[2024-01-24 14:39:14,839] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:39:14,842] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:39:14,844] [INFO] DQC Reference Directory: /var/lib/cwl/stg3812ed80-b929-4eb7-93de-5f0a39926ae9/dqc_reference
[2024-01-24 14:39:16,157] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:39:16,158] [INFO] Task started: Prodigal
[2024-01-24 14:39:16,159] [INFO] Running command: gunzip -c /var/lib/cwl/stg6b0c5d73-4669-41b3-aee1-143468cdea8c/GCF_019669985.1_ASM1966998v1_genomic.fna.gz | prodigal -d GCF_019669985.1_ASM1966998v1_genomic.fna/cds.fna -a GCF_019669985.1_ASM1966998v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:39:37,439] [INFO] Task succeeded: Prodigal
[2024-01-24 14:39:37,439] [INFO] Task started: HMMsearch
[2024-01-24 14:39:37,439] [INFO] Running command: hmmsearch --tblout GCF_019669985.1_ASM1966998v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3812ed80-b929-4eb7-93de-5f0a39926ae9/dqc_reference/reference_markers.hmm GCF_019669985.1_ASM1966998v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:39:37,770] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:39:37,772] [INFO] Found 6/6 markers.
[2024-01-24 14:39:37,811] [INFO] Query marker FASTA was written to GCF_019669985.1_ASM1966998v1_genomic.fna/markers.fasta
[2024-01-24 14:39:37,811] [INFO] Task started: Blastn
[2024-01-24 14:39:37,811] [INFO] Running command: blastn -query GCF_019669985.1_ASM1966998v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3812ed80-b929-4eb7-93de-5f0a39926ae9/dqc_reference/reference_markers.fasta -out GCF_019669985.1_ASM1966998v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:39:38,849] [INFO] Task succeeded: Blastn
[2024-01-24 14:39:38,852] [INFO] Selected 19 target genomes.
[2024-01-24 14:39:38,853] [INFO] Target genome list was writen to GCF_019669985.1_ASM1966998v1_genomic.fna/target_genomes.txt
[2024-01-24 14:39:38,862] [INFO] Task started: fastANI
[2024-01-24 14:39:38,862] [INFO] Running command: fastANI --query /var/lib/cwl/stg6b0c5d73-4669-41b3-aee1-143468cdea8c/GCF_019669985.1_ASM1966998v1_genomic.fna.gz --refList GCF_019669985.1_ASM1966998v1_genomic.fna/target_genomes.txt --output GCF_019669985.1_ASM1966998v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:39:54,752] [INFO] Task succeeded: fastANI
[2024-01-24 14:39:54,753] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3812ed80-b929-4eb7-93de-5f0a39926ae9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:39:54,753] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3812ed80-b929-4eb7-93de-5f0a39926ae9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:39:54,772] [INFO] Found 19 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:39:54,773] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:39:54,773] [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
Methylogaea oryzae	strain=E10	GCA_019669985.1	1295382	1295382	type	True	100.0	1338	1339	95	conclusive
Methylogaea oryzae	strain=JCM 16910	GCA_001312345.1	1295382	1295382	type	True	99.4217	773	1339	95	conclusive
Methylococcus geothermalis	strain=IM1	GCA_012769535.1	2681310	2681310	type	True	78.1946	258	1339	95	below_threshold
Methylococcus capsulatus	strain=ATCC 19069	GCA_000424685.1	414	414	type	True	77.8529	221	1339	95	below_threshold
Methylomagnum ishizawai	strain=RS11D-Pr	GCA_019670005.1	1760988	1760988	type	True	77.6036	303	1339	95	below_threshold
Methyloterricola oryzae	strain=73a	GCA_000934725.1	1495050	1495050	type	True	77.5708	279	1339	95	below_threshold
Methylococcus capsulatus	strain=Texas	GCA_000297615.1	414	414	type	True	77.3715	220	1339	95	below_threshold
Thioalkalivibrio sulfidiphilus	strain=HL-EbGR7	GCA_000021985.1	1033854	1033854	type	True	77.2137	180	1339	95	below_threshold
Pseudomonas hydrolytica	strain=DSWY01	GCA_021495345.2	2493633	2493633	type	True	76.9194	178	1339	95	below_threshold
Thiohalobacter thiocyanaticus	strain=Hrh1	GCA_003932505.1	585455	585455	type	True	76.8396	175	1339	95	below_threshold
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	76.8318	186	1339	95	below_threshold
Thiohalocapsa marina	strain=DSM 19078	GCA_008632335.1	424902	424902	type	True	76.7644	148	1339	95	below_threshold
Pseudomonas delhiensis	strain=CCM 7361	GCA_900099945.1	366289	366289	type	True	76.678	228	1339	95	below_threshold
Pseudomonas sagittaria	strain=JCM 18195	GCA_900115715.1	1135990	1135990	type	True	76.6564	189	1339	95	below_threshold
Pseudomonas aeruginosa	strain=DSM 50071	GCA_024169805.1	287	287	type	True	76.6338	195	1339	95	below_threshold
Pseudomonas aeruginosa	strain=JCM 5962	GCA_022496575.1	287	287	type	True	76.4533	186	1339	95	below_threshold
Pseudomonas guryensis	strain=SR9	GCA_014164785.1	2759165	2759165	type	True	76.3801	141	1339	95	below_threshold
Pseudomonas aeruginosa	strain=DSM 50071	GCA_012987025.1	287	287	type	True	76.3692	190	1339	95	below_threshold
Pseudomonas aeruginosa	strain=DSM 50071	GCA_900167195.1	287	287	type	True	76.3227	196	1339	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:39:54,775] [INFO] DFAST Taxonomy check result was written to GCF_019669985.1_ASM1966998v1_genomic.fna/tc_result.tsv
[2024-01-24 14:39:54,775] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:39:54,776] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:39:54,776] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3812ed80-b929-4eb7-93de-5f0a39926ae9/dqc_reference/checkm_data
[2024-01-24 14:39:54,777] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:39:54,821] [INFO] Task started: CheckM
