[2024-01-24 13:40:42,383] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:42,385] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:42,386] [INFO] DQC Reference Directory: /var/lib/cwl/stge5fbb7f5-fed8-4276-ab3a-998416e34173/dqc_reference
[2024-01-24 13:40:43,741] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:43,744] [INFO] Task started: Prodigal
[2024-01-24 13:40:43,745] [INFO] Running command: gunzip -c /var/lib/cwl/stgdd66569b-ab2d-4ebd-b1f4-202fe186241e/GCF_002749615.1_ASM274961v1_genomic.fna.gz | prodigal -d GCF_002749615.1_ASM274961v1_genomic.fna/cds.fna -a GCF_002749615.1_ASM274961v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:40:56,118] [INFO] Task succeeded: Prodigal
[2024-01-24 13:40:56,118] [INFO] Task started: HMMsearch
[2024-01-24 13:40:56,118] [INFO] Running command: hmmsearch --tblout GCF_002749615.1_ASM274961v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge5fbb7f5-fed8-4276-ab3a-998416e34173/dqc_reference/reference_markers.hmm GCF_002749615.1_ASM274961v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:40:56,437] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:40:56,438] [INFO] Found 6/6 markers.
[2024-01-24 13:40:56,481] [INFO] Query marker FASTA was written to GCF_002749615.1_ASM274961v1_genomic.fna/markers.fasta
[2024-01-24 13:40:56,481] [INFO] Task started: Blastn
[2024-01-24 13:40:56,481] [INFO] Running command: blastn -query GCF_002749615.1_ASM274961v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge5fbb7f5-fed8-4276-ab3a-998416e34173/dqc_reference/reference_markers.fasta -out GCF_002749615.1_ASM274961v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:40:57,569] [INFO] Task succeeded: Blastn
[2024-01-24 13:40:57,573] [INFO] Selected 19 target genomes.
[2024-01-24 13:40:57,573] [INFO] Target genome list was writen to GCF_002749615.1_ASM274961v1_genomic.fna/target_genomes.txt
[2024-01-24 13:40:57,579] [INFO] Task started: fastANI
[2024-01-24 13:40:57,580] [INFO] Running command: fastANI --query /var/lib/cwl/stgdd66569b-ab2d-4ebd-b1f4-202fe186241e/GCF_002749615.1_ASM274961v1_genomic.fna.gz --refList GCF_002749615.1_ASM274961v1_genomic.fna/target_genomes.txt --output GCF_002749615.1_ASM274961v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:18,902] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:18,903] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge5fbb7f5-fed8-4276-ab3a-998416e34173/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:18,903] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge5fbb7f5-fed8-4276-ab3a-998416e34173/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:18,922] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:41:18,922] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:41:18,923] [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
Caulobacter mirabilis	strain=FWC 38	GCA_002749615.1	69666	69666	type	True	100.0	1521	1525	95	conclusive
Caulobacter hibisci	strain=KACC 18849	GCA_016135805.1	2035993	2035993	type	True	80.7174	766	1525	95	below_threshold
Caulobacter soli	strain=Ji-3-8	GCA_011045195.1	2708539	2708539	type	True	80.5137	759	1525	95	below_threshold
Caulobacter segnis	strain=TK0059	GCA_003015125.1	88688	88688	type	True	80.4996	699	1525	95	below_threshold
Caulobacter segnis	strain=ATCC 21756	GCA_000092285.1	88688	88688	type	True	80.4868	699	1525	95	below_threshold
Caulobacter radicis	strain=695	GCA_003094615.1	2172650	2172650	type	True	80.4508	806	1525	95	below_threshold
Caulobacter rhizosphaerae	strain=KCTC 52515	GCA_010977555.1	2010972	2010972	type	True	80.4401	781	1525	95	below_threshold
Caulobacter zeae	strain=410	GCA_002858925.1	2055137	2055137	type	True	80.4319	784	1525	95	below_threshold
Caulobacter rhizosphaerae	strain=CGMCC 1.15915	GCA_014645055.1	2010972	2010972	type	True	80.4253	766	1525	95	below_threshold
Caulobacter vibrioides	strain=DSM 9893	GCA_002858865.1	155892	155892	type	True	80.1199	665	1525	95	below_threshold
Phenylobacterium hankyongense	strain=HKS-05	GCA_003254505.1	1813876	1813876	type	True	79.9945	619	1525	95	below_threshold
Phenylobacterium soli	strain=LX32	GCA_003254475.1	2170551	2170551	type	True	79.8625	597	1525	95	below_threshold
Phenylobacterium zucineum	strain=HLK1	GCA_000017265.1	284016	284016	type	True	79.6718	668	1525	95	below_threshold
Phenylobacterium kunshanense	strain=BUT-10	GCA_003254525.1	1445034	1445034	type	True	79.4263	609	1525	95	below_threshold
Phenylobacterium aquaticum	strain=KACC 18306	GCA_022695515.1	1763816	1763816	type	True	79.3438	666	1525	95	below_threshold
Phenylobacterium glaciei	strain=20VBR1	GCA_016772415.2	2803784	2803784	type	True	79.2544	610	1525	95	below_threshold
Brevundimonas guildfordensis	strain=Sa3CVA3	GCA_014836405.1	2762241	2762241	type	True	79.0844	413	1525	95	below_threshold
Phenylobacterium parvum	strain=HYN0004	GCA_003150835.1	2201350	2201350	type	True	78.747	443	1525	95	below_threshold
Starkeya novella	strain=DSM 506	GCA_000092925.1	921	921	type	True	76.5636	288	1525	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:18,926] [INFO] DFAST Taxonomy check result was written to GCF_002749615.1_ASM274961v1_genomic.fna/tc_result.tsv
