[2024-01-24 12:44:19,019] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:44:19,021] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:44:19,021] [INFO] DQC Reference Directory: /var/lib/cwl/stg7e45fa20-867f-4038-86a0-c0f458a71929/dqc_reference
[2024-01-24 12:44:20,231] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:44:20,232] [INFO] Task started: Prodigal
[2024-01-24 12:44:20,232] [INFO] Running command: gunzip -c /var/lib/cwl/stg2117443c-bae3-42f7-aff1-ea65a3c9b36a/GCF_007995055.1_ASM799505v1_genomic.fna.gz | prodigal -d GCF_007995055.1_ASM799505v1_genomic.fna/cds.fna -a GCF_007995055.1_ASM799505v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:44:28,587] [INFO] Task succeeded: Prodigal
[2024-01-24 12:44:28,588] [INFO] Task started: HMMsearch
[2024-01-24 12:44:28,588] [INFO] Running command: hmmsearch --tblout GCF_007995055.1_ASM799505v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7e45fa20-867f-4038-86a0-c0f458a71929/dqc_reference/reference_markers.hmm GCF_007995055.1_ASM799505v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:44:28,838] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:44:28,839] [INFO] Found 6/6 markers.
[2024-01-24 12:44:28,867] [INFO] Query marker FASTA was written to GCF_007995055.1_ASM799505v1_genomic.fna/markers.fasta
[