[2024-01-25 18:10:35,870] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:10:35,872] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:10:35,872] [INFO] DQC Reference Directory: /var/lib/cwl/stgddf911b2-3984-4bf8-8c8e-9bd72c4b027a/dqc_reference
[2024-01-25 18:10:37,020] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:10:37,021] [INFO] Task started: Prodigal
[2024-01-25 18:10:37,021] [INFO] Running command: gunzip -c /var/lib/cwl/stgc8e608b3-f60b-4135-b78d-521217e7ced2/GCF_000785705.2_ASM78570v2_genomic.fna.gz | prodigal -d GCF_000785705.2_ASM78570v2_genomic.fna/cds.fna -a GCF_000785705.2_ASM78570v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:10:50,943] [INFO] Task succeeded: Prodigal
[2024-01-25 18:10:50,944] [INFO] Task started: HMMsearch
[2024-01-25 18:10:50,944] [INFO] Running command: hmmsearch --tblout GCF_000785705.2_ASM78570v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgddf911b2-3984-4bf8-8c8e-9bd72c4b027a/dqc_reference/reference_markers.hmm GCF_000785705.2_ASM78570v2_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:10:51,244] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:10:51,245] [INFO] Found 6/6 markers.
[2024-01-25 18:10:51,288] [INFO] Query marker FASTA was written to GCF_000785705.2_ASM78570v2_genomic.fna/markers.fasta
[2024-01-25 18:10:51,288] [INFO] Task started: Blastn
[2024-01-25 18:10:51,289] [INFO] Running command: blastn -query GCF_000785705.2_ASM78570v2_genomic.fna/markers.fasta -db /var/lib/cwl/stgddf911b2-3984-4bf8-8c8e-9bd72c4b027a/dqc_reference/reference_markers.fasta -out GCF_000785705.2_ASM78570v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:10:51,869] [INFO] Task succeeded: Blastn
[2024-01-25 18:10:51,871] [INFO] Selected 15 target genomes.
[2024-01-25 18:10:51,872] [INFO] Target genome list was writen to GCF_000785705.2_ASM78570v2_genomic.fna/target_genomes.txt
[2024-01-25 18:10:51,886] [INFO] Task started: fastANI
[2024-01-25 18:10:51,886] [INFO] Running command: fastANI --query /var/lib/cwl/stgc8e608b3-f60b-4135-b78d-521217e7ced2/GCF_000785705.2_ASM78570v2_genomic.fna.gz --refList GCF_000785705.2_ASM78570v2_genomic.fna/target_genomes.txt --output GCF_000785705.2_ASM78570v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:11:06,307] [INFO] Task succeeded: fastANI
[2024-01-25 18:11:06,308] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgddf911b2-3984-4bf8-8c8e-9bd72c4b027a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:11:06,308] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgddf911b2-3984-4bf8-8c8e-9bd72c4b027a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:11:06,325] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:11:06,325] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:11:06,325] [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
Methylomonas denitrificans	strain=FJG1	GCA_000785705.2	1538553	1538553	type	True	100.0	1718	1724	95	conclusive
Methylomonas albis	strain=EbA	GCA_014850955.1	1854563	1854563	type	True	86.3144	1209	1724	95	below_threshold
Methylomonas koyamae	strain=Fw12E-Y	GCA_019669905.1	702114	702114	suspected-type	True	80.074	760	1724	95	below_threshold
Methylomonas koyamae	strain=JCM 16701	GCA_001312005.1	702114	702114	suspected-type	True	79.9227	690	1724	95	below_threshold
Methylomonas rhizoryzae	strain=GJ1	GCA_008632455.1	2608981	2608981	type	True	78.181	345	1724	95	below_threshold
Methylomarinum vadi	strain=IT-4	GCA_000733935.1	438855	438855	type	True	77.3143	188	1724	95	below_threshold
Methylobacter marinus	strain=A45	GCA_000383855.1	34058	34058	type	True	77.1734	167	1724	95	below_threshold
Methylosarcina fibrata	strain=AML-C10	GCA_000372865.1	105972	105972	type	True	77.1686	176	1724	95	below_threshold
Methylotuvimicrobium alcaliphilum	strain=20Z	GCA_000968535.1	271065	271065	type	True	77.0413	137	1724	95	below_threshold
Methylomicrobium lacus	strain=LW14	GCA_000527095.1	136992	136992	type	True	76.9865	195	1724	95	below_threshold
