[2024-01-24 13:41:10,516] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:41:10,517] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:41:10,518] [INFO] DQC Reference Directory: /var/lib/cwl/stg0699ca16-5600-4e75-be29-716504b73d00/dqc_reference
[2024-01-24 13:41:11,790] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:41:11,791] [INFO] Task started: Prodigal
[2024-01-24 13:41:11,792] [INFO] Running command: gunzip -c /var/lib/cwl/stg27540e32-baf8-4e1a-9d89-6203d0590ac1/GCF_014925385.1_ASM1492538v1_genomic.fna.gz | prodigal -d GCF_014925385.1_ASM1492538v1_genomic.fna/cds.fna -a GCF_014925385.1_ASM1492538v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:41:28,175] [INFO] Task succeeded: Prodigal
[2024-01-24 13:41:28,176] [INFO] Task started: HMMsearch
[2024-01-24 13:41:28,176] [INFO] Running command: hmmsearch --tblout GCF_014925385.1_ASM1492538v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0699ca16-5600-4e75-be29-716504b73d00/dqc_reference/reference_markers.hmm GCF_014925385.1_ASM1492538v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:41:28,446] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:41:28,447] [INFO] Found 6/6 markers.
[2024-01-24 13:41:28,494] [INFO] Query marker FASTA was written to GCF_014925385.1_ASM1492538v1_genomic.fna/markers.fasta
[2024-01-24 13:41:28,494] [INFO] Task started: Blastn
[2024-01-24 13:41:28,494] [INFO] Running command: blastn -query GCF_014925385.1_ASM1492538v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0699ca16-5600-4e75-be29-716504b73d00/dqc_reference/reference_markers.fasta -out GCF_014925385.1_ASM1492538v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:29,494] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:29,497] [INFO] Selected 21 target genomes.
[2024-01-24 13:41:29,498] [INFO] Target genome list was writen to GCF_014925385.1_ASM1492538v1_genomic.fna/target_genomes.txt
[2024-01-24 13:41:29,504] [INFO] Task started: fastANI
[2024-01-24 13:41:29,504] [INFO] Running command: fastANI --query /var/lib/cwl/stg27540e32-baf8-4e1a-9d89-6203d0590ac1/GCF_014925385.1_ASM1492538v1_genomic.fna.gz --refList GCF_014925385.1_ASM1492538v1_genomic.fna/target_genomes.txt --output GCF_014925385.1_ASM1492538v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:50,511] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:50,511] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0699ca16-5600-4e75-be29-716504b73d00/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:50,512] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0699ca16-5600-4e75-be29-716504b73d00/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:50,528] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:41:50,528] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:41:50,528] [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
Pelagibius marinus	strain=NBU2595	GCA_014925385.1	2762760	2762760	type	True	100.0	1792	1794	95	conclusive
Pelagibius litoralis	strain=DSM 21314	GCA_011683915.1	374515	374515	type	True	80.5732	841	1794	95	below_threshold
Tistlia consotensis	strain=DSM 21585	GCA_900188055.1	1321365	1321365	type	True	78.7738	724	1794	95	below_threshold
Tistlia consotensis	strain=USBA 355	GCA_900177295.1	1321365	1321365	type	True	78.7472	729	1794	95	below_threshold
Rhodovibrio sodomensis	strain=DSM 9895	GCA_016583645.1	1088	1088	type	True	77.7912	428	1794	95	below_threshold
Algihabitans albus	strain=HHTR 118	GCA_003572205.1	2164067	2164067	type	True	77.6103	347	1794	95	below_threshold
Ferruginivarius sediminum	strain=WD2A32	GCA_003344765.1	2661937	2661937	type	True	77.6009	369	1794	95	below_threshold
Fodinicurvata fenggangensis	strain=DSM 21160	GCA_000686045.1	1121830	1121830	type	True	77.5913	231	1794	95	below_threshold
Azospirillum picis	strain=IMMIB TAR-3	GCA_017876115.1	488438	488438	type	True	77.4004	460	1794	95	below_threshold
Hypericibacter adhaerens	strain=R5959	GCA_008728835.1	2602016	2602016	type	True	77.3932	418	1794	95	below_threshold
Fodinicurvata sediminis	strain=DSM 21159	GCA_000420625.1	1121832	1121832	type	True	77.362	201	1794	95	below_threshold
Azospirillum agricola	strain=CC-HIH038	GCA_017876095.1	1720247	1720247	type	True	77.2339	536	1794	95	below_threshold
Stella humosa	strain=ATCC 43930	GCA_006738645.1	94	94	type	True	77.0628	417	1794	95	below_threshold
Stella humosa	strain=DSM 5900	GCA_003751345.1	94	94	type	True	77.0489	420	1794	95	below_threshold
Oceanicella actignis	strain=DSM 22673	GCA_008124525.1	1189325	1189325	type	True	76.7931	340	1794	95	below_threshold
Rhodospirillum rubrum	strain=DSM 467	GCA_019134555.1	1085	1085	type	True	76.7121	225	1794	95	below_threshold
Rhodospirillum rubrum	strain=ATCC 11170	GCA_000013085.1	1085	1085	type	True	76.6918	227	1794	95	below_threshold
Azospirillum cavernae	strain=K2W22B-5	GCA_003590795.1	2320860	2320860	type	True	76.507	323	1794	95	below_threshold
Roseomonas rubea	strain=MO17	GCA_016106015.1	2748666	2748666	type	True	76.4668	253	1794	95	below_threshold
Pseudaminobacter soli	strain=19-2017	GCA_018310375.1	2831468	2831468	type	True	76.357	238	1794	95	below_threshold
Pseudaminobacter soli	strain=HC19	GCA_014595955.1	2831468	2831468	type	True	76.357	238	1794	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:50,530] [INFO] DFAST Taxonomy check result was written to GCF_014925385.1_ASM1492538v1_genomic.fna/tc_result.tsv
