[2024-01-24 11:58:51,864] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:58:51,868] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:58:51,868] [INFO] DQC Reference Directory: /var/lib/cwl/stg15d7d3c7-d00d-40e7-a1ad-0fe99fc06b1e/dqc_reference
[2024-01-24 11:58:53,140] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:58:53,141] [INFO] Task started: Prodigal
[2024-01-24 11:58:53,142] [INFO] Running command: gunzip -c /var/lib/cwl/stg29148b28-216b-49b1-b631-356e1998324a/GCF_003149435.1_ASM314943v1_genomic.fna.gz | prodigal -d GCF_003149435.1_ASM314943v1_genomic.fna/cds.fna -a GCF_003149435.1_ASM314943v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:59:04,488] [INFO] Task succeeded: Prodigal
[2024-01-24 11:59:04,488] [INFO] Task started: HMMsearch
[2024-01-24 11:59:04,488] [INFO] Running command: hmmsearch --tblout GCF_003149435.1_ASM314943v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg15d7d3c7-d00d-40e7-a1ad-0fe99fc06b1e/dqc_reference/reference_markers.hmm GCF_003149435.1_ASM314943v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:59:04,800] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:59:04,801] [INFO] Found 6/6 markers.
[2024-01-24 11:59:04,853] [INFO] Query marker FASTA was written to GCF_003149435.1_ASM314943v1_genomic.fna/markers.fasta
[2024-01-24 11:59:04,854] [INFO] Task started: Blastn
[2024-01-24 11:59:04,854] [INFO] Running command: blastn -query GCF_003149435.1_ASM314943v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg15d7d3c7-d00d-40e7-a1ad-0fe99fc06b1e/dqc_reference/reference_markers.fasta -out GCF_003149435.1_ASM314943v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:59:05,833] [INFO] Task succeeded: Blastn
[2024-01-24 11:59:05,836] [INFO] Selected 19 target genomes.
[2024-01-24 11:59:05,836] [INFO] Target genome list was writen to GCF_003149435.1_ASM314943v1_genomic.fna/target_genomes.txt
[2024-01-24 11:59:05,844] [INFO] Task started: fastANI
[2024-01-24 11:59:05,844] [INFO] Running command: fastANI --query /var/lib/cwl/stg29148b28-216b-49b1-b631-356e1998324a/GCF_003149435.1_ASM314943v1_genomic.fna.gz --refList GCF_003149435.1_ASM314943v1_genomic.fna/target_genomes.txt --output GCF_003149435.1_ASM314943v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:59:17,876] [INFO] Task succeeded: fastANI
[2024-01-24 11:59:17,877] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg15d7d3c7-d00d-40e7-a1ad-0fe99fc06b1e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:59:17,877] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg15d7d3c7-d00d-40e7-a1ad-0fe99fc06b1e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:59:17,891] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:59:17,892] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:59:17,892] [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
Arhodomonas aquaeolei	strain=DSM 8974	GCA_000374645.1	2369	2369	type	True	79.3094	437	1343	95	below_threshold
Spiribacter aquaticus	strain=SP30	GCA_007625215.1	1935996	1935996	type	True	78.3488	284	1343	95	below_threshold
Halorhodospira neutriphila	strain=DSM 15116	GCA_016584055.1	168379	168379	type	True	78.3088	245	1343	95	below_threshold
Spiribacter vilamensis	strain=DSM 21056	GCA_007625165.1	531306	531306	type	True	78.1086	253	1343	95	below_threshold
Spiribacter vilamensis	strain=DSM 21056	GCA_004217415.1	531306	531306	type	True	78.0444	254	1343	95	below_threshold
Thioalbus denitrificans	strain=DSM 26407	GCA_003337735.1	547122	547122	type	True	78.027	264	1343	95	below_threshold
Spiribacter curvatus	strain=UAH-SP71	GCA_000485905.1	1335757	1335757	type	True	78.0046	207	1343	95	below_threshold
Spiribacter salinus	strain=M19-40	GCA_000319575.2	1335746	1335746	type	True	77.6107	183	1343	95	below_threshold
Methylonatrum kenyense	strain=AMT 1	GCA_023195885.1	455253	455253	type	True	77.5824	186	1343	95	below_threshold
Inmirania thermothiophila	strain=DSM 100275	GCA_003751635.1	1750597	1750597	type	True	77.5773	314	1343	95	below_threshold
Natronocella acetinitrilica	strain=ANL 6-2	GCA_024170285.1	414046	414046	type	True	77.1223	216	1343	95	below_threshold
Halomonas campaniensis	strain=5AG	GCA_014193375.1	213554	213554	type	True	77.1021	268	1343	95	below_threshold
Thioalkalivibrio versutus	strain=AL 2	GCA_001999325.1	106634	106634	type	True	76.9318	153	1343	95	below_threshold
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	76.4872	258	1343	95	below_threshold
Pseudomonas cavernae	strain=K2W31S-8	GCA_003595175.1	2320867	2320867	type	True	76.2425	174	1343	95	below_threshold
Pseudomonas insulae	strain=UL073	GCA_016901015.1	2809017	2809017	type	True	76.0125	178	1343	95	below_threshold
Aromatoleum tolulyticum	strain=ATCC 51758	GCA_900156155.1	34027	34027	type	True	75.8801	161	1343	95	below_threshold
Aromatoleum toluolicum	strain=T	GCA_012911005.2	90060	90060	type	True	75.8539	162	1343	95	below_threshold
Aromatoleum toluvorans	strain=Td21	GCA_012910905.1	92002	92002	type	True	75.7557	173	1343	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:59:17,896] [INFO] DFAST Taxonomy check result was written to GCF_003149435.1_ASM314943v1_genomic.fna/tc_result.tsv
[2024-01-24 11:59:17,896] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:59:17,897] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:59:17,897] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg15d7d3c7-d00d-40e7-a1ad-0fe99fc06b1e/dqc_reference/checkm_data
