[2024-01-24 11:50:49,644] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:50:49,646] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:50:49,646] [INFO] DQC Reference Directory: /var/lib/cwl/stg81ceb86a-97f3-461d-9335-4f9891e6ff74/dqc_reference
[2024-01-24 11:50:50,851] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:50:50,852] [INFO] Task started: Prodigal
[2024-01-24 11:50:50,853] [INFO] Running command: gunzip -c /var/lib/cwl/stg08ae6ed9-aa4e-4961-b60c-a0281e0aab09/GCF_019623905.1_ASM1962390v1_genomic.fna.gz | prodigal -d GCF_019623905.1_ASM1962390v1_genomic.fna/cds.fna -a GCF_019623905.1_ASM1962390v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:51:05,227] [INFO] Task succeeded: Prodigal
[2024-01-24 11:51:05,227] [INFO] Task started: HMMsearch
[2024-01-24 11:51:05,228] [INFO] Running command: hmmsearch --tblout GCF_019623905.1_ASM1962390v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg81ceb86a-97f3-461d-9335-4f9891e6ff74/dqc_reference/reference_markers.hmm GCF_019623905.1_ASM1962390v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:51:05,509] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:51:05,511] [INFO] Found 6/6 markers.
[2024-01-24 11:51:05,554] [INFO] Query marker FASTA was written to GCF_019623905.1_ASM1962390v1_genomic.fna/markers.fasta
[2024-01-24 11:51:05,554] [INFO] Task started: Blastn
[2024-01-24 11:51:05,554] [INFO] Running command: blastn -query GCF_019623905.1_ASM1962390v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg81ceb86a-97f3-461d-9335-4f9891e6ff74/dqc_reference/reference_markers.fasta -out GCF_019623905.1_ASM1962390v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:51:06,404] [INFO] Task succeeded: Blastn
[2024-01-24 11:51:06,407] [INFO] Selected 24 target genomes.
[2024-01-24 11:51:06,408] [INFO] Target genome list was writen to GCF_019623905.1_ASM1962390v1_genomic.fna/target_genomes.txt
[2024-01-24 11:51:06,418] [INFO] Task started: fastANI
[2024-01-24 11:51:06,418] [INFO] Running command: fastANI --query /var/lib/cwl/stg08ae6ed9-aa4e-4961-b60c-a0281e0aab09/GCF_019623905.1_ASM1962390v1_genomic.fna.gz --refList GCF_019623905.1_ASM1962390v1_genomic.fna/target_genomes.txt --output GCF_019623905.1_ASM1962390v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:51:25,310] [INFO] Task succeeded: fastANI
[2024-01-24 11:51:25,311] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg81ceb86a-97f3-461d-9335-4f9891e6ff74/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:51:25,311] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg81ceb86a-97f3-461d-9335-4f9891e6ff74/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:51:25,329] [INFO] Found 24 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:51:25,329] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:51:25,329] [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
Rhodobacter amnigenus	strain=HSP-20	GCA_019130055.1	2852097	2852097	type	True	80.077	644	1461	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_009908265.2	2852097	2852097	type	True	80.0719	645	1461	95	below_threshold
Rhodobacter flagellatus	strain=SYSU G03088	GCA_008271465.1	2593021	2593021	type	True	80.002	659	1461	95	below_threshold
Rhodobacter thermarum	strain=YIM 73036	GCA_003574395.1	2670345	2670345	type	True	79.8291	642	1461	95	below_threshold
Rhodobacter ruber	strain=CCP-1	GCA_009908315.1	1985673	1985673	type	True	79.692	631	1461	95	below_threshold
Rhodobacter calidifons	strain=M37P	GCA_011174775.1	2715277	2715277	type	True	79.6881	669	1461	95	below_threshold
Cereibacter changlensis	strain=JA139	GCA_003034985.1	402884	402884	type	True	79.5709	604	1461	95	below_threshold
Cereibacter changlensis	strain=DSM 18774	GCA_003254335.1	402884	402884	type	True	79.4771	632	1461	95	below_threshold
Gemmobacter caeruleus	strain=N8	GCA_008271655.1	2595004	2595004	type	True	79.4458	600	1461	95	below_threshold
Gemmobacter straminiformis	strain=CAM-8	GCA_014243445.1	2045119	2045119	type	True	79.2087	607	1461	95	below_threshold
Cereibacter sediminicola	strain=JA983	GCA_007668225.1	2584941	2584941	type	True	79.1206	518	1461	95	below_threshold
Gemmobacter aquatilis	strain=DSM 3857	GCA_900110025.1	933059	933059	type	True	79.1174	597	1461	95	below_threshold
Gemmobacter caeni	strain=DSM 21823	GCA_003054195.1	589035	589035	type	True	79.1133	568	1461	95	below_threshold
Gemmobacter caeni	strain=CGMCC 1.7745	GCA_007830625.1	589035	589035	type	True	79.0482	578	1461	95	below_threshold
Gemmobacter lutimaris	strain=YJ-T1-11	GCA_003570715.1	2306023	2306023	type	True	79.0339	600	1461	95	below_threshold
Tabrizicola algicola	strain=ETT8	GCA_010915705.1	2709381	2709381	type	True	79.0322	556	1461	95	below_threshold
Gemmobacter aquarius	strain=HYN0069	GCA_003060865.1	2169400	2169400	type	True	78.9666	544	1461	95	below_threshold
Cereibacter sphaeroides	strain=2.4.1	GCA_000273405.1	1063	1063	type	True	78.9564	531	1461	95	below_threshold
Frigidibacter albus	strain=CGMCC 1.13995	GCA_014640395.1	1465486	1465486	type	True	78.7141	548	1461	95	below_threshold
Frigidibacter albus	strain=SP32	GCA_009881095.1	1465486	1465486	type	True	78.6385	555	1461	95	below_threshold
Frigidibacter albus	strain=SP32	GCA_010993795.1	1465486	1465486	type	True	78.6322	555	1461	95	below_threshold
Frigidibacter albus	strain=SP32	GCA_009908165.1	1465486	1465486	type	True	78.5946	552	1461	95	below_threshold
Paracoccus fontiphilus	strain=MVW-1	GCA_017356265.1	1815556	1815556	type	True	78.481	394	1461	95	below_threshold
Paracoccus aerius	strain=KCTC 42845	GCA_016757275.1	1915382	1915382	type	True	78.375	377	1461	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:51:25,332] [INFO] DFAST Taxonomy check result was written to GCF_019623905.1_ASM1962390v1_genomic.fna/tc_result.tsv
[2024-01-24 11:51:25,333] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:51:25,333] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:51:25,334] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg81ceb86a-97f3-461d-9335-4f9891e6ff74/dqc_reference/checkm_data
