[2024-01-24 11:35:34,604] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:35:34,606] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:35:34,607] [INFO] DQC Reference Directory: /var/lib/cwl/stg0accfe34-d629-40df-925f-1897989fcf05/dqc_reference
[2024-01-24 11:35:35,852] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:35:35,853] [INFO] Task started: Prodigal
[2024-01-24 11:35:35,853] [INFO] Running command: gunzip -c /var/lib/cwl/stg9ebb70ea-1f57-42fa-a498-05cc400ce0c9/GCF_006175985.1_ASM617598v1_genomic.fna.gz | prodigal -d GCF_006175985.1_ASM617598v1_genomic.fna/cds.fna -a GCF_006175985.1_ASM617598v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:35:49,857] [INFO] Task succeeded: Prodigal
[2024-01-24 11:35:49,858] [INFO] Task started: HMMsearch
[2024-01-24 11:35:49,858] [INFO] Running command: hmmsearch --tblout GCF_006175985.1_ASM617598v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0accfe34-d629-40df-925f-1897989fcf05/dqc_reference/reference_markers.hmm GCF_006175985.1_ASM617598v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:35:50,125] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:35:50,126] [INFO] Found 6/6 markers.
[2024-01-24 11:35:50,166] [INFO] Query marker FASTA was written to GCF_006175985.1_ASM617598v1_genomic.fna/markers.fasta
[2024-01-24 11:35:50,167] [INFO] Task started: Blastn
[2024-01-24 11:35:50,167] [INFO] Running command: blastn -query GCF_006175985.1_ASM617598v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0accfe34-d629-40df-925f-1897989fcf05/dqc_reference/reference_markers.fasta -out GCF_006175985.1_ASM617598v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:35:51,044] [INFO] Task succeeded: Blastn
[2024-01-24 11:35:51,048] [INFO] Selected 23 target genomes.
[2024-01-24 11:35:51,049] [INFO] Target genome list was writen to GCF_006175985.1_ASM617598v1_genomic.fna/target_genomes.txt
[2024-01-24 11:35:51,059] [INFO] Task started: fastANI
[2024-01-24 11:35:51,059] [INFO] Running command: fastANI --query /var/lib/cwl/stg9ebb70ea-1f57-42fa-a498-05cc400ce0c9/GCF_006175985.1_ASM617598v1_genomic.fna.gz --refList GCF_006175985.1_ASM617598v1_genomic.fna/target_genomes.txt --output GCF_006175985.1_ASM617598v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:36:06,442] [INFO] Task succeeded: fastANI
[2024-01-24 11:36:06,443] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0accfe34-d629-40df-925f-1897989fcf05/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:36:06,443] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0accfe34-d629-40df-925f-1897989fcf05/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:36:06,465] [INFO] Found 23 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:36:06,465] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:36:06,466] [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
Methylotetracoccus oryzae	strain=C50C1	GCA_006175985.1	1919059	1919059	type	True	100.0	1592	1592	95	conclusive
Methylococcus geothermalis	strain=IM1	GCA_012769535.1	2681310	2681310	type	True	77.6025	215	1592	95	below_threshold
Methylococcus capsulatus	strain=ATCC 19069	GCA_000424685.1	414	414	type	True	77.3087	192	1592	95	below_threshold
Methyloterricola oryzae	strain=73a	GCA_000934725.1	1495050	1495050	type	True	77.168	177	1592	95	below_threshold
Methylococcus capsulatus	strain=Texas	GCA_000297615.1	414	414	type	True	77.0433	189	1592	95	below_threshold
Methylomagnum ishizawai	strain=RS11D-Pr	GCA_019670005.1	1760988	1760988	type	True	76.7813	171	1592	95	below_threshold
Methylomarinum vadi	strain=IT-4	GCA_000733935.1	438855	438855	type	True	76.3838	53	1592	95	below_threshold
Dyella telluris	strain=G9	GCA_014297575.1	2763498	2763498	type	True	76.2646	63	1592	95	below_threshold
Thiohalobacter thiocyanaticus	strain=Hrh1	GCA_003932505.1	585455	585455	type	True	76.2467	74	1592	95	below_threshold
Thiocapsa marina	strain=5811	GCA_000223985.2	244573	244573	type	True	76.2446	99	1592	95	below_threshold
Lysobacter luteus	strain=CECT 30171	GCA_907164845.1	2822368	2822368	type	True	76.1095	76	1592	95	below_threshold
Methylonatrum kenyense	strain=AMT 1	GCA_023195885.1	455253	455253	type	True	76.1029	68	1592	95	below_threshold
Thiocystis violacea	strain=DSM 207	GCA_016583575.1	13725	13725	type	True	76.1013	98	1592	95	below_threshold
Lysobacter solisilvae	strain=R19	GCA_016613535.2	2763317	2763317	type	True	76.0676	78	1592	95	below_threshold
Arenimonas soli	strain=CGMCC 1.15905	GCA_014643775.1	2269504	2269504	type	True	76.036	60	1592	95	below_threshold
Methylomonas koyamae	strain=Fw12E-Y	GCA_019669905.1	702114	702114	suspected-type	True	76.0274	76	1592	95	below_threshold
Halomonas aestuarii	strain=Hb3	GCA_001886615.1	1897729	1897729	type	True	76.0079	65	1592	95	below_threshold
Chitiniphilus shinanonensis	strain=DSM 23277	GCA_000374805.1	553088	553088	type	True	75.9873	72	1592	95	below_threshold
Halomonas denitrificans	strain=DSM 18045	GCA_003056305.1	370769	370769	type	True	75.8368	72	1592	95	below_threshold
Methylomonas koyamae	strain=JCM 16701	GCA_001312005.1	702114	702114	suspected-type	True	75.7999	73	1592	95	below_threshold
Jeongeupia naejangsanensis	strain=DSM 24253	GCA_016865585.1	613195	613195	type	True	75.7496	54	1592	95	below_threshold
Pseudomonas sputi	strain=BML-PP014	GCA_021603585.1	2892325	2892325	type	True	75.2511	52	1592	95	below_threshold
Pseudomonas pharyngis	strain=BML-PP036	GCA_021602345.1	2892333	2892333	type	True	74.9217	60	1592	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:36:06,467] [INFO] DFAST Taxonomy check result was written to GCF_006175985.1_ASM617598v1_genomic.fna/tc_result.tsv
[2024-01-24 11:36:06,468] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:36:06,468] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:36:06,468] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0accfe34-d629-40df-925f-1897989fcf05/dqc_reference/checkm_data
