[2024-01-25 17:34:50,961] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:34:50,964] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:34:50,964] [INFO] DQC Reference Directory: /var/lib/cwl/stg1829ff12-4c0a-4436-8b80-828194250f52/dqc_reference
[2024-01-25 17:34:52,163] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:34:52,164] [INFO] Task started: Prodigal
[2024-01-25 17:34:52,164] [INFO] Running command: gunzip -c /var/lib/cwl/stg018acae6-15c9-45fa-9348-aa0e04697e86/GCF_016124105.1_ASM1612410v1_genomic.fna.gz | prodigal -d GCF_016124105.1_ASM1612410v1_genomic.fna/cds.fna -a GCF_016124105.1_ASM1612410v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:35:02,978] [INFO] Task succeeded: Prodigal
[2024-01-25 17:35:02,978] [INFO] Task started: HMMsearch
[2024-01-25 17:35:02,978] [INFO] Running command: hmmsearch --tblout GCF_016124105.1_ASM1612410v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1829ff12-4c0a-4436-8b80-828194250f52/dqc_reference/reference_markers.hmm GCF_016124105.1_ASM1612410v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:35:03,239] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:35:03,240] [INFO] Found 6/6 markers.
[2024-01-25 17:35:03,279] [INFO] Query marker FASTA was written to GCF_016124105.1_ASM1612410v1_genomic.fna/markers.fasta
[2024-01-25 17:35:03,279] [INFO] Task started: Blastn
[2024-01-25 17:35:03,279] [INFO] Running command: blastn -query GCF_016124105.1_ASM1612410v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1829ff12-4c0a-4436-8b80-828194250f52/dqc_reference/reference_markers.fasta -out GCF_016124105.1_ASM1612410v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:35:04,165] [INFO] Task succeeded: Blastn
[2024-01-25 17:35:04,168] [INFO] Selected 19 target genomes.
[2024-01-25 17:35:04,168] [INFO] Target genome list was writen to GCF_016124105.1_ASM1612410v1_genomic.fna/target_genomes.txt
[2024-01-25 17:35:04,199] [INFO] Task started: fastANI
[2024-01-25 17:35:04,199] [INFO] Running command: fastANI --query /var/lib/cwl/stg018acae6-15c9-45fa-9348-aa0e04697e86/GCF_016124105.1_ASM1612410v1_genomic.fna.gz --refList GCF_016124105.1_ASM1612410v1_genomic.fna/target_genomes.txt --output GCF_016124105.1_ASM1612410v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:35:25,014] [INFO] Task succeeded: fastANI
[2024-01-25 17:35:25,015] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1829ff12-4c0a-4436-8b80-828194250f52/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:35:25,015] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1829ff12-4c0a-4436-8b80-828194250f52/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:35:25,027] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:35:25,029] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:35:25,030] [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
Aquamicrobium zhengzhouense	strain=cd-1	GCA_016124105.1	2781738	2781738	type	True	100.0	1341	1344	95	conclusive
Mesorhizobium sediminum	strain=KCTC 42205	GCA_013240295.1	1849104	1849104	type	True	78.3451	421	1344	95	below_threshold
Aquamicrobium defluvii	strain=DSM 11603	GCA_004363725.1	69279	69279	type	True	78.2285	314	1344	95	below_threshold
Aminobacter aganoensis	strain=DSM 7051	GCA_014206975.1	83264	83264	type	True	77.9646	332	1344	95	below_threshold
Aminobacter niigataensis	strain=DSM 7050	GCA_014200015.1	83265	83265	type	True	77.9082	327	1344	95	below_threshold
Aquibium oceanicum	strain=B7	GCA_001889605.1	1670800	1670800	type	True	77.8453	266	1344	95	below_threshold
Aquibium microcysteis	strain=NIBR3	GCA_014495845.1	675281	675281	type	True	77.6926	318	1344	95	below_threshold
Mesorhizobium atlanticum	strain=CNPSo 3140	GCA_003289965.1	2233532	2233532	type	True	77.687	291	1344	95	below_threshold
Mesorhizobium carmichaelinearum	strain=ICMP 18942	GCA_900199455.1	1208188	1208188	type	True	77.6559	305	1344	95	below_threshold
Mesorhizobium silamurunense	strain=CCBAU 01550	GCA_014843825.1	499528	499528	type	True	77.6043	281	1344	95	below_threshold
Mesorhizobium hawassense	strain=AC99b	GCA_003289945.1	1209954	1209954	type	True	77.5993	295	1344	95	below_threshold
Mesorhizobium zhangyense	strain=CGMCC 1.15528	GCA_011045115.1	1776730	1776730	type	True	77.5916	316	1344	95	below_threshold
Aquibium carbonis	strain=B2.3	GCA_003970795.1	2495581	2495581	type	True	77.5396	300	1344	95	below_threshold
Ciceribacter ferrooxidans	strain=F8825	GCA_004137355.1	2509717	2509717	type	True	77.5335	177	1344	95	below_threshold
Mesorhizobium albiziae	strain=DSM 21822	GCA_900114255.1	335020	335020	type	True	77.5138	281	1344	95	below_threshold
Mesorhizobium comanense	strain=3P27G6	GCA_005503535.1	2502215	2502215	type	True	77.4958	294	1344	95	below_threshold
Mesorhizobium camelthorni	strain=CCNWXJ 40-4	GCA_011045125.1	475069	475069	type	True	77.418	314	1344	95	below_threshold
Mesorhizobium erdmanii	strain=USDA 3471	GCA_000472705.1	1777866	1777866	type	True	77.4154	283	1344	95	below_threshold
Mesorhizobium onobrychidis	strain=OM4	GCA_024707545.1	2775404	2775404	type	True	77.2209	284	1344	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:35:25,031] [INFO] DFAST Taxonomy check result was written to GCF_016124105.1_ASM1612410v1_genomic.fna/tc_result.tsv