[2024-01-24 11:59:17,898] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:59:17,939] [INFO] Task started: CheckM
[2024-01-24 11:59:17,939] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003149435.1_ASM314943v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003149435.1_ASM314943v1_genomic.fna/checkm_input GCF_003149435.1_ASM314943v1_genomic.fna/checkm_result
[2024-01-24 11:59:55,025] [INFO] Task succeeded: CheckM
[2024-01-24 11:59:55,026] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:59:55,047] [INFO] ===== Completeness check finished =====
[2024-01-24 11:59:55,047] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:59:55,047] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003149435.1_ASM314943v1_genomic.fna/markers.fasta)
[2024-01-24 11:59:55,047] [INFO] Task started: Blastn
[2024-01-24 11:59:55,047] [INFO] Running command: blastn -query GCF_003149435.1_ASM314943v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg15d7d3c7-d00d-40e7-a1ad-0fe99fc06b1e/dqc_reference/reference_markers_gtdb.fasta -out GCF_003149435.1_ASM314943v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:59:56,936] [INFO] Task succeeded: Blastn
[2024-01-24 11:59:56,940] [INFO] Selected 15 target genomes.
[2024-01-24 11:59:56,940] [INFO] Target genome list was writen to GCF_003149435.1_ASM314943v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:59:56,951] [INFO] Task started: fastANI
[2024-01-24 11:59:56,952] [INFO] Running command: fastANI --query /var/lib/cwl/stg29148b28-216b-49b1-b631-356e1998324a/GCF_003149435.1_ASM314943v1_genomic.fna.gz --refList GCF_003149435.1_ASM314943v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003149435.1_ASM314943v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:00:06,130] [INFO] Task succeeded: fastANI
[2024-01-24 12:00:06,142] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:00:06,142] [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_003149435.1	s__E85 sp003149435	100.0	1336	1343	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrococcales;f__Nitrococcaceae;g__E85	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000374645.1	s__Arhodomonas aquaeolei	79.3433	435	1343	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrococcales;f__Nitrococcaceae;g__Arhodomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013519935.1	s__WFHF3C12 sp013519935	78.6949	366	1343	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrococcales;f__Nitrococcaceae;g__WFHF3C12	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002813635.1	s__Spiribacter roseus	78.6163	272	1343	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrococcales;f__Nitrococcaceae;g__Spiribacter	95.0	98.20	97.75	0.92	0.91	7	-
GCF_016584055.1	s__Halorhodospira neutriphila	78.308	244	1343	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrococcales;f__Halorhodospiraceae;g__Halorhodospira	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009676705.1	s__Spiribacter sp009676705	78.2321	239	1343	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrococcales;f__Nitrococcaceae;g__Spiribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009295635.1	s__S0819 sp009295635	78.0582	277	1343	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrococcales;f__AK92;g__S0819	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004217415.1	s__Spiribacter vilamensis	78.0434	254	1343	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrococcales;f__Nitrococcaceae;g__Spiribacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000485905.1	s__Spiribacter curvatus	78.0221	206	1343	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrococcales;f__Nitrococcaceae;g__Spiribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014762505.1	s__SpSt-1174 sp014762505	77.7523	250	1343	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	-
GCF_003751635.1	s__Inmirania thermothiophila	77.6071	311	1343	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__DSM-100275;f__DSM-100275;g__Inmirania	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007127935.1	s__SKYL01 sp007127935	77.1408	129	1343	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrococcales;f__Halorhodospiraceae;g__SKYL01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000801295.1	s__MONJU sp000801295	77.1384	151	1343	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Sedimenticolaceae;g__MONJU	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012911005.1	s__Aromatoleum toluolicum	75.8606	163	1343	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Aromatoleum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012910905.1	s__Aromatoleum toluvorans	75.749	174	1343	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Aromatoleum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:00:06,144] [INFO] GTDB search result was written to GCF_003149435.1_ASM314943v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:00:06,145] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:00:06,149] [INFO] DFAST_QC result json was written to GCF_003149435.1_ASM314943v1_genomic.fna/dqc_result.json
[2024-01-24 12:00:06,149] [INFO] DFAST_QC completed!
[2024-01-24 12:00:06,149] [INFO] Total running time: 0h1m14s