[2024-01-24 11:36:06,469] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:36:06,515] [INFO] Task started: CheckM
[2024-01-24 11:36:06,515] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_006175985.1_ASM617598v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_006175985.1_ASM617598v1_genomic.fna/checkm_input GCF_006175985.1_ASM617598v1_genomic.fna/checkm_result
[2024-01-24 11:36:48,707] [INFO] Task succeeded: CheckM
[2024-01-24 11:36:48,708] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:36:48,726] [INFO] ===== Completeness check finished =====
[2024-01-24 11:36:48,726] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:36:48,726] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_006175985.1_ASM617598v1_genomic.fna/markers.fasta)
[2024-01-24 11:36:48,727] [INFO] Task started: Blastn
[2024-01-24 11:36:48,727] [INFO] Running command: blastn -query GCF_006175985.1_ASM617598v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0accfe34-d629-40df-925f-1897989fcf05/dqc_reference/reference_markers_gtdb.fasta -out GCF_006175985.1_ASM617598v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:36:50,397] [INFO] Task succeeded: Blastn
[2024-01-24 11:36:50,401] [INFO] Selected 20 target genomes.
[2024-01-24 11:36:50,402] [INFO] Target genome list was writen to GCF_006175985.1_ASM617598v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:36:50,462] [INFO] Task started: fastANI
[2024-01-24 11:36:50,463] [INFO] Running command: fastANI --query /var/lib/cwl/stg9ebb70ea-1f57-42fa-a498-05cc400ce0c9/GCF_006175985.1_ASM617598v1_genomic.fna.gz --refList GCF_006175985.1_ASM617598v1_genomic.fna/target_genomes_gtdb.txt --output GCF_006175985.1_ASM617598v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:37:04,330] [INFO] Task succeeded: fastANI
[2024-01-24 11:37:04,351] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:37:04,351] [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_006175985.1	s__Methylotetracoccus oryzae	100.0	1592	1592	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylococcaceae;g__Methylotetracoccus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_004168015.1	s__Methylotetracoccus sp004168015	94.8296	972	1592	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylococcaceae;g__Methylotetracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012769535.1	s__Methylococcus sp012769535	77.6314	213	1592	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylococcaceae;g__Methylococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000424685.1	s__Methylococcus capsulatus	77.3087	192	1592	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylococcaceae;g__Methylococcus	95.0	99.39	98.77	0.98	0.95	3	-
GCF_016106025.1	s__Methylococcus sp016106025	77.173	156	1592	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylococcaceae;g__Methylococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016925495.1	s__EFPC2 sp016925495	77.1697	195	1592	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylococcaceae;g__EFPC2	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000427385.1	s__Methylocaldum szegediense	76.8818	93	1592	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylococcaceae;g__Methylocaldum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900155475.1	s__Methylomagnum ishizawai	76.8295	164	1592	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylococcaceae;g__Methylomagnum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002005105.1	s__Methylocaldum sp002005105	76.5146	137	1592	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylococcaceae;g__Methylocaldum	95.0	98.51	98.17	0.91	0.88	6	-
GCF_009498235.1	s__Methylospira mobilis	76.5136	87	1592	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylococcaceae;g__Methylospira	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000733935.1	s__Methylomarinum vadi	76.3838	53	1592	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methylomarinum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011371455.1	s__DRQN01 sp011371455	76.2576	52	1592	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SZUA-152;f__SZUA-152;g__DRQN01	95.0	97.38	97.35	0.90	0.88	5	-
GCF_016583575.1	s__Thiocystis violacea	76.1013	98	1592	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Thiocystis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015494295.1	s__Thiogranum sp015494295	76.0412	83	1592	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__DSM-19610;f__DSM-19610;g__Thiogranum	95.0	99.47	99.47	0.86	0.86	2	-
GCF_000374805.1	s__Chitiniphilus shinanonensis	75.9873	72	1592	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinibacteraceae;g__Chitiniphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008033135.1	s__Chitinolyticbacter meiyuanensis	75.9686	59	1592	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinibacteraceae;g__Chitinolyticbacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001312005.1	s__Methylomonas koyamae	75.7999	73	1592	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methylomonas	95.0	96.46	95.49	0.87	0.86	5	-
GCF_016865585.1	s__Jeongeupia naejangsanensis	75.7004	56	1592	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinibacteraceae;g__Jeongeupia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002929135.1	s__Methylomonas sp002929135	75.4036	52	1592	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methylomonas	95.0	99.96	99.88	0.95	0.87	5	-
--------------------------------------------------------------------------------
[2024-01-24 11:37:04,353] [INFO] GTDB search result was written to GCF_006175985.1_ASM617598v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:37:04,353] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:37:04,357] [INFO] DFAST_QC result json was written to GCF_006175985.1_ASM617598v1_genomic.fna/dqc_result.json
[2024-01-24 11:37:04,357] [INFO] DFAST_QC completed!
[2024-01-24 11:37:04,357] [INFO] Total running time: 0h1m30s