-01-24 11:21:24,930] [INFO] Task started: fastANI
[2024-01-24 11:21:24,930] [INFO] Running command: fastANI --query /var/lib/cwl/stgd55152d3-9a3a-4497-b3eb-4c1dd0511acd/GCF_003722355.1_ASM372235v1_genomic.fna.gz --refList GCF_003722355.1_ASM372235v1_genomic.fna/target_genomes.txt --output GCF_003722355.1_ASM372235v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:21:37,305] [INFO] Task succeeded: fastANI
[2024-01-24 11:21:37,306] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4e5c4250-5412-419b-a76b-4b518ee4bbbd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:21:37,306] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4e5c4250-5412-419b-a76b-4b518ee4bbbd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:21:37,318] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:21:37,318] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:21:37,319] [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
Methylocystis hirsuta	strain=CSC1	GCA_003722355.1	369798	369798	type	True	100.0	1400	1402	95	conclusive
Methylocystis silviterrae	strain=FS	GCA_013350005.1	2743612	2743612	type	True	94.1628	1060	1402	95	below_threshold
Methylocystis rosea	strain=SV97	GCA_000372845.1	173366	173366	type	True	92.2195	1020	1402	95	below_threshold
Methylocystis parvus	strain=OBBP	GCA_000283235.1	134	134	type	True	79.6992	613	1402	95	below_threshold
Methylosinus trichosporium	strain=OB3b	GCA_000178815.2	426	426	type	True	78.9231	533	1402	95	below_threshold
Methylosinus sporium	strain=DSM 17706	GCA_003113265.1	428	428	type	True	78.8949	488	1402	95	below_threshold
Methylosinus trichosporium	strain=OB3b	GCA_002752655.1	426	426	type	True	78.8909	537	1402	95	below_threshold
Methylocystis heyeri	strain=H2	GCA_004802635.2	391905	391905	type	True	78.3722	421	1402	95	below_threshold
Methylovirgula ligni	strain=BW863	GCA_004135935.1	569860	569860	type	True	77.7258	223	1402	95	below_threshold
Methylovirgula ligni	strain=BW863	GCA_003387225.1	569860	569860	type	True	77.6897	221	1402	95	below_threshold
Candidatus Rhodoblastus alkanivorans		GCA_022760755.1	2954117	2954117	type	True	77.3437	275	1402	95	below_threshold
Methylobacterium dankookense	strain=DSM 22415	GCA_022179165.1	560405	560405	type	True	76.6967	227	1402	95	below_threshold
Methylobacterium gregans	strain=NBRC 103626	GCA_022179245.1	374424	374424	type	True	76.6749	206	1402	95	below_threshold
Methylobacterium oxalidis	strain=DSM 24028	GCA_022179505.1	944322	944322	type	True	76.6427	225	1402	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:21:37,321] [INFO] DFAST Taxonomy check result was written to GCF_003722355.1_ASM372235v1_genomic.fna/tc_result.tsv
[2024-01-24 11:21:37,321] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:21:37,322] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:21:37,322] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4e5c4250-5412-419b-a76b-4b518ee4bbbd/dqc_reference/checkm_data
[2024-01-24 11:21:37,324] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:21:37,365] [INFO] Task started: CheckM
[2024-01-24 11:21:37,365] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003722355.1_ASM372235v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003722355.1_ASM372235v1_genomic.fna/checkm_input GCF_003722355.1_ASM372235v1_genomic.fna/checkm_result
[2024-01-24 11:22:14,692] [INFO] Task succeeded: CheckM
[2024-01-24 11:22:14,693] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 8.33%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2024-01-24 11:22:14,712] [INFO] ===== Completeness check finished =====
[2024-01-24 11:22:14,712] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:22:14,712] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003722355.1_ASM372235v1_genomic.fna/markers.fasta)
[2024-01-24 11:22:14,713] [INFO] Task started: Blastn
[2024-01-24 11:22:14,713] [INFO] Running command: blastn -query GCF_003722355.1_ASM372235v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4e5c4250-5412-419b-a76b-4b518ee4bbbd/dqc_reference/reference_markers_gtdb.fasta -out GCF_003722355.1_ASM372235v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:22:16,057] [INFO] Task succeeded: Blastn
[2024-01-24 11:22:16,061] [INFO] Selected 9 target genomes.
[2024-01-24 11:22:16,061] [INFO] Target genome list was writen to GCF_003722355.1_ASM372235v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:22:16,074] [INFO] Task started: fastANI
[2024-01-24 11:22:16,074] [INFO] Running command: fastANI --query /var/lib/cwl/stgd55152d3-9a3a-4497-b3eb-4c1dd0511acd/GCF_003722355.1_ASM372235v1_genomic.fna.gz --refList GCF_003722355.1_ASM372235v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003722355.1_ASM372235v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:22:25,511] [INFO] Task succeeded: fastANI
[2024-01-24 11:22:25,525] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:22:25,525] [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_003722355.1	s__Methylocystis hirsuta	100.0	1398	1402	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylocystis	95.0	95.95	95.95	0.95	0.95	2	conclusive
GCF_013350005.1	s__Methylocystis sp013350005	94.1628	1060	1402	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylocystis	95.0	96.16	96.16	0.88	0.88	2	-
GCF_000304315.1	s__Methylocystis sp000304315	92.8027	1050	1402	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylocystis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000372845.1	s__Methylocystis rosea	92.2311	1020	1402	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylocystis	95.0	95.62	95.24	0.85	0.83	5	-
GCF_015709515.1	s__Methylocystis sp015709515	92.1488	1050	1402	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylocystis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015709525.1	s__Methylocystis sp015709525	92.114	1026	1402	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylocystis	95.0	100.00	100.00	1.00	1.00	2	-
GCA_009773555.1	s__Methylocystis sp009773555	92.0997	1003	1402	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylocystis	95.0	99.69	99.47	0.95	0.93	3	-
GCA_016869595.1	s__Methylocystis sp016869595	85.3297	824	1402	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylocystis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016869435.1	s__Methylocystis sp016869435	85.2077	773	1402	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylocystis	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:22:25,526] [INFO] GTDB search result was written to GCF_003722355.1_ASM372235v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:22:25,527] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:22:25,531] [INFO] DFAST_QC result json was written to GCF_003722355.1_ASM372235v1_genomic.fna/dqc_result.json
[2024-01-24 11:22:25,531] [INFO] DFAST_QC completed!
[2024-01-24 11:22:25,531] [INFO] Total running time: 0h1m18s