[2024-01-24 14:11:50,840] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:11:50,844] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:11:50,844] [INFO] DQC Reference Directory: /var/lib/cwl/stgc3ba3209-67a0-4bb0-bc8e-9f7812c40980/dqc_reference
[2024-01-24 14:11:52,273] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:11:52,274] [INFO] Task started: Prodigal
[2024-01-24 14:11:52,274] [INFO] Running command: gunzip -c /var/lib/cwl/stg06c85cec-8561-4704-a8d8-21e95a7d9ac1/GCF_004362995.1_ASM436299v1_genomic.fna.gz | prodigal -d GCF_004362995.1_ASM436299v1_genomic.fna/cds.fna -a GCF_004362995.1_ASM436299v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:12:06,241] [INFO] Task succeeded: Prodigal
[2024-01-24 14:12:06,242] [INFO] Task started: HMMsearch
[2024-01-24 14:12:06,242] [INFO] Running command: hmmsearch --tblout GCF_004362995.1_ASM436299v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc3ba3209-67a0-4bb0-bc8e-9f7812c40980/dqc_reference/reference_markers.hmm GCF_004362995.1_ASM436299v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:12:06,650] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:12:06,651] [INFO] Found 6/6 markers.
[2024-01-24 14:12:06,713] [INFO] Query marker FASTA was written to GCF_004362995.1_ASM436299v1_genomic.fna/markers.fasta
[2024-01-24 14:12:06,714] [INFO] Task started: Blastn
[2024-01-24 14:12:06,714] [INFO] Running command: blastn -query GCF_004362995.1_ASM436299v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc3ba3209-67a0-4bb0-bc8e-9f7812c40980/dqc_reference/reference_markers.fasta -out GCF_004362995.1_ASM436299v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:12:07,807] [INFO] Task succeeded: Blastn
[2024-01-24 14:12:07,811] [INFO] Selected 20 target genomes.
[2024-01-24 14:12:07,812] [INFO] Target genome list was writen to GCF_004362995.1_ASM436299v1_genomic.fna/target_genomes.txt
[2024-01-24 14:12:07,823] [INFO] Task started: fastANI
[2024-01-24 14:12:07,823] [INFO] Running command: fastANI --query /var/lib/cwl/stg06c85cec-8561-4704-a8d8-21e95a7d9ac1/GCF_004362995.1_ASM436299v1_genomic.fna.gz --refList GCF_004362995.1_ASM436299v1_genomic.fna/target_genomes.txt --output GCF_004362995.1_ASM436299v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:12:30,813] [INFO] Task succeeded: fastANI
[2024-01-24 14:12:30,814] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc3ba3209-67a0-4bb0-bc8e-9f7812c40980/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:12:30,815] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc3ba3209-67a0-4bb0-bc8e-9f7812c40980/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:12:30,919] [INFO] Found 20 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:12:30,919] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:12:30,919] [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
Zavarzinia compransoris	strain=DSM 1231	GCA_004362995.1	1264899	1264899	type	True	100.0	1570	1570	95	conclusive
Zavarzinia compransoris	strain=DSM 1231	GCA_003173055.1	1264899	1264899	type	True	99.9977	1561	1570	95	conclusive
Zavarzinia aquatilis	strain=HR-AS	GCA_003173035.1	2211142	2211142	type	True	83.7086	987	1570	95	below_threshold
Nisaea sediminum	strain=NBU1469	GCA_014904705.1	2775867	2775867	type	True	76.9371	232	1570	95	below_threshold
Xanthobacter aminoxidans	strain=ATCC BAA-299	GCA_023571765.1	186280	186280	type	True	76.761	316	1570	95	below_threshold
Oceanibacterium hippocampi	strain=CECT 7691	GCA_900172325.1	745714	745714	type	True	76.7366	306	1570	95	below_threshold
Skermanella rosea	strain=KEMB 2255-458	GCA_016806835.2	1817965	1817965	type	True	76.5865	400	1570	95	below_threshold
Chelatococcus caeni	strain=DSM 103737	GCA_014196925.1	1348468	1348468	type	True	76.5651	347	1570	95	below_threshold
Jiella sonneratiae	strain=MQZ13P-4	GCA_017353515.1	2816856	2816856	type	True	76.3836	322	1570	95	below_threshold
Thalassobaculum fulvum	strain=KCTC 42651	GCA_014652915.1	1633335	1633335	type	True	76.3457	397	1570	95	below_threshold
Chelatococcus composti	strain=DSM 101465	GCA_018398355.1	1743235	1743235	type	True	76.3449	230	1570	95	below_threshold
Methylobacterium terrae	strain=17Sr1-28	GCA_003173755.1	2202827	2202827	type	True	76.2458	403	1570	95	below_threshold
Pararhodospirillum photometricum	strain=DSM 122	GCA_000284415.2	1084	1084	type	True	76.2297	166	1570	95	below_threshold
Methylobacterium dankookense	strain=DSM 22415	GCA_022179165.1	560405	560405	type	True	76.1868	337	1570	95	below_threshold
Pararhodospirillum oryzae	strain=NBRC 107573	GCA_007992075.1	478448	478448	type	True	76.1687	193	1570	95	below_threshold
Rhodovastum atsumiense	strain=G2-11	GCA_937425535.1	504468	504468	type	True	76.1531	386	1570	95	below_threshold
Methylobacterium dankookense	strain=SW08-7	GCA_902141855.1	560405	560405	type	True	76.1427	350	1570	95	below_threshold
Rhodovarius crocodyli	strain=CCP-6	GCA_004005855.1	1979269	1979269	type	True	76.064	271	1570	95	below_threshold
Roseococcus pinisoli	strain=XZZS9	GCA_018413645.1	2835040	2835040	type	True	75.8052	283	1570	95	below_threshold
Sphingomonas jatrophae	strain=S5-249	GCA_900113315.1	1166337	1166337	type	True	75.6278	215	1570	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:12:30,921] [INFO] DFAST Taxonomy check result was written to GCF_004362995.1_ASM436299v1_genomic.fna/tc_result.tsv
[2024-01-24 14:12:30,922] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:12:30,922] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:12:30,922] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc3ba3209-67a0-4bb0-bc8e-9f7812c40980/dqc_reference/checkm_data
