[2024-01-24 13:49:27,300] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:49:27,308] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:49:27,308] [INFO] DQC Reference Directory: /var/lib/cwl/stg40466759-2339-4127-97c2-657e29f3f0d9/dqc_reference
[2024-01-24 13:49:28,716] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:28,717] [INFO] Task started: Prodigal
[2024-01-24 13:49:28,717] [INFO] Running command: gunzip -c /var/lib/cwl/stga15e09ce-3f80-484a-b420-ad3b09964a35/GCF_002088945.1_ASM208894v1_genomic.fna.gz | prodigal -d GCF_002088945.1_ASM208894v1_genomic.fna/cds.fna -a GCF_002088945.1_ASM208894v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:49:39,112] [INFO] Task succeeded: Prodigal
[2024-01-24 13:49:39,113] [INFO] Task started: HMMsearch
[2024-01-24 13:49:39,113] [INFO] Running command: hmmsearch --tblout GCF_002088945.1_ASM208894v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg40466759-2339-4127-97c2-657e29f3f0d9/dqc_reference/reference_markers.hmm GCF_002088945.1_ASM208894v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:49:39,437] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:49:39,438] [INFO] Found 6/6 markers.
[2024-01-24 13:49:39,473] [INFO] Query marker FASTA was written to GCF_002088945.1_ASM208894v1_genomic.fna/markers.fasta
[2024-01-24 13:49:39,473] [INFO] Task started: Blastn
[2024-01-24 13:49:39,473] [INFO] Running command: blastn -query GCF_002088945.1_ASM208894v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg40466759-2339-4127-97c2-657e29f3f0d9/dqc_reference/reference_markers.fasta -out GCF_002088945.1_ASM208894v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:40,386] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:40,389] [INFO] Selected 15 target genomes.
[2024-01-24 13:49:40,389] [INFO] Target genome list was writen to GCF_002088945.1_ASM208894v1_genomic.fna/target_genomes.txt
[2024-01-24 13:49:40,401] [INFO] Task started: fastANI
[2024-01-24 13:49:40,401] [INFO] Running command: fastANI --query /var/lib/cwl/stga15e09ce-3f80-484a-b420-ad3b09964a35/GCF_002088945.1_ASM208894v1_genomic.fna.gz --refList GCF_002088945.1_ASM208894v1_genomic.fna/target_genomes.txt --output GCF_002088945.1_ASM208894v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:49:52,979] [INFO] Task succeeded: fastANI
[2024-01-24 13:49:52,979] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg40466759-2339-4127-97c2-657e29f3f0d9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:49:52,979] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg40466759-2339-4127-97c2-657e29f3f0d9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:49:52,991] [INFO] Found 13 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:49:52,991] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:49:52,991] [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 pelagia	strain=LA220	GCA_002088945.1	1977912	1977912	type	True	100.0	1140	1141	95	conclusive
Henriciella pelagia	strain=CGMCC 1.15928	GCA_014644035.1	1977912	1977912	type	True	99.9937	1137	1141	95	conclusive
Henriciella litoralis	strain=DSM 22014	GCA_002088935.1	568102	568102	type	True	80.3293	503	1141	95	below_threshold
Henriciella mobilis	strain=M65	GCA_003576315.1	2305467	2305467	type	True	80.2188	569	1141	95	below_threshold
Henriciella aquimarina	strain=LMG 24711	GCA_002088975.1	545261	545261	type	True	80.1756	572	1141	95	below_threshold
Henriciella algicola	strain=CCUG67844	GCA_003576245.1	1608422	1608422	type	True	79.4058	473	1141	95	below_threshold
Henriciella barbarensis	strain=CCUG66934	GCA_003576345.1	86342	86342	type	True	79.1895	426	1141	95	below_threshold
Hyphomonas chukchiensis	strain=BH-BN04-4	GCA_000682695.1	1280947	1280947	type	True	77.2257	259	1141	95	below_threshold
Hyphomonas johnsonii	strain=MHS-2	GCA_000685275.1	81031	81031	type	True	77.1666	224	1141	95	below_threshold
Bradyrhizobium cenepequi	strain=CNPSo 4026	GCA_020329485.1	2821403	2821403	type	True	76.2313	64	1141	95	below_threshold
Bradyrhizobium septentrionale	strain=1S1	GCA_011516645.4	1404411	1404411	type	True	76.2184	75	1141	95	below_threshold
Cereibacter sediminicola	strain=JA983	GCA_007668225.1	2584941	2584941	type	True	76.1713	52	1141	95	below_threshold
Parvularcula marina	strain=SM1705	GCA_003399445.1	2292771	2292771	type	True	75.8968	58	1141	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:49:52,993] [INFO] DFAST Taxonomy check result was written to GCF_002088945.1_ASM208894v1_genomic.fna/tc_result.tsv