[2024-01-25 17:35:25,032] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:35:25,032] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:35:25,032] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1829ff12-4c0a-4436-8b80-828194250f52/dqc_reference/checkm_data
[2024-01-25 17:35:25,033] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:35:25,075] [INFO] Task started: CheckM
[2024-01-25 17:35:25,075] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016124105.1_ASM1612410v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016124105.1_ASM1612410v1_genomic.fna/checkm_input GCF_016124105.1_ASM1612410v1_genomic.fna/checkm_result
[2024-01-25 17:35:58,424] [INFO] Task succeeded: CheckM
[2024-01-25 17:35:58,425] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:35:58,439] [INFO] ===== Completeness check finished =====
[2024-01-25 17:35:58,440] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:35:58,440] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016124105.1_ASM1612410v1_genomic.fna/markers.fasta)
[2024-01-25 17:35:58,440] [INFO] Task started: Blastn
[2024-01-25 17:35:58,440] [INFO] Running command: blastn -query GCF_016124105.1_ASM1612410v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1829ff12-4c0a-4436-8b80-828194250f52/dqc_reference/reference_markers_gtdb.fasta -out GCF_016124105.1_ASM1612410v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:36:00,022] [INFO] Task succeeded: Blastn
[2024-01-25 17:36:00,025] [INFO] Selected 14 target genomes.
[2024-01-25 17:36:00,026] [INFO] Target genome list was writen to GCF_016124105.1_ASM1612410v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:36:00,036] [INFO] Task started: fastANI
[2024-01-25 17:36:00,036] [INFO] Running command: fastANI --query /var/lib/cwl/stg018acae6-15c9-45fa-9348-aa0e04697e86/GCF_016124105.1_ASM1612410v1_genomic.fna.gz --refList GCF_016124105.1_ASM1612410v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016124105.1_ASM1612410v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:36:14,052] [INFO] Task succeeded: fastANI
[2024-01-25 17:36:14,061] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:36:14,061] [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_016124105.1	s__Aquamicrobium_A sp016124105	100.0	1341	1344	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aquamicrobium_A	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000526635.1	s__Aquamicrobium_A sp000526635	80.8884	770	1344	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aquamicrobium_A	95.0	99.33	98.68	0.94	0.89	3	-
GCF_900113935.1	s__Aquamicrobium_A aerolatum	79.23	375	1344	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aquamicrobium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008180155.1	s__Aquamicrobium_A microcysteis	78.485	431	1344	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aquamicrobium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013240295.1	s__Aquamicrobium_A sediminum	78.3461	421	1344	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aquamicrobium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003577315.1	s__Aquamicrobium_A sp003577315	78.2993	350	1344	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aquamicrobium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018555685.1	s__Aminobacter anthyllidis	78.0611	320	1344	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aminobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003148475.1	s__Pseudaminobacter salicylatoxidans	77.9454	323	1344	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Pseudaminobacter	95.0	97.95	97.95	0.90	0.90	2	-
GCF_008727715.1	s__Mesorhizobium terrae	77.8194	309	1344	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	99.80	99.17	0.95	0.89	9	-
GCA_004020545.1	s__Mesorhizobium sp004020545	77.7744	293	1344	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	98.24	97.54	0.89	0.86	9	-
GCF_017874015.1	s__Pseudaminobacter sp017874015	77.7659	301	1344	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Pseudaminobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003012705.1	s__Pseudaminobacter soli	77.6739	326	1344	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Pseudaminobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003952485.1	s__Mesorhizobium sp003952485	77.6081	309	1344	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	98.38	98.21	0.91	0.89	5	-
GCA_017305925.1	s__JAFKJW01 sp017305925	77.4418	256	1344	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__JAFKJW01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:36:14,063] [INFO] GTDB search result was written to GCF_016124105.1_ASM1612410v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:36:14,063] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:36:14,066] [INFO] DFAST_QC result json was written to GCF_016124105.1_ASM1612410v1_genomic.fna/dqc_result.json
[2024-01-25 17:36:14,066] [INFO] DFAST_QC completed!
[2024-01-25 17:36:14,066] [INFO] Total running time: 0h1m23s