Methylomagnum ishizawai	strain=RS11D-Pr	GCA_019670005.1	1760988	1760988	type	True	76.2386	88	1724	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:11:06,338] [INFO] DFAST Taxonomy check result was written to GCF_000785705.2_ASM78570v2_genomic.fna/tc_result.tsv
[2024-01-25 18:11:06,341] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:11:06,341] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:11:06,342] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgddf911b2-3984-4bf8-8c8e-9bd72c4b027a/dqc_reference/checkm_data
[2024-01-25 18:11:06,343] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:11:06,392] [INFO] Task started: CheckM
[2024-01-25 18:11:06,393] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000785705.2_ASM78570v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000785705.2_ASM78570v2_genomic.fna/checkm_input GCF_000785705.2_ASM78570v2_genomic.fna/checkm_result
[2024-01-25 18:11:45,570] [INFO] Task succeeded: CheckM
[2024-01-25 18:11:45,571] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.96%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:11:45,588] [INFO] ===== Completeness check finished =====
[2024-01-25 18:11:45,588] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:11:45,589] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000785705.2_ASM78570v2_genomic.fna/markers.fasta)
[2024-01-25 18:11:45,589] [INFO] Task started: Blastn
[2024-01-25 18:11:45,589] [INFO] Running command: blastn -query GCF_000785705.2_ASM78570v2_genomic.fna/markers.fasta -db /var/lib/cwl/stgddf911b2-3984-4bf8-8c8e-9bd72c4b027a/dqc_reference/reference_markers_gtdb.fasta -out GCF_000785705.2_ASM78570v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:11:46,420] [INFO] Task succeeded: Blastn
[2024-01-25 18:11:46,422] [INFO] Selected 6 target genomes.
[2024-01-25 18:11:46,423] [INFO] Target genome list was writen to GCF_000785705.2_ASM78570v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:11:46,431] [INFO] Task started: fastANI
[2024-01-25 18:11:46,431] [INFO] Running command: fastANI --query /var/lib/cwl/stgc8e608b3-f60b-4135-b78d-521217e7ced2/GCF_000785705.2_ASM78570v2_genomic.fna.gz --refList GCF_000785705.2_ASM78570v2_genomic.fna/target_genomes_gtdb.txt --output GCF_000785705.2_ASM78570v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:11:54,769] [INFO] Task succeeded: fastANI
[2024-01-25 18:11:54,775] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:11:54,775] [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
GCA_001644045.1	s__Methylomonas methanica	99.9393	1610	1724	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methylomonas	95.0	99.99	99.99	1.00	0.99	3	conclusive
GCF_001644035.1	s__Methylomonas methanica_A	88.4273	1274	1724	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methylomonas	95.0	95.96	95.96	0.85	0.85	2	-
GCF_000515215.1	s__Methylomonas sp000515215	87.4304	1302	1724	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methylomonas	95.0	95.46	95.46	0.83	0.83	2	-
GCF_016865255.1	s__Methylomonas sp000702925	86.5074	1265	1724	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methylomonas	95.0	97.47	95.82	0.92	0.86	5	-
GCF_903064685.1	s__Methylomonas sp903064685	86.4095	1288	1724	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methylomonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_903064715.1	s__Methylomonas sp903064715	86.2873	1210	1724	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methylomonas	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-25 18:11:54,780] [INFO] GTDB search result was written to GCF_000785705.2_ASM78570v2_genomic.fna/result_gtdb.tsv
[2024-01-25 18:11:54,780] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:11:54,783] [INFO] DFAST_QC result json was written to GCF_000785705.2_ASM78570v2_genomic.fna/dqc_result.json
[2024-01-25 18:11:54,783] [INFO] DFAST_QC completed!
[2024-01-25 18:11:54,783] [INFO] Total running time: 0h1m19s