[2024-01-24 13:22:40,396] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:22:40,398] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:22:40,398] [INFO] DQC Reference Directory: /var/lib/cwl/stgf44fe234-8688-41bc-ac51-01b1bed50d18/dqc_reference
[2024-01-24 13:22:41,679] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:22:41,680] [INFO] Task started: Prodigal
[2024-01-24 13:22:41,680] [INFO] Running command: gunzip -c /var/lib/cwl/stgaaa14b4d-9042-49de-90b1-4e2948977159/GCF_027913035.1_ASM2791303v1_genomic.fna.gz | prodigal -d GCF_027913035.1_ASM2791303v1_genomic.fna/cds.fna -a GCF_027913035.1_ASM2791303v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:22:53,341] [INFO] Task succeeded: Prodigal
[2024-01-24 13:22:53,342] [INFO] Task started: HMMsearch
[2024-01-24 13:22:53,342] [INFO] Running command: hmmsearch --tblout GCF_027913035.1_ASM2791303v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf44fe234-8688-41bc-ac51-01b1bed50d18/dqc_reference/reference_markers.hmm GCF_027913035.1_ASM2791303v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:22:53,639] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:22:53,640] [INFO] Found 6/6 markers.
[2024-01-24 13:22:53,678] [INFO] Query marker FASTA was written to GCF_027913035.1_ASM2791303v1_genomic.fna/markers.fasta
[2024-01-24 13:22:53,678] [INFO] Task started: Blastn
[2024-01-24 13:22:53,679] [INFO] Running command: blastn -query GCF_027913035.1_ASM2791303v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf44fe234-8688-41bc-ac51-01b1bed50d18/dqc_reference/reference_markers.fasta -out GCF_027913035.1_ASM2791303v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:22:54,585] [INFO] Task succeeded: Blastn
[2024-01-24 13:22:54,590] [INFO] Selected 23 target genomes.
[2024-01-24 13:22:54,591] [INFO] Target genome list was writen to GCF_027913035.1_ASM2791303v1_genomic.fna/target_genomes.txt
[2024-01-24 13:22:54,600] [INFO] Task started: fastANI
[2024-01-24 13:22:54,600] [INFO] Running command: fastANI --query /var/lib/cwl/stgaaa14b4d-9042-49de-90b1-4e2948977159/GCF_027913035.1_ASM2791303v1_genomic.fna.gz --refList GCF_027913035.1_ASM2791303v1_genomic.fna/target_genomes.txt --output GCF_027913035.1_ASM2791303v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:23:13,122] [INFO] Task succeeded: fastANI
[2024-01-24 13:23:13,122] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf44fe234-8688-41bc-ac51-01b1bed50d18/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:23:13,122] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf44fe234-8688-41bc-ac51-01b1bed50d18/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:23:13,142] [INFO] Found 23 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:23:13,142] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:23:13,142] [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
Paracoccus aurantiacus	strain=TK008	GCA_007993065.1	2599412	2599412	type	True	80.8991	610	1252	95	below_threshold
Paracoccus isoporae	strain=DSM 22220	GCA_900101865.1	591205	591205	type	True	80.6327	584	1252	95	below_threshold
Paracoccus xiamenensis	strain=12-3	GCA_011308835.1	2714901	2714901	type	True	80.3788	604	1252	95	below_threshold
Paracoccus jeotgali	strain=CBA4604	GCA_002865605.1	2065379	2065379	type	True	79.5064	499	1252	95	below_threshold
Paracoccus halophilus	strain=CGMCC 1.6117	GCA_900111785.1	376733	376733	type	True	79.0087	365	1252	95	below_threshold
Paracoccus halophilus	strain=JCM 14014	GCA_000763905.1	376733	376733	type	True	78.9647	358	1252	95	below_threshold
Paracoccus tegillarcae	strain=BM15	GCA_002847305.1	1529068	1529068	type	True	78.7512	342	1252	95	below_threshold
Paracoccus caeni	strain=MJ17	GCA_016629665.1	657651	657651	type	True	78.6465	350	1252	95	below_threshold
Paracoccus siganidrum	strain=M26	GCA_003709565.1	1276757	1276757	type	True	78.5125	385	1252	95	below_threshold
Paracoccus denitrificans	strain=NBRC 102528	GCA_007989485.1	266	266	type	True	78.2923	346	1252	95	below_threshold
Paracoccus versutus	strain=DSM 582	GCA_000763885.1	34007	34007	type	True	78.2727	344	1252	95	below_threshold
Paracoccus litorisediminis	strain=NBRC 112902	GCA_009711205.1	2006130	2006130	type	True	78.2057	372	1252	95	below_threshold
Paracoccus solventivorans	strain=DSM 6637	GCA_900142875.1	53463	53463	type	True	77.94	265	1252	95	below_threshold
Paracoccus salsus	strain=EGI L200073	GCA_021556615.1	2911061	2911061	type	True	77.9115	309	1252	95	below_threshold
Thioclava pacifica	strain=DSM 10166	GCA_000714535.1	285109	285109	type	True	77.7331	211	1252	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	77.613	184	1252	95	below_threshold
Gemmobacter fulva	strain=con5	GCA_018798885.1	2840474	2840474	type	True	77.5497	247	1252	95	below_threshold
Sinirhodobacter hankyongi	strain=BO-81	GCA_003664585.1	2294033	2294033	type	True	77.472	223	1252	95	below_threshold
Halovulum dunhuangense	strain=YYQ-30	GCA_013093415.1	1505036	1505036	type	True	77.2749	153	1252	95	below_threshold
Gemmobacter aquatilis	strain=DSM 3857	GCA_900110025.1	933059	933059	type	True	77.1753	243	1252	95	below_threshold