[2024-01-24 14:39:54,822] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019669985.1_ASM1966998v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019669985.1_ASM1966998v1_genomic.fna/checkm_input GCF_019669985.1_ASM1966998v1_genomic.fna/checkm_result
[2024-01-24 14:40:54,699] [INFO] Task succeeded: CheckM
[2024-01-24 14:40:54,701] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.96%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:40:54,722] [INFO] ===== Completeness check finished =====
[2024-01-24 14:40:54,723] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:40:54,723] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019669985.1_ASM1966998v1_genomic.fna/markers.fasta)
[2024-01-24 14:40:54,724] [INFO] Task started: Blastn
[2024-01-24 14:40:54,724] [INFO] Running command: blastn -query GCF_019669985.1_ASM1966998v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3812ed80-b929-4eb7-93de-5f0a39926ae9/dqc_reference/reference_markers_gtdb.fasta -out GCF_019669985.1_ASM1966998v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:40:56,615] [INFO] Task succeeded: Blastn
[2024-01-24 14:40:56,619] [INFO] Selected 19 target genomes.
[2024-01-24 14:40:56,620] [INFO] Target genome list was writen to GCF_019669985.1_ASM1966998v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:40:56,635] [INFO] Task started: fastANI
[2024-01-24 14:40:56,636] [INFO] Running command: fastANI --query /var/lib/cwl/stg6b0c5d73-4669-41b3-aee1-143468cdea8c/GCF_019669985.1_ASM1966998v1_genomic.fna.gz --refList GCF_019669985.1_ASM1966998v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019669985.1_ASM1966998v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:41:10,726] [INFO] Task succeeded: fastANI
[2024-01-24 14:41:10,742] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:41:10,742] [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_001312345.1	s__Methylogaea oryzae	99.4125	774	1339	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylococcaceae;g__Methylogaea	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_004299145.1	s__Methylogaea sp004299145	79.5077	490	1339	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylococcaceae;g__Methylogaea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016925495.1	s__EFPC2 sp016925495	78.5036	278	1339	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylococcaceae;g__EFPC2	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012769535.1	s__Methylococcus sp012769535	78.2158	257	1339	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylococcaceae;g__Methylococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012026715.1	s__VEPB01 sp012026715	77.72	236	1339	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylococcaceae;g__VEPB01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900155475.1	s__Methylomagnum ishizawai	77.7073	296	1339	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylococcaceae;g__Methylomagnum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016106025.1	s__Methylococcus sp016106025	77.5875	196	1339	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylococcaceae;g__Methylococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000934725.1	s__Methyloterricola oryzae	77.5371	281	1339	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylococcaceae;g__Methyloterricola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000021985.1	s__Thioalkalivibrio_A sulfidiphilus	77.2494	179	1339	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Ectothiorhodospiraceae;g__Thioalkalivibrio_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002943415.1	s__Perlucidibaca sp002943415	77.249	92	1339	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Perlucidibaca	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014762505.1	s__SpSt-1174 sp014762505	77.2375	178	1339	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SpSt-1174;f__SpSt-1174;g__SpSt-1174	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015491615.1	s__S140-43 sp015491615	76.9803	113	1339	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__S140-43;f__S140-43;g__S140-43	95.0	99.42	99.32	0.88	0.87	3	-
GCF_008632335.1	s__Thiohalocapsa marina	76.7268	147	1339	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Thiohalocapsa	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900115715.1	s__Pseudomonas_K sagittaria	76.6802	187	1339	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_K	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000378965.1	s__Thioalkalivibrio_A thiocyanodenitrificans	76.6712	109	1339	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Ectothiorhodospiraceae;g__Thioalkalivibrio_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001457615.1	s__Pseudomonas aeruginosa	76.6581	194	1339	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.0	99.12	97.38	0.94	0.84	5623	-
GCA_004168015.1	s__Methylotetracoccus sp004168015	76.6566	101	1339	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylococcaceae;g__Methylotetracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018435665.1	s__M0108 sp018435665	76.3054	142	1339	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__M0108	95.0	99.16	99.16	0.79	0.79	2	-
GCA_009928645.1	s__M0108 sp009928645	76.0632	105	1339	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__M0108	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:41:10,744] [INFO] GTDB search result was written to GCF_019669985.1_ASM1966998v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:41:10,744] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:41:10,749] [INFO] DFAST_QC result json was written to GCF_019669985.1_ASM1966998v1_genomic.fna/dqc_result.json
[2024-01-24 14:41:10,749] [INFO] DFAST_QC completed!
[2024-01-24 14:41:10,749] [INFO] Total running time: 0h1m56s