[2024-01-24 13:49:30,670] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:49:30,674] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:49:30,675] [INFO] DQC Reference Directory: /var/lib/cwl/stg855f8132-641c-40d9-9c12-ff8954a0c2cf/dqc_reference
[2024-01-24 13:49:31,962] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:31,963] [INFO] Task started: Prodigal
[2024-01-24 13:49:31,963] [INFO] Running command: gunzip -c /var/lib/cwl/stgb6049b6a-47a7-498b-83c8-7e599dba5383/GCF_014863405.1_ASM1486340v1_genomic.fna.gz | prodigal -d GCF_014863405.1_ASM1486340v1_genomic.fna/cds.fna -a GCF_014863405.1_ASM1486340v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:49:50,271] [INFO] Task succeeded: Prodigal
[2024-01-24 13:49:50,271] [INFO] Task started: HMMsearch
[2024-01-24 13:49:50,271] [INFO] Running command: hmmsearch --tblout GCF_014863405.1_ASM1486340v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg855f8132-641c-40d9-9c12-ff8954a0c2cf/dqc_reference/reference_markers.hmm GCF_014863405.1_ASM1486340v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:49:50,637] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:49:50,638] [INFO] Found 6/6 markers.
[2024-01-24 13:49:50,680] [INFO] Query marker FASTA was written to GCF_014863405.1_ASM1486340v1_genomic.fna/markers.fasta
[2024-01-24 13:49:50,681] [INFO] Task started: Blastn
[2024-01-24 13:49:50,681] [INFO] Running command: blastn -query GCF_014863405.1_ASM1486340v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg855f8132-641c-40d9-9c12-ff8954a0c2cf/dqc_reference/reference_markers.fasta -out GCF_014863405.1_ASM1486340v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:51,727] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:51,730] [INFO] Selected 13 target genomes.
[2024-01-24 13:49:51,731] [INFO] Target genome list was writen to GCF_014863405.1_ASM1486340v1_genomic.fna/target_genomes.txt
[2024-01-24 13:49:51,736] [INFO] Task started: fastANI
[2024-01-24 13:49:51,736] [INFO] Running command: fastANI --query /var/lib/cwl/stgb6049b6a-47a7-498b-83c8-7e599dba5383/GCF_014863405.1_ASM1486340v1_genomic.fna.gz --refList GCF_014863405.1_ASM1486340v1_genomic.fna/target_genomes.txt --output GCF_014863405.1_ASM1486340v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:50:05,820] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:05,821] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg855f8132-641c-40d9-9c12-ff8954a0c2cf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:50:05,821] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg855f8132-641c-40d9-9c12-ff8954a0c2cf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:50:05,832] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:50:05,832] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:50:05,833] [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
Dyella acidiphila	strain=7MK23	GCA_014863405.1	2775866	2775866	type	True	100.0	1673	1675	95	conclusive
Dyella flava	strain=DHOC52	GCA_016904955.1	1920170	1920170	type	True	83.4082	996	1675	95	below_threshold
Dyella mobilis	strain=DHON07	GCA_016904945.1	1849582	1849582	type	True	83.3368	1051	1675	95	below_threshold
Dyella caseinilytica	strain=CGMCC 1.15434	GCA_014642815.1	1849581	1849581	type	True	83.0302	1036	1675	95	below_threshold
Dyella caseinilytica	strain=DHOB09	GCA_016865235.1	1849581	1849581	type	True	83.0195	1041	1675	95	below_threshold
Dyella psychrodurans	strain=4MSK11	GCA_003363265.1	1927960	1927960	type	True	82.3271	889	1675	95	below_threshold
Dyella choica	strain=4 M-K27	GCA_003977665.1	1927959	1927959	type	True	81.8669	917	1675	95	below_threshold
Dyella japonica	strain=DSM 16301	GCA_001010355.1	231455	231455	type	True	80.8629	624	1675	95	below_threshold
Dyella telluris	strain=G9	GCA_014297575.1	2763498	2763498	type	True	80.7769	726	1675	95	below_threshold
Rhodanobacter spathiphylli	strain=B39	GCA_000264295.1	347483	347483	type	True	80.6534	637	1675	95	below_threshold
Frateuria flava	strain=MAH-13	GCA_017837635.1	2821489	2821489	type	True	80.5665	606	1675	95	below_threshold
Dyella tabacisoli	strain=L4-6	GCA_003350925.1	2282381	2282381	type	True	79.1748	556	1675	95	below_threshold