Pseudooceanicola nanhaiensis	strain=CGMCC 1.6293	GCA_014645095.1	375761	375761	type	True	77.105	186	1252	95	below_threshold
Roseovarius litoreus	strain=DSM 28249	GCA_900142765.1	1155722	1155722	type	True	77.0999	175	1252	95	below_threshold
Pseudooceanicola nanhaiensis	strain=DSM 18065	GCA_000688295.1	375761	375761	type	True	77.0699	188	1252	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:23:13,144] [INFO] DFAST Taxonomy check result was written to GCF_027913035.1_ASM2791303v1_genomic.fna/tc_result.tsv
[2024-01-24 13:23:13,144] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:23:13,145] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:23:13,145] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf44fe234-8688-41bc-ac51-01b1bed50d18/dqc_reference/checkm_data
[2024-01-24 13:23:13,146] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:23:13,188] [INFO] Task started: CheckM
[2024-01-24 13:23:13,188] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_027913035.1_ASM2791303v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_027913035.1_ASM2791303v1_genomic.fna/checkm_input GCF_027913035.1_ASM2791303v1_genomic.fna/checkm_result
[2024-01-24 13:23:50,235] [INFO] Task succeeded: CheckM
[2024-01-24 13:23:50,237] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:23:50,259] [INFO] ===== Completeness check finished =====
[2024-01-24 13:23:50,259] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:23:50,260] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_027913035.1_ASM2791303v1_genomic.fna/markers.fasta)
[2024-01-24 13:23:50,260] [INFO] Task started: Blastn
[2024-01-24 13:23:50,260] [INFO] Running command: blastn -query GCF_027913035.1_ASM2791303v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf44fe234-8688-41bc-ac51-01b1bed50d18/dqc_reference/reference_markers_gtdb.fasta -out GCF_027913035.1_ASM2791303v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:23:51,837] [INFO] Task succeeded: Blastn
[2024-01-24 13:23:51,840] [INFO] Selected 15 target genomes.
[2024-01-24 13:23:51,840] [INFO] Target genome list was writen to GCF_027913035.1_ASM2791303v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:23:51,890] [INFO] Task started: fastANI
[2024-01-24 13:23:51,890] [INFO] Running command: fastANI --query /var/lib/cwl/stgaaa14b4d-9042-49de-90b1-4e2948977159/GCF_027913035.1_ASM2791303v1_genomic.fna.gz --refList GCF_027913035.1_ASM2791303v1_genomic.fna/target_genomes_gtdb.txt --output GCF_027913035.1_ASM2791303v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:24:02,055] [INFO] Task succeeded: fastANI
[2024-01-24 13:24:02,080] [INFO] Found 15 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:24:02,081] [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
GCA_005768755.1	s__Paracoccus denitrificans_B	80.9812	647	1252	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007993065.1	s__Paracoccus aurantiacus	80.9032	609	1252	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900101865.1	s__Paracoccus isoporae	80.6327	584	1252	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011308835.1	s__Paracoccus xiamenensis	80.3813	603	1252	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013868135.1	s__Paracoccus sp013868135	80.145	566	1252	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002865605.1	s__Paracoccus jeotgali	79.4824	497	1252	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	96.34	96.34	0.97	0.97	2	-
GCF_000763905.1	s__Paracoccus halophilus	78.9629	360	1252	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	100.00	100.00	0.99	0.99	2	-
GCF_009711265.1	s__Paracoccus sp009711265	78.5412	363	1252	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_009711205.1	s__Paracoccus litorisediminis	78.2296	369	1252	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	97.39	97.39	0.92	0.92	2	-
GCA_018056045.1	s__Paracoccus sp018056045	78.2292	240	1252	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001447385.1	s__Paracoccus sp001447385	78.0346	384	1252	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003664585.1	s__Paenirhodobacter hankyongi	77.4462	225	1252	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paenirhodobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016869835.1	s__KMS-5 sp016869835	77.102	142	1252	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__KMS-5	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000688295.1	s__Pseudooceanicola nanhaiensis	77.0693	188	1252	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	100.00	100.00	1.00	1.00	2	-
GCA_001314715.1	s__Pararhodobacter sp001314715	76.9441	175	1252	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pararhodobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:24:02,082] [INFO] GTDB search result was written to GCF_027913035.1_ASM2791303v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:24:02,083] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:24:02,087] [INFO] DFAST_QC result json was written to GCF_027913035.1_ASM2791303v1_genomic.fna/dqc_result.json
[2024-01-24 13:24:02,087] [INFO] DFAST_QC completed!
[2024-01-24 13:24:02,087] [INFO] Total running time: 0h1m22s