[2024-01-24 14:12:30,929] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:12:30,997] [INFO] Task started: CheckM
[2024-01-24 14:12:30,998] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004362995.1_ASM436299v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004362995.1_ASM436299v1_genomic.fna/checkm_input GCF_004362995.1_ASM436299v1_genomic.fna/checkm_result
[2024-01-24 14:13:15,243] [INFO] Task succeeded: CheckM
[2024-01-24 14:13:15,245] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:13:15,268] [INFO] ===== Completeness check finished =====
[2024-01-24 14:13:15,269] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:13:15,269] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004362995.1_ASM436299v1_genomic.fna/markers.fasta)
[2024-01-24 14:13:15,269] [INFO] Task started: Blastn
[2024-01-24 14:13:15,270] [INFO] Running command: blastn -query GCF_004362995.1_ASM436299v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc3ba3209-67a0-4bb0-bc8e-9f7812c40980/dqc_reference/reference_markers_gtdb.fasta -out GCF_004362995.1_ASM436299v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:13:17,557] [INFO] Task succeeded: Blastn
[2024-01-24 14:13:17,564] [INFO] Selected 19 target genomes.
[2024-01-24 14:13:17,565] [INFO] Target genome list was writen to GCF_004362995.1_ASM436299v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:13:17,579] [INFO] Task started: fastANI
[2024-01-24 14:13:17,580] [INFO] Running command: fastANI --query /var/lib/cwl/stg06c85cec-8561-4704-a8d8-21e95a7d9ac1/GCF_004362995.1_ASM436299v1_genomic.fna.gz --refList GCF_004362995.1_ASM436299v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004362995.1_ASM436299v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:13:36,339] [INFO] Task succeeded: fastANI
[2024-01-24 14:13:36,401] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:13:36,401] [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_003173055.1	s__Zavarzinia compransoris	99.9977	1561	1570	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Zavarziniales;f__Zavarziniaceae;g__Zavarzinia	95.0	100.00	100.00	0.99	0.99	2	conclusive
GCF_003173035.1	s__Zavarzinia aquatilis	83.7415	983	1570	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Zavarziniales;f__Zavarziniaceae;g__Zavarzinia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003590945.1	s__Zavarzinia sp003590945	81.5397	942	1570	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Zavarziniales;f__Zavarziniaceae;g__Zavarzinia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000283655.1	s__Azospirillum lipoferum_C	77.0659	447	1570	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017307375.1	s__JAFKFH01 sp017307375	76.9686	493	1570	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Ferrovibrionales;f__Ferrovibrionaceae;g__JAFKFH01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003116035.1	s__Azospirillum sp003116035	76.9363	451	1570	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008630065.1	s__Blastochloris sulfoviridis	76.7536	291	1570	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Blastochloris	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003576705.1	s__SYSU-D60015 sp003576705	76.7095	405	1570	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Ferrovibrionales;f__Ferrovibrionaceae;g__SYSU-D60015	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016595245.1	s__Azospirillum sp016595245	76.6451	496	1570	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_006739055.1	s__Stella vacuolata	76.5581	444	1570	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__ATCC43930;f__Stellaceae;g__Stella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002480495.1	s__Parvibaculum sp002480495	76.5391	161	1570	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__Parvibaculaceae;g__Parvibaculum	95.0	99.50	98.87	0.94	0.88	9	-
GCF_008330945.1	s__Labrys sp008330945	76.4826	286	1570	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Labraceae;g__Labrys	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102465.1	s__Thalassobaculum litoreum	76.3944	330	1570	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__Thalassobaculum	95.0	98.83	98.83	0.96	0.96	2	-
GCF_001424705.1	s__Methylobacterium sp001424705	76.3609	280	1570	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	98.56	98.52	0.92	0.91	5	-
GCF_000284415.1	s__Pararhodospirillum photometricum	76.2378	166	1570	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__Pararhodospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007992075.1	s__Pararhodospirillum oryzae	76.1929	191	1570	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__Pararhodospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902141855.1	s__Methylobacterium dankookense	76.1592	348	1570	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011048875.1	s__Rhodovulum sp011048875	75.9846	152	1570	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016793965.1	s__JAEULF01 sp016793965	75.8574	227	1570	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__JAEULF01;f__JAEULF01;g__JAEULF01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:13:36,403] [INFO] GTDB search result was written to GCF_004362995.1_ASM436299v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:13:36,403] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:13:36,407] [INFO] DFAST_QC result json was written to GCF_004362995.1_ASM436299v1_genomic.fna/dqc_result.json
[2024-01-24 14:13:36,408] [INFO] DFAST_QC completed!
[2024-01-24 14:13:36,408] [INFO] Total running time: 0h1m46s