[2024-01-24 12:06:18,895] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:06:18,897] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:06:18,897] [INFO] DQC Reference Directory: /var/lib/cwl/stgdd52d3c0-6930-47b9-aa6e-b43336f34587/dqc_reference
[2024-01-24 12:06:20,110] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:06:20,111] [INFO] Task started: Prodigal
[2024-01-24 12:06:20,111] [INFO] Running command: gunzip -c /var/lib/cwl/stg172d5a3f-84a0-403f-b2a3-75cbeff8fb26/GCF_003576345.1_ASM357634v1_genomic.fna.gz | prodigal -d GCF_003576345.1_ASM357634v1_genomic.fna/cds.fna -a GCF_003576345.1_ASM357634v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:06:29,717] [INFO] Task succeeded: Prodigal
[2024-01-24 12:06:29,717] [INFO] Task started: HMMsearch
[2024-01-24 12:06:29,717] [INFO] Running command: hmmsearch --tblout GCF_003576345.1_ASM357634v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdd52d3c0-6930-47b9-aa6e-b43336f34587/dqc_reference/reference_markers.hmm GCF_003576345.1_ASM357634v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:06:29,953] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:06:29,954] [INFO] Found 6/6 markers.
[2024-01-24 12:06:29,981] [INFO] Query marker FASTA was written to GCF_003576345.1_ASM357634v1_genomic.fna/markers.fasta
[2024-01-24 12:06:29,982] [INFO] Task started: Blastn
[2024-01-24 12:06:29,982] [INFO] Running command: blastn -query GCF_003576345.1_ASM357634v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdd52d3c0-6930-47b9-aa6e-b43336f34587/dqc_reference/reference_markers.fasta -out GCF_003576345.1_ASM357634v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:06:30,807] [INFO] Task succeeded: Blastn
[2024-01-24 12:06:30,811] [INFO] Selected 17 target genomes.
[2024-01-24 12:06:30,811] [INFO] Target genome list was writen to GCF_003576345.1_ASM357634v1_genomic.fna/target_genomes.txt
[2024-01-24 12:06:30,822] [INFO] Task started: fastANI
[2024-01-24 12:06:30,822] [INFO] Running command: fastANI --query /var/lib/cwl/stg172d5a3f-84a0-403f-b2a3-75cbeff8fb26/GCF_003576345.1_ASM357634v1_genomic.fna.gz --refList GCF_003576345.1_ASM357634v1_genomic.fna/target_genomes.txt --output GCF_003576345.1_ASM357634v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:06:43,419] [INFO] Task succeeded: fastANI
[2024-01-24 12:06:43,420] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdd52d3c0-6930-47b9-aa6e-b43336f34587/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:06:43,420] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdd52d3c0-6930-47b9-aa6e-b43336f34587/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:06:43,437] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:06:43,437] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:06:43,437] [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
Henriciella barbarensis	strain=CCUG66934	GCA_003576345.1	86342	86342	type	True	100.0	1100	1102	95	conclusive
Henriciella algicola	strain=CCUG67844	GCA_003576245.1	1608422	1608422	type	True	85.9653	887	1102	95	below_threshold
Henriciella marina	strain=DSM 19595	GCA_000376805.1	453851	453851	type	True	82.963	758	1102	95	below_threshold
Henriciella pelagia	strain=LA220	GCA_002088945.1	1977912	1977912	type	True	79.254	413	1102	95	below_threshold
Henriciella aquimarina	strain=LMG 24711	GCA_002088975.1	545261	545261	type	True	79.2514	488	1102	95	below_threshold
Henriciella pelagia	strain=CGMCC 1.15928	GCA_014644035.1	1977912	1977912	type	True	79.2254	412	1102	95	below_threshold
Henriciella mobilis	strain=M65	GCA_003576315.1	2305467	2305467	type	True	79.08	466	1102	95	below_threshold
Henriciella litoralis	strain=DSM 22014	GCA_002088935.1	568102	568102	type	True	79.0652	482	1102	95	below_threshold
Hyphomonas chukchiensis	strain=BH-BN04-4	GCA_000682695.1	1280947	1280947	type	True	77.0867	206	1102	95	below_threshold
Hyphomonas polymorpha	strain=PS728	GCA_000685315.1	74319	74319	type	True	77.0488	181	1102	95	below_threshold
Hyphomonas sediminis	strain=WL0036	GCA_019679475.1	2866160	2866160	type	True	77.0305	166	1102	95	below_threshold
Hyphomonas oceanitis	strain=SCH89	GCA_000685295.1	81033	81033	type	True	76.857	204	1102	95	below_threshold
Phenylobacterium glaciei	strain=20VBR1	GCA_016772415.2	2803784	2803784	type	True	76.2879	58	1102	95	below_threshold
Stappia albiluteola	strain=F7233	GCA_014050225.1	2758565	2758565	type	True	76.2296	70	1102	95	below_threshold
