[2024-01-24 14:05:32,364] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:05:32,365] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:05:32,366] [INFO] DQC Reference Directory: /var/lib/cwl/stg393af6cb-c421-4507-9624-65122754cd5d/dqc_reference
[2024-01-24 14:05:33,650] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:05:33,650] [INFO] Task started: Prodigal
[2024-01-24 14:05:33,651] [INFO] Running command: gunzip -c /var/lib/cwl/stg3c3d045e-f6cd-462e-8057-d27362164c0f/GCF_002088975.1_ASM208897v1_genomic.fna.gz | prodigal -d GCF_002088975.1_ASM208897v1_genomic.fna/cds.fna -a GCF_002088975.1_ASM208897v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:05:45,836] [INFO] Task succeeded: Prodigal
[2024-01-24 14:05:45,837] [INFO] Task started: HMMsearch
[2024-01-24 14:05:45,837] [INFO] Running command: hmmsearch --tblout GCF_002088975.1_ASM208897v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg393af6cb-c421-4507-9624-65122754cd5d/dqc_reference/reference_markers.hmm GCF_002088975.1_ASM208897v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:05:46,154] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:05:46,156] [INFO] Found 6/6 markers.
[2024-01-24 14:05:46,198] [INFO] Query marker FASTA was written to GCF_002088975.1_ASM208897v1_genomic.fna/markers.fasta
[2024-01-24 14:05:46,199] [INFO] Task started: Blastn
[2024-01-24 14:05:46,199] [INFO] Running command: blastn -query GCF_002088975.1_ASM208897v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg393af6cb-c421-4507-9624-65122754cd5d/dqc_reference/reference_markers.fasta -out GCF_002088975.1_ASM208897v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:05:47,145] [INFO] Task succeeded: Blastn
[2024-01-24 14:05:47,148] [INFO] Selected 18 target genomes.
[2024-01-24 14:05:47,149] [INFO] Target genome list was writen to GCF_002088975.1_ASM208897v1_genomic.fna/target_genomes.txt
[2024-01-24 14:05:47,170] [INFO] Task started: fastANI
[2024-01-24 14:05:47,170] [INFO] Running command: fastANI --query /var/lib/cwl/stg3c3d045e-f6cd-462e-8057-d27362164c0f/GCF_002088975.1_ASM208897v1_genomic.fna.gz --refList GCF_002088975.1_ASM208897v1_genomic.fna/target_genomes.txt --output GCF_002088975.1_ASM208897v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:06:02,087] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:02,087] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg393af6cb-c421-4507-9624-65122754cd5d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:06:02,088] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg393af6cb-c421-4507-9624-65122754cd5d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:06:02,101] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:06:02,101] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:06:02,102] [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 aquimarina	strain=LMG 24711	GCA_002088975.1	545261	545261	type	True	100.0	1367	1373	95	conclusive
Henriciella mobilis	strain=M65	GCA_003576315.1	2305467	2305467	type	True	82.2048	706	1373	95	below_threshold
Henriciella pelagia	strain=LA220	GCA_002088945.1	1977912	1977912	type	True	80.0855	578	1373	95	below_threshold
Henriciella pelagia	strain=CGMCC 1.15928	GCA_014644035.1	1977912	1977912	type	True	80.0816	575	1373	95	below_threshold
Henriciella litoralis	strain=DSM 22014	GCA_002088935.1	568102	568102	type	True	79.8549	536	1373	95	below_threshold
Henriciella marina	strain=DSM 19595	GCA_000376805.1	453851	453851	type	True	79.384	536	1373	95	below_threshold
Henriciella algicola	strain=CCUG67844	GCA_003576245.1	1608422	1608422	type	True	79.33	549	1373	95	below_threshold
Henriciella barbarensis	strain=CCUG66934	GCA_003576345.1	86342	86342	type	True	79.2596	472	1373	95	below_threshold
Hyphomonas oceanitis	strain=SCH89	GCA_000685295.1	81033	81033	type	True	77.9213	308	1373	95	below_threshold
Hyphomonas adhaerens	strain=MHS-3	GCA_000685235.1	81029	81029	type	True	77.7721	298	1373	95	below_threshold
Hyphomonas sediminis	strain=WL0036	GCA_019679475.1	2866160	2866160	type	True	77.5748	253	1373	95	below_threshold
Hyphomonas johnsonii	strain=MHS-2	GCA_000685275.1	81031	81031	type	True	77.5437	291	1373	95	below_threshold
Oricola indica	strain=JL-62	GCA_019966595.1	2872591	2872591	type	True	76.7397	117	1373	95	below_threshold
Starkeya novella	strain=DSM 506	GCA_000092925.1	921	921	type	True	76.6737	136	1373	95	below_threshold
Starkeya koreensis	strain=Jip08	GCA_023016525.1	266121	266121	type	True	76.505	128	1373	95	below_threshold
Methylobacterium mesophilicum	strain=NBRC 15688	GCA_022179445.1	39956	39956	type	True	75.9505	111	1373	95	below_threshold
