[2024-01-24 13:19:13,165] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:19:13,167] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:19:13,167] [INFO] DQC Reference Directory: /var/lib/cwl/stg20588ebd-af14-4596-9349-70ffd6d47e64/dqc_reference
[2024-01-24 13:19:14,427] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:19:14,428] [INFO] Task started: Prodigal
[2024-01-24 13:19:14,428] [INFO] Running command: gunzip -c /var/lib/cwl/stg3be4b1cd-5913-4f35-a334-84ad0c289ba0/GCF_014842925.1_ASM1484292v1_genomic.fna.gz | prodigal -d GCF_014842925.1_ASM1484292v1_genomic.fna/cds.fna -a GCF_014842925.1_ASM1484292v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:19:28,290] [INFO] Task succeeded: Prodigal
[2024-01-24 13:19:28,291] [INFO] Task started: HMMsearch
[2024-01-24 13:19:28,291] [INFO] Running command: hmmsearch --tblout GCF_014842925.1_ASM1484292v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg20588ebd-af14-4596-9349-70ffd6d47e64/dqc_reference/reference_markers.hmm GCF_014842925.1_ASM1484292v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:19:28,575] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:19:28,577] [INFO] Found 6/6 markers.
[2024-01-24 13:19:28,620] [INFO] Query marker FASTA was written to GCF_014842925.1_ASM1484292v1_genomic.fna/markers.fasta
[2024-01-24 13:19:28,620] [INFO] Task started: Blastn
[2024-01-24 13:19:28,621] [INFO] Running command: blastn -query GCF_014842925.1_ASM1484292v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg20588ebd-af14-4596-9349-70ffd6d47e64/dqc_reference/reference_markers.fasta -out GCF_014842925.1_ASM1484292v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:29,529] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:29,533] [INFO] Selected 18 target genomes.
[2024-01-24 13:19:29,534] [INFO] Target genome list was writen to GCF_014842925.1_ASM1484292v1_genomic.fna/target_genomes.txt
[2024-01-24 13:19:29,542] [INFO] Task started: fastANI
[2024-01-24 13:19:29,543] [INFO] Running command: fastANI --query /var/lib/cwl/stg3be4b1cd-5913-4f35-a334-84ad0c289ba0/GCF_014842925.1_ASM1484292v1_genomic.fna.gz --refList GCF_014842925.1_ASM1484292v1_genomic.fna/target_genomes.txt --output GCF_014842925.1_ASM1484292v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:19:45,523] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:45,524] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg20588ebd-af14-4596-9349-70ffd6d47e64/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:19:45,524] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg20588ebd-af14-4596-9349-70ffd6d47e64/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:19:45,540] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:19:45,541] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:19:45,541] [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
Roseibium polysiphoniae	strain=KACC 19711	GCA_014842925.1	2571221	2571221	type	True	100.0	1522	1522	95	conclusive
Roseibium suaedae	strain=DSM 22153	GCA_900142725.1	735517	735517	type	True	78.7999	507	1522	95	below_threshold
Roseibium litorale	strain=4C16A	GCA_014842915.1	2803841	2803841	type	True	78.7189	509	1522	95	below_threshold
Roseibium aestuarii	strain=SYSU M00256-3	GCA_008477545.1	2600299	2600299	type	True	78.5632	482	1522	95	below_threshold
Roseibium limicola	strain=CAU 1637	GCA_017313085.1	2816037	2816037	type	True	78.3544	409	1522	95	below_threshold
Roseibium marinum	strain=DSM 17023	GCA_002906165.1	281252	281252	type	True	78.0725	417	1522	95	below_threshold
Roseibium aggregatum	strain=IAM 12614	GCA_000168975.1	187304	187304	suspected-type	True	78.0714	470	1522	95	below_threshold
Pannonibacter phragmitetus	strain=NCTC13350	GCA_900454465.1	121719	121719	suspected-type	True	77.8027	368	1522	95	below_threshold
Pannonibacter phragmitetus	strain=DSM 14782	GCA_000382365.1	121719	121719	suspected-type	True	77.7189	366	1522	95	below_threshold
Roseibium album	strain=CECT 5095	GCA_001404515.1	311410	311410	type	True	77.6624	305	1522	95	below_threshold
Stappia taiwanensis	strain=DSM 23284	GCA_013868145.1	992267	992267	type	True	77.4498	270	1522	95	below_threshold
Aurantimonas endophytica	strain=KCTC 52296	GCA_024105745.1	1522175	1522175	type	True	76.3746	127	1522	95	below_threshold
Microvirga splendida	strain=BT325	GCA_016427565.1	2795727	2795727	type	True	76.1564	88	1522	95	below_threshold
Bradyrhizobium betae	strain=CECT 5829	GCA_024806875.1	244734	244734	type	True	76.1365	107	1522	95	below_threshold
Jiella sonneratiae	strain=MQZ13P-4	GCA_017353515.1	2816856	2816856	type	True	76.119	141	1522	95	below_threshold
Methylobacterium terricola	strain=17Sr1-39	GCA_006151805.1	2583531	2583531	type	True	75.825	115	1522	95	below_threshold