[2024-01-24 11:51:25,335] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:51:25,380] [INFO] Task started: CheckM
[2024-01-24 11:51:25,380] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019623905.1_ASM1962390v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019623905.1_ASM1962390v1_genomic.fna/checkm_input GCF_019623905.1_ASM1962390v1_genomic.fna/checkm_result
[2024-01-24 11:52:23,346] [INFO] Task succeeded: CheckM
[2024-01-24 11:52:23,347] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:52:23,370] [INFO] ===== Completeness check finished =====
[2024-01-24 11:52:23,370] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:52:23,370] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019623905.1_ASM1962390v1_genomic.fna/markers.fasta)
[2024-01-24 11:52:23,371] [INFO] Task started: Blastn
[2024-01-24 11:52:23,371] [INFO] Running command: blastn -query GCF_019623905.1_ASM1962390v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg81ceb86a-97f3-461d-9335-4f9891e6ff74/dqc_reference/reference_markers_gtdb.fasta -out GCF_019623905.1_ASM1962390v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:52:24,677] [INFO] Task succeeded: Blastn
[2024-01-24 11:52:24,681] [INFO] Selected 22 target genomes.
[2024-01-24 11:52:24,681] [INFO] Target genome list was writen to GCF_019623905.1_ASM1962390v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:52:24,699] [INFO] Task started: fastANI
[2024-01-24 11:52:24,699] [INFO] Running command: fastANI --query /var/lib/cwl/stg08ae6ed9-aa4e-4961-b60c-a0281e0aab09/GCF_019623905.1_ASM1962390v1_genomic.fna.gz --refList GCF_019623905.1_ASM1962390v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019623905.1_ASM1962390v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:52:43,693] [INFO] Task succeeded: fastANI
[2024-01-24 11:52:43,712] [INFO] Found 22 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 11:52:43,712] [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
GCA_013693875.1	s__SSD5 sp013693875	86.5387	1040	1461	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__SSD5	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011043545.1	s__JAAKGP01 sp011043545	80.5881	701	1461	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JAAKGP01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014859945.1	s__UBA1943 sp014859945	80.2108	576	1461	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__UBA1943	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009908265.2	s__Gemmobacter_B sp009908265	80.0792	643	1461	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter_B	95.0	100.00	100.00	1.00	1.00	2	-
GCA_018058035.1	s__JAAKGP01 sp018058035	79.9341	605	1461	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JAAKGP01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002855575.1	s__Gemmobacter_B sp002855575	79.6873	668	1461	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000500915.1	s__Gemmobacter_B sp000500915	79.6632	564	1461	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003993775.1	s__Frigidibacter sp003993775	79.6153	539	1461	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Frigidibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003034985.1	s__Cereibacter changlensis	79.5462	608	1461	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cereibacter	95.0	98.07	96.18	0.89	0.78	3	-
GCA_016704435.1	s__JAAKGP01 sp016704435	79.5109	617	1461	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JAAKGP01	95.0	99.06	99.06	0.93	0.93	2	-
GCF_008271655.1	s__Gemmobacter caeruleus	79.4906	597	1461	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014763725.1	s__JACXUX01 sp014763725	79.4749	482	1461	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JACXUX01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004799285.1	s__Gemmobacter_D aestuarii	79.4299	625	1461	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter_D	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014879735.1	s__Pseudogemmobacter sp014879735	79.3121	557	1461	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudogemmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014243445.1	s__Gemmobacter_B straminiformis	79.2339	603	1461	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003054195.1	s__Gemmobacter caeni	79.0794	571	1461	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter	95.0	98.77	98.23	0.88	0.79	5	-
GCA_016792685.1	s__Tabrizicola sp016792685	79.0125	504	1461	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tabrizicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003060865.1	s__Gemmobacter_B sp003060865	78.9352	539	1461	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002423245.1	s__Frigidibacter sp002423245	78.641	456	1461	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Frigidibacter	95.0	98.55	98.55	0.85	0.85	2	-
GCF_017356265.1	s__Paracoccus fontiphilus	78.4997	393	1461	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015654855.1	s__JAATGA01 sp015654855	78.2452	353	1461	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JAATGA01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007131945.1	s__Pararhodobacter sp007131945	77.899	331	1461	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pararhodobacter	95.0	99.16	99.15	0.86	0.82	3	-
--------------------------------------------------------------------------------
[2024-01-24 11:52:43,714] [INFO] GTDB search result was written to GCF_019623905.1_ASM1962390v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:52:43,715] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:52:43,719] [INFO] DFAST_QC result json was written to GCF_019623905.1_ASM1962390v1_genomic.fna/dqc_result.json
[2024-01-24 11:52:43,720] [INFO] DFAST_QC completed!
[2024-01-24 11:52:43,720] [INFO] Total running time: 0h1m54s