Tahibacter caeni	strain=BUT-6	GCA_024609805.1	1453545	1453545	type	True	78.107	333	1675	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:50:05,834] [INFO] DFAST Taxonomy check result was written to GCF_014863405.1_ASM1486340v1_genomic.fna/tc_result.tsv
[2024-01-24 13:50:05,835] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:50:05,835] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:50:05,835] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg855f8132-641c-40d9-9c12-ff8954a0c2cf/dqc_reference/checkm_data
[2024-01-24 13:50:05,836] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:50:05,892] [INFO] Task started: CheckM
[2024-01-24 13:50:05,892] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014863405.1_ASM1486340v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014863405.1_ASM1486340v1_genomic.fna/checkm_input GCF_014863405.1_ASM1486340v1_genomic.fna/checkm_result
[2024-01-24 13:50:58,627] [INFO] Task succeeded: CheckM
[2024-01-24 13:50:58,628] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:50:58,649] [INFO] ===== Completeness check finished =====
[2024-01-24 13:50:58,650] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:50:58,650] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014863405.1_ASM1486340v1_genomic.fna/markers.fasta)
[2024-01-24 13:50:58,650] [INFO] Task started: Blastn
[2024-01-24 13:50:58,651] [INFO] Running command: blastn -query GCF_014863405.1_ASM1486340v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg855f8132-641c-40d9-9c12-ff8954a0c2cf/dqc_reference/reference_markers_gtdb.fasta -out GCF_014863405.1_ASM1486340v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:51:00,620] [INFO] Task succeeded: Blastn
[2024-01-24 13:51:00,625] [INFO] Selected 11 target genomes.
[2024-01-24 13:51:00,625] [INFO] Target genome list was writen to GCF_014863405.1_ASM1486340v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:51:00,648] [INFO] Task started: fastANI
[2024-01-24 13:51:00,648] [INFO] Running command: fastANI --query /var/lib/cwl/stgb6049b6a-47a7-498b-83c8-7e599dba5383/GCF_014863405.1_ASM1486340v1_genomic.fna.gz --refList GCF_014863405.1_ASM1486340v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014863405.1_ASM1486340v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:51:12,425] [INFO] Task succeeded: fastANI
[2024-01-24 13:51:12,437] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:51:12,437] [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_014863405.1	s__Dyella_B sp014863405	100.0	1673	1675	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella_B	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_016904955.1	s__Dyella_B flava	83.4348	993	1675	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016904945.1	s__Dyella_B mobilis	83.3243	1052	1675	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016865235.1	s__Dyella_B caseinilytica	83.0323	1038	1675	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella_B	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003363265.1	s__Dyella_B psychrodurans	82.3157	890	1675	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014873315.1	s__Dyella_B sp014873315	82.1622	990	1675	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003977665.1	s__Dyella_B choica	81.8743	916	1675	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012275375.1	s__Dyella sp012275375	81.8036	851	1675	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella	95.0	96.64	95.58	0.92	0.90	4	-
GCF_900112865.1	s__Dyella marensis	81.6762	816	1675	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella	95.0	99.99	99.99	1.00	1.00	2	-
GCF_001182895.1	s__Frateuria_B defendens	81.2019	658	1675	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Frateuria_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014842975.1	s__Rhodanobacter sp014842975	81.1138	730	1675	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Rhodanobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:51:12,439] [INFO] GTDB search result was written to GCF_014863405.1_ASM1486340v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:51:12,439] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:51:12,443] [INFO] DFAST_QC result json was written to GCF_014863405.1_ASM1486340v1_genomic.fna/dqc_result.json
[2024-01-24 13:51:12,443] [INFO] DFAST_QC completed!
[2024-01-24 13:51:12,443] [INFO] Total running time: 0h1m42s