[2024-01-24 13:49:52,993] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:49:52,993] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:49:52,993] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg40466759-2339-4127-97c2-657e29f3f0d9/dqc_reference/checkm_data
[2024-01-24 13:49:52,994] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:49:53,032] [INFO] Task started: CheckM
[2024-01-24 13:49:53,032] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002088945.1_ASM208894v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002088945.1_ASM208894v1_genomic.fna/checkm_input GCF_002088945.1_ASM208894v1_genomic.fna/checkm_result
[2024-01-24 13:50:28,447] [INFO] Task succeeded: CheckM
[2024-01-24 13:50:28,448] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:50:28,464] [INFO] ===== Completeness check finished =====
[2024-01-24 13:50:28,464] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:50:28,465] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002088945.1_ASM208894v1_genomic.fna/markers.fasta)
[2024-01-24 13:50:28,465] [INFO] Task started: Blastn
[2024-01-24 13:50:28,465] [INFO] Running command: blastn -query GCF_002088945.1_ASM208894v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg40466759-2339-4127-97c2-657e29f3f0d9/dqc_reference/reference_markers_gtdb.fasta -out GCF_002088945.1_ASM208894v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:29,923] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:29,927] [INFO] Selected 13 target genomes.
[2024-01-24 13:50:29,927] [INFO] Target genome list was writen to GCF_002088945.1_ASM208894v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:50:29,939] [INFO] Task started: fastANI
[2024-01-24 13:50:29,939] [INFO] Running command: fastANI --query /var/lib/cwl/stga15e09ce-3f80-484a-b420-ad3b09964a35/GCF_002088945.1_ASM208894v1_genomic.fna.gz --refList GCF_002088945.1_ASM208894v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002088945.1_ASM208894v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:50:38,666] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:38,677] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:50:38,678] [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_002088945.1	s__Henriciella pelagia	100.0	1140	1141	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Henriciella	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_003576285.1	s__Henriciella sp003576285	80.6937	590	1141	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	80.3208	502	1141	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Henriciella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002088975.1	s__Henriciella aquimarina	80.1855	571	1141	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	79.6664	474	1141	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Henriciella	95.0	99.93	99.93	0.95	0.95	2	-
GCF_003576245.1	s__Henriciella algicola	79.3828	473	1141	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Henriciella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017792385.1	s__Hyphomonas sp017792385	79.3087	282	1141	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002733705.1	s__Henriciella sp002733705	79.2594	433	1141	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Henriciella	95.0	99.60	99.22	0.83	0.79	5	-
GCF_000376805.1	s__Henriciella marina	78.9131	469	1141	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Henriciella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000961695.1	s__Hyphomonas sp000961695	77.4565	248	1141	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000685275.1	s__Hyphomonas johnsonii	77.1666	224	1141	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018830285.1	s__Hyphomonas sp018830285	76.886	213	1141	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013213825.1	s__Henriciella sp013213825	75.9833	69	1141	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Henriciella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:50:38,679] [INFO] GTDB search result was written to GCF_002088945.1_ASM208894v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:50:38,680] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:50:38,683] [INFO] DFAST_QC result json was written to GCF_002088945.1_ASM208894v1_genomic.fna/dqc_result.json
[2024-01-24 13:50:38,684] [INFO] DFAST_QC completed!
[2024-01-24 13:50:38,684] [INFO] Total running time: 0h1m11s