Shinella sumterensis	strain=MEC087	GCA_004514425.2	1967501	1967501	type	True	75.9821	66	1102	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:06:43,440] [INFO] DFAST Taxonomy check result was written to GCF_003576345.1_ASM357634v1_genomic.fna/tc_result.tsv
[2024-01-24 12:06:43,440] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:06:43,440] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:06:43,441] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdd52d3c0-6930-47b9-aa6e-b43336f34587/dqc_reference/checkm_data
[2024-01-24 12:06:43,441] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:06:43,473] [INFO] Task started: CheckM
[2024-01-24 12:06:43,473] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003576345.1_ASM357634v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003576345.1_ASM357634v1_genomic.fna/checkm_input GCF_003576345.1_ASM357634v1_genomic.fna/checkm_result
[2024-01-24 12:07:15,685] [INFO] Task succeeded: CheckM
[2024-01-24 12:07:15,686] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:07:15,706] [INFO] ===== Completeness check finished =====
[2024-01-24 12:07:15,706] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:07:15,707] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003576345.1_ASM357634v1_genomic.fna/markers.fasta)
[2024-01-24 12:07:15,707] [INFO] Task started: Blastn
[2024-01-24 12:07:15,707] [INFO] Running command: blastn -query GCF_003576345.1_ASM357634v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdd52d3c0-6930-47b9-aa6e-b43336f34587/dqc_reference/reference_markers_gtdb.fasta -out GCF_003576345.1_ASM357634v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:07:17,125] [INFO] Task succeeded: Blastn
[2024-01-24 12:07:17,128] [INFO] Selected 10 target genomes.
[2024-01-24 12:07:17,129] [INFO] Target genome list was writen to GCF_003576345.1_ASM357634v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:07:17,147] [INFO] Task started: fastANI
[2024-01-24 12:07:17,147] [INFO] Running command: fastANI --query /var/lib/cwl/stg172d5a3f-84a0-403f-b2a3-75cbeff8fb26/GCF_003576345.1_ASM357634v1_genomic.fna.gz --refList GCF_003576345.1_ASM357634v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003576345.1_ASM357634v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:07:24,854] [INFO] Task succeeded: fastANI
[2024-01-24 12:07:24,867] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:07:24,867] [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_003576345.1	s__Henriciella barbarensis	100.0	1100	1102	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Henriciella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003576245.1	s__Henriciella algicola	85.9569	888	1102	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Henriciella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012960415.1	s__Henriciella sp012960415	85.7743	895	1102	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Henriciella	95.0	99.93	99.93	0.95	0.95	2	-
GCF_000376805.1	s__Henriciella marina	82.9631	758	1102	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Henriciella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002733705.1	s__Henriciella sp002733705	80.9277	624	1102	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Henriciella	95.0	99.60	99.22	0.83	0.79	5	-
GCF_003576285.1	s__Henriciella sp003576285	79.2611	459	1102	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Henriciella	95.0	97.82	97.80	0.89	0.89	3	-
GCF_002088935.1	s__Henriciella litoralis	79.0838	480	1102	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Henriciella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000682695.1	s__Hyphomonas chukchiensis	77.1125	204	1102	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000685315.1	s__Hyphomonas polymorpha	77.0488	181	1102	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	98.45	98.45	0.90	0.90	2	-
GCF_000685295.1	s__Hyphomonas oceanitis	76.857	204	1102	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:07:24,869] [INFO] GTDB search result was written to GCF_003576345.1_ASM357634v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:07:24,869] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:07:24,876] [INFO] DFAST_QC result json was written to GCF_003576345.1_ASM357634v1_genomic.fna/dqc_result.json
[2024-01-24 12:07:24,876] [INFO] DFAST_QC completed!
[2024-01-24 12:07:24,876] [INFO] Total running time: 0h1m6s