[2023-06-30 22:23:02,132] [INFO] DFAST_QC pipeline started.
[2023-06-30 22:23:02,141] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 22:23:02,142] [INFO] DQC Reference Directory: /var/lib/cwl/stg1c0de1eb-fbc4-4134-bb39-1fd1f9d830f8/dqc_reference
[2023-06-30 22:23:03,785] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 22:23:03,786] [INFO] Task started: Prodigal
[2023-06-30 22:23:03,786] [INFO] Running command: gunzip -c /var/lib/cwl/stg65f02ff3-14f8-4667-bf37-ad121f8b5e60/GCA_024511045.1_ASM2451104v1_genomic.fna.gz | prodigal -d GCA_024511045.1_ASM2451104v1_genomic.fna/cds.fna -a GCA_024511045.1_ASM2451104v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 22:23:10,394] [INFO] Task succeeded: Prodigal
[2023-06-30 22:23:10,395] [INFO] Task started: HMMsearch
[2023-06-30 22:23:10,395] [INFO] Running command: hmmsearch --tblout GCA_024511045.1_ASM2451104v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1c0de1eb-fbc4-4134-bb39-1fd1f9d830f8/dqc_reference/reference_markers.hmm GCA_024511045.1_ASM2451104v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 22:23:10,662] [INFO] Task succeeded: HMMsearch
[2023-06-30 22:23:10,664] [INFO] Found 6/6 markers.
[2023-06-30 22:23:10,689] [INFO] Query marker FASTA was written to GCA_024511045.1_ASM2451104v1_genomic.fna/markers.fasta
[2023-06-30 22:23:10,689] [INFO] Task started: Blastn
[2023-06-30 22:23:10,690] [INFO] Running command: blastn -query GCA_024511045.1_ASM2451104v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1c0de1eb-fbc4-4134-bb39-1fd1f9d830f8/dqc_reference/reference_markers.fasta -out GCA_024511045.1_ASM2451104v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 22:23:11,430] [INFO] Task succeeded: Blastn
[2023-06-30 22:23:11,434] [INFO] Selected 30 target genomes.
[2023-06-30 22:23:11,435] [INFO] Target genome list was writen to GCA_024511045.1_ASM2451104v1_genomic.fna/target_genomes.txt
[2023-06-30 22:23:11,439] [INFO] Task started: fastANI
[2023-06-30 22:23:11,439] [INFO] Running command: fastANI --query /var/lib/cwl/stg65f02ff3-14f8-4667-bf37-ad121f8b5e60/GCA_024511045.1_ASM2451104v1_genomic.fna.gz --refList GCA_024511045.1_ASM2451104v1_genomic.fna/target_genomes.txt --output GCA_024511045.1_ASM2451104v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 22:23:29,950] [INFO] Task succeeded: fastANI
[2023-06-30 22:23:29,951] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1c0de1eb-fbc4-4134-bb39-1fd1f9d830f8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 22:23:29,951] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1c0de1eb-fbc4-4134-bb39-1fd1f9d830f8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 22:23:29,966] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 22:23:29,966] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 22:23:29,966] [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
Methyloterricola oryzae	strain=73a	GCA_000934725.1	1495050	1495050	type	True	76.8209	67	642	95	below_threshold
Methylogaea oryzae	strain=E10	GCA_019669985.1	1295382	1295382	type	True	76.8154	77	642	95	below_threshold
Methylogaea oryzae	strain=JCM 16910	GCA_001312345.1	1295382	1295382	type	True	76.7121	59	642	95	below_threshold
Methylobacter marinus	strain=A45	GCA_000383855.1	34058	34058	type	True	76.5829	100	642	95	below_threshold
Methylosarcina fibrata	strain=AML-C10	GCA_000372865.1	105972	105972	type	True	76.3685	95	642	95	below_threshold
Sulfurivermis fontis	strain=JG42	GCA_004001245.1	1972068	1972068	type	True	76.3622	56	642	95	below_threshold
Methylomicrobium lacus	strain=LW14	GCA_000527095.1	136992	136992	type	True	76.3074	98	642	95	below_threshold
Methylococcus geothermalis	strain=IM1	GCA_012769535.1	2681310	2681310	type	True	76.2971	80	642	95	below_threshold
Methylococcus capsulatus	strain=Texas	GCA_000297615.1	414	414	type	True	76.1944	65	642	95	below_threshold
Methylococcus capsulatus	strain=ATCC 19069	GCA_000424685.1	414	414	type	True	76.1842	66	642	95	below_threshold
Thioalbus denitrificans	strain=DSM 26407	GCA_003337735.1	547122	547122	type	True	76.1265	58	642	95	below_threshold
Thiohalobacter thiocyanaticus	strain=Hrh1	GCA_003932505.1	585455	585455	type	True	76.0885	57	642	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 22:23:29,969] [INFO] DFAST Taxonomy check result was written to GCA_024511045.1_ASM2451104v1_genomic.fna/tc_result.tsv
[2023-06-30 22:23:29,969] [INFO] ===== Taxonomy check completed =====
[2023-06-30 22:23:29,969] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 22:23:29,970] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1c0de1eb-fbc4-4134-bb39-1fd1f9d830f8/dqc_reference/checkm_data
[2023-06-30 22:23:29,971] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 22:23:30,005] [INFO] Task started: CheckM
[2023-06-30 22:23:30,006] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_024511045.1_ASM2451104v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_024511045.1_ASM2451104v1_genomic.fna/checkm_input GCA_024511045.1_ASM2451104v1_genomic.fna/checkm_result
[2023-06-30 22:23:55,569] [INFO] Task succeeded: CheckM