[2024-01-24 13:41:18,927] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:18,927] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:18,928] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge5fbb7f5-fed8-4276-ab3a-998416e34173/dqc_reference/checkm_data
[2024-01-24 13:41:18,929] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:18,981] [INFO] Task started: CheckM
[2024-01-24 13:41:18,981] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002749615.1_ASM274961v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002749615.1_ASM274961v1_genomic.fna/checkm_input GCF_002749615.1_ASM274961v1_genomic.fna/checkm_result
[2024-01-24 13:41:59,350] [INFO] Task succeeded: CheckM
[2024-01-24 13:41:59,352] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:41:59,373] [INFO] ===== Completeness check finished =====
[2024-01-24 13:41:59,374] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:41:59,374] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002749615.1_ASM274961v1_genomic.fna/markers.fasta)
[2024-01-24 13:41:59,374] [INFO] Task started: Blastn
[2024-01-24 13:41:59,375] [INFO] Running command: blastn -query GCF_002749615.1_ASM274961v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge5fbb7f5-fed8-4276-ab3a-998416e34173/dqc_reference/reference_markers_gtdb.fasta -out GCF_002749615.1_ASM274961v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:42:01,537] [INFO] Task succeeded: Blastn
[2024-01-24 13:42:01,542] [INFO] Selected 16 target genomes.
[2024-01-24 13:42:01,542] [INFO] Target genome list was writen to GCF_002749615.1_ASM274961v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:42:01,566] [INFO] Task started: fastANI
[2024-01-24 13:42:01,566] [INFO] Running command: fastANI --query /var/lib/cwl/stgdd66569b-ab2d-4ebd-b1f4-202fe186241e/GCF_002749615.1_ASM274961v1_genomic.fna.gz --refList GCF_002749615.1_ASM274961v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002749615.1_ASM274961v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:42:17,362] [INFO] Task succeeded: fastANI
[2024-01-24 13:42:17,380] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:42:17,380] [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_002749615.1	s__Caulobacter mirabilis	100.0	1521	1525	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Caulobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_016234625.1	s__Caulobacter sp016234625	82.3088	685	1525	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Caulobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903858185.1	s__Caulobacter sp903858185	82.2545	734	1525	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Caulobacter	95.0	99.71	99.71	0.95	0.95	2	-
GCF_000281955.1	s__Caulobacter sp000281955	80.5802	772	1525	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Caulobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017418605.1	s__CAISGS01 sp017418605	80.5785	745	1525	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__CAISGS01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001556515.1	s__Caulobacter sp001556515	80.5375	656	1525	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Caulobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002742635.1	s__Caulobacter sp002742635	80.5071	717	1525	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Caulobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010977555.1	s__Caulobacter rhizosphaerae	80.4465	775	1525	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Caulobacter	95.0	98.18	95.88	0.94	0.91	4	-
GCF_016467375.1	s__Caulobacter sp016467375	80.4125	617	1525	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Caulobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016125585.1	s__Caulobacter sp016125585	80.3424	746	1525	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Caulobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000744465.1	s__Caulobacter henricii_A	80.0683	742	1525	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Caulobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003254505.1	s__Phenylobacterium hankyongense	80.0207	616	1525	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014349105.1	s__17J80-11 sp014349105	79.4081	590	1525	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__17J80-11	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018821435.1	s__Phenylobacterium sp018821435	79.1441	654	1525	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	99.99	99.99	0.99	0.99	6	-
GCF_018135625.1	s__BOG-935 sp018135625	79.0827	619	1525	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__BOG-935	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004799515.1	s__Phenylobacterium sp004799515	79.0551	626	1525	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:42:17,382] [INFO] GTDB search result was written to GCF_002749615.1_ASM274961v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:42:17,383] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:42:17,387] [INFO] DFAST_QC result json was written to GCF_002749615.1_ASM274961v1_genomic.fna/dqc_result.json
[2024-01-24 13:42:17,387] [INFO] DFAST_QC completed!
[2024-01-24 13:42:17,387] [INFO] Total running time: 0h1m35s