Falsiroseomonas tokyonensis	strain=K-20	GCA_019024325.1	430521	430521	type	True	75.913	107	1373	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:06:02,103] [INFO] DFAST Taxonomy check result was written to GCF_002088975.1_ASM208897v1_genomic.fna/tc_result.tsv
[2024-01-24 14:06:02,104] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:06:02,104] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:06:02,104] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg393af6cb-c421-4507-9624-65122754cd5d/dqc_reference/checkm_data
[2024-01-24 14:06:02,105] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:06:02,149] [INFO] Task started: CheckM
[2024-01-24 14:06:02,149] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002088975.1_ASM208897v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002088975.1_ASM208897v1_genomic.fna/checkm_input GCF_002088975.1_ASM208897v1_genomic.fna/checkm_result
[2024-01-24 14:06:42,899] [INFO] Task succeeded: CheckM
[2024-01-24 14:06:42,901] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:06:42,937] [INFO] ===== Completeness check finished =====
[2024-01-24 14:06:42,937] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:06:42,938] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002088975.1_ASM208897v1_genomic.fna/markers.fasta)
[2024-01-24 14:06:42,938] [INFO] Task started: Blastn
[2024-01-24 14:06:42,938] [INFO] Running command: blastn -query GCF_002088975.1_ASM208897v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg393af6cb-c421-4507-9624-65122754cd5d/dqc_reference/reference_markers_gtdb.fasta -out GCF_002088975.1_ASM208897v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:44,745] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:44,750] [INFO] Selected 13 target genomes.
[2024-01-24 14:06:44,750] [INFO] Target genome list was writen to GCF_002088975.1_ASM208897v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:06:44,768] [INFO] Task started: fastANI
[2024-01-24 14:06:44,768] [INFO] Running command: fastANI --query /var/lib/cwl/stg3c3d045e-f6cd-462e-8057-d27362164c0f/GCF_002088975.1_ASM208897v1_genomic.fna.gz --refList GCF_002088975.1_ASM208897v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002088975.1_ASM208897v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:06:54,862] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:54,885] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:06:54,885] [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_002088975.1	s__Henriciella aquimarina	100.0	1367	1373	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_003576285.1	s__Henriciella sp003576285	82.2833	722	1373	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Henriciella	95.0	97.82	97.80	0.89	0.89	3	-
GCA_002733705.1	s__Henriciella sp002733705	80.1538	549	1373	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Henriciella	95.0	99.60	99.22	0.83	0.79	5	-
GCA_012960415.1	s__Henriciella sp012960415	80.1335	537	1373	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Henriciella	95.0	99.93	99.93	0.95	0.95	2	-
GCF_002088945.1	s__Henriciella pelagia	80.091	577	1373	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Henriciella	95.0	100.00	100.00	1.00	1.00	2	-
GCA_017792385.1	s__Hyphomonas sp017792385	79.6764	360	1373	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000376805.1	s__Henriciella marina	79.386	537	1373	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Henriciella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003576245.1	s__Henriciella algicola	79.3346	549	1373	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Henriciella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003576345.1	s__Henriciella barbarensis	79.2789	474	1373	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Henriciella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000685295.1	s__Hyphomonas oceanitis	77.91	309	1373	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000961795.1	s__Hyphomonas sp000961795	77.8839	302	1373	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000685235.1	s__Hyphomonas adhaerens	77.7455	301	1373	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	97.03	96.92	0.83	0.82	4	-
GCF_000685275.1	s__Hyphomonas johnsonii	77.5437	291	1373	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 14:06:54,887] [INFO] GTDB search result was written to GCF_002088975.1_ASM208897v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:06:54,888] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:06:54,891] [INFO] DFAST_QC result json was written to GCF_002088975.1_ASM208897v1_genomic.fna/dqc_result.json
[2024-01-24 14:06:54,892] [INFO] DFAST_QC completed!
[2024-01-24 14:06:54,892] [INFO] Total running time: 0h1m23s