[2024-01-24 13:41:50,531] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:50,531] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:50,531] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0699ca16-5600-4e75-be29-716504b73d00/dqc_reference/checkm_data
[2024-01-24 13:41:50,532] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:50,584] [INFO] Task started: CheckM
[2024-01-24 13:41:50,584] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014925385.1_ASM1492538v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014925385.1_ASM1492538v1_genomic.fna/checkm_input GCF_014925385.1_ASM1492538v1_genomic.fna/checkm_result
[2024-01-24 13:42:33,913] [INFO] Task succeeded: CheckM
[2024-01-24 13:42:33,914] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:42:33,932] [INFO] ===== Completeness check finished =====
[2024-01-24 13:42:33,932] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:42:33,933] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014925385.1_ASM1492538v1_genomic.fna/markers.fasta)
[2024-01-24 13:42:33,933] [INFO] Task started: Blastn
[2024-01-24 13:42:33,933] [INFO] Running command: blastn -query GCF_014925385.1_ASM1492538v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0699ca16-5600-4e75-be29-716504b73d00/dqc_reference/reference_markers_gtdb.fasta -out GCF_014925385.1_ASM1492538v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:42:35,902] [INFO] Task succeeded: Blastn
[2024-01-24 13:42:35,905] [INFO] Selected 14 target genomes.
[2024-01-24 13:42:35,905] [INFO] Target genome list was writen to GCF_014925385.1_ASM1492538v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:42:35,944] [INFO] Task started: fastANI
[2024-01-24 13:42:35,945] [INFO] Running command: fastANI --query /var/lib/cwl/stg27540e32-baf8-4e1a-9d89-6203d0590ac1/GCF_014925385.1_ASM1492538v1_genomic.fna.gz --refList GCF_014925385.1_ASM1492538v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014925385.1_ASM1492538v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:42:51,143] [INFO] Task succeeded: fastANI
[2024-01-24 13:42:51,156] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:42:51,157] [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_014925385.1	s__WHTV01 sp014925385	100.0	1792	1794	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Kiloniellales;f__Kiloniellaceae;g__WHTV01	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_009377535.1	s__WHTV01 sp009377535	83.8802	1006	1794	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Kiloniellales;f__Kiloniellaceae;g__WHTV01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001657395.1	s__Pelagibius sp001657395	81.4157	920	1794	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Kiloniellales;f__Kiloniellaceae;g__Pelagibius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011683915.1	s__Pelagibius litoralis	80.5988	837	1794	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Kiloniellales;f__Kiloniellaceae;g__Pelagibius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900177295.1	s__Tistlia consotensis	78.7312	731	1794	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Kiloniellales;f__DSM-21159;g__Tistlia	95.0	99.99	99.99	0.99	0.99	2	-
GCF_016583645.1	s__Rhodovibrio sodomensis	77.7992	427	1794	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Kiloniellales;f__Rhodovibrionaceae;g__Rhodovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008728835.1	s__Hypericibacter adhaerens	77.4044	418	1794	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Dongiales;f__Dongiaceae;g__Hypericibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003693905.1	s__J153 sp003693905	77.3658	201	1794	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Kiloniellales;f__J153;g__J153	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007004665.1	s__Denitrobaculum tricleocarpae	77.306	291	1794	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Kiloniellales;f__Kiloniellaceae;g__Denitrobaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_006738865.1	s__Stella sp006738865	77.126	371	1794	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__ATCC43930;f__Stellaceae;g__Stella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015232025.1	s__JADFZP01 sp015232025	77.0415	230	1794	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__JADFZP01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008124525.1	s__Oceanicella actignis	76.7798	343	1794	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Oceanicella	95.0	98.87	98.87	0.96	0.96	3	-
GCA_016212565.1	s__JACRFY01 sp016212565	76.7569	292	1794	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__JACRFY01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016793965.1	s__JAEULF01 sp016793965	76.3734	290	1794	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 13:42:51,158] [INFO] GTDB search result was written to GCF_014925385.1_ASM1492538v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:42:51,159] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:42:51,163] [INFO] DFAST_QC result json was written to GCF_014925385.1_ASM1492538v1_genomic.fna/dqc_result.json
[2024-01-24 13:42:51,164] [INFO] DFAST_QC completed!
[2024-01-24 13:42:51,164] [INFO] Total running time: 0h1m41s