Niveispirillum cyanobacteriorum	strain=CGMCC 1.12958	GCA_014640215.1	1612173	1612173	type	True	75.5902	59	1522	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:19:45,542] [INFO] DFAST Taxonomy check result was written to GCF_014842925.1_ASM1484292v1_genomic.fna/tc_result.tsv
[2024-01-24 13:19:45,543] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:19:45,543] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:19:45,543] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg20588ebd-af14-4596-9349-70ffd6d47e64/dqc_reference/checkm_data
[2024-01-24 13:19:45,544] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:19:45,587] [INFO] Task started: CheckM
[2024-01-24 13:19:45,587] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014842925.1_ASM1484292v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014842925.1_ASM1484292v1_genomic.fna/checkm_input GCF_014842925.1_ASM1484292v1_genomic.fna/checkm_result
[2024-01-24 13:20:28,677] [INFO] Task succeeded: CheckM
[2024-01-24 13:20:28,679] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:20:28,699] [INFO] ===== Completeness check finished =====
[2024-01-24 13:20:28,700] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:20:28,700] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014842925.1_ASM1484292v1_genomic.fna/markers.fasta)
[2024-01-24 13:20:28,701] [INFO] Task started: Blastn
[2024-01-24 13:20:28,701] [INFO] Running command: blastn -query GCF_014842925.1_ASM1484292v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg20588ebd-af14-4596-9349-70ffd6d47e64/dqc_reference/reference_markers_gtdb.fasta -out GCF_014842925.1_ASM1484292v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:20:30,396] [INFO] Task succeeded: Blastn
[2024-01-24 13:20:30,400] [INFO] Selected 12 target genomes.
[2024-01-24 13:20:30,401] [INFO] Target genome list was writen to GCF_014842925.1_ASM1484292v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:20:30,432] [INFO] Task started: fastANI
[2024-01-24 13:20:30,432] [INFO] Running command: fastANI --query /var/lib/cwl/stg3be4b1cd-5913-4f35-a334-84ad0c289ba0/GCF_014842925.1_ASM1484292v1_genomic.fna.gz --refList GCF_014842925.1_ASM1484292v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014842925.1_ASM1484292v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:20:42,959] [INFO] Task succeeded: fastANI
[2024-01-24 13:20:42,979] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:20:42,979] [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_014842925.1	s__Roseibium polysiphoniae	100.0	1522	1522	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Roseibium	95.0	96.20	96.20	0.93	0.93	2	conclusive
GCF_009650605.1	s__Roseibium sp009650605	92.9091	1360	1522	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Roseibium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142725.1	s__Roseibium suaedae	78.7917	508	1522	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Roseibium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014842915.1	s__Roseibium litorale	78.7273	508	1522	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Roseibium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014692675.1	s__Roseibium aggregatum_C	78.7172	527	1522	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Roseibium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008477545.1	s__Roseibium aestuarii	78.5547	483	1522	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Roseibium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001999245.1	s__Roseibium aggregatum_A	78.2649	452	1522	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Roseibium	95.0	97.61	96.85	0.93	0.89	16	-
GCF_008107695.1	s__Roseibium sp008107695	78.0844	462	1522	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Roseibium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000168975.1	s__Roseibium aggregatum	78.0712	470	1522	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Roseibium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002906165.1	s__Roseibium marinum	78.064	418	1522	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Roseibium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001624695.1	s__Roseibium sp001624695	77.9349	432	1522	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Roseibium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000382365.1	s__Pannonibacter phragmitetus	77.7104	367	1522	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Pannonibacter	95.0	99.99	99.99	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:20:42,981] [INFO] GTDB search result was written to GCF_014842925.1_ASM1484292v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:20:42,982] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:20:42,985] [INFO] DFAST_QC result json was written to GCF_014842925.1_ASM1484292v1_genomic.fna/dqc_result.json
[2024-01-24 13:20:42,986] [INFO] DFAST_QC completed!
[2024-01-24 13:20:42,986] [INFO] Total running time: 0h1m30s