[2023-06-30 22:23:55,570] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 22:23:55,592] [INFO] ===== Completeness check finished =====
[2023-06-30 22:23:55,593] [INFO] ===== Start GTDB Search =====
[2023-06-30 22:23:55,593] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_024511045.1_ASM2451104v1_genomic.fna/markers.fasta)
[2023-06-30 22:23:55,594] [INFO] Task started: Blastn
[2023-06-30 22:23:55,594] [INFO] Running command: blastn -query GCA_024511045.1_ASM2451104v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1c0de1eb-fbc4-4134-bb39-1fd1f9d830f8/dqc_reference/reference_markers_gtdb.fasta -out GCA_024511045.1_ASM2451104v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 22:23:56,878] [INFO] Task succeeded: Blastn
[2023-06-30 22:23:56,884] [INFO] Selected 34 target genomes.
[2023-06-30 22:23:56,884] [INFO] Target genome list was writen to GCA_024511045.1_ASM2451104v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 22:23:56,901] [INFO] Task started: fastANI
[2023-06-30 22:23:56,902] [INFO] Running command: fastANI --query /var/lib/cwl/stg65f02ff3-14f8-4667-bf37-ad121f8b5e60/GCA_024511045.1_ASM2451104v1_genomic.fna.gz --refList GCA_024511045.1_ASM2451104v1_genomic.fna/target_genomes_gtdb.txt --output GCA_024511045.1_ASM2451104v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 22:24:17,876] [INFO] Task succeeded: fastANI
[2023-06-30 22:24:17,903] [INFO] Found 18 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-30 22:24:17,903] [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_000934725.1	s__Methyloterricola oryzae	76.8209	67	642	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylococcaceae;g__Methyloterricola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000745375.1	s__Methylobacter whittenburyi	76.7545	95	642	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methylobacter	95.0	98.49	98.36	0.89	0.88	3	-
GCF_001312345.1	s__Methylogaea oryzae	76.7121	59	642	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylococcaceae;g__Methylogaea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011321775.1	s__Thiogranum sp011321775	76.6257	59	642	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__DSM-19610;f__DSM-19610;g__Thiogranum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011051715.1	s__HyVt-443 sp011051715	76.5554	60	642	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Sedimenticolaceae;g__HyVt-443	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002843155.1	s__PGZD01 sp002843155	76.5446	64	642	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__PGZD01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002929135.1	s__Methylomonas sp002929135	76.4517	76	642	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methylomonas	95.0	99.96	99.88	0.95	0.87	5	-
GCF_000372865.1	s__Methylosarcina fibrata	76.3523	96	642	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methylosarcina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000527095.1	s__Methylomicrobium lacus	76.3074	98	642	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methylomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006483455.1	s__Methylomonas koyamae_B	76.2669	59	642	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methylomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016745425.1	s__Methylomicrobium sp016745425	76.2067	98	642	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methylomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000424685.1	s__Methylococcus capsulatus	76.1842	66	642	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylococcaceae;g__Methylococcus	95.0	99.39	98.77	0.98	0.95	3	-
GCF_000733855.1	s__Methylomicrobium agile	76.1406	98	642	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methylomicrobium	95.0	99.08	99.08	0.92	0.92	2	-
GCF_001644025.1	s__Methylomonas koyamae_A	76.0702	51	642	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methylomonas	95.0	97.40	97.36	0.85	0.85	3	-
GCF_015476545.1	s__Methylobacter sp015476545	75.9925	85	642	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methylobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000214665.1	s__Methylomonas methanica_B	75.7744	62	642	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methylomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006788925.1	s__Methylotuvimicrobium kenyense	75.7653	69	642	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methylotuvimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018335995.1	s__Methylomonas sp018335995	75.6695	57	642	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methylomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 22:24:17,905] [INFO] GTDB search result was written to GCA_024511045.1_ASM2451104v1_genomic.fna/result_gtdb.tsv
[2023-06-30 22:24:17,906] [INFO] ===== GTDB Search completed =====
[2023-06-30 22:24:17,910] [INFO] DFAST_QC result json was written to GCA_024511045.1_ASM2451104v1_genomic.fna/dqc_result.json
[2023-06-30 22:24:17,910] [INFO] DFAST_QC completed!
[2023-06-30 22:24:17,910] [INFO] Total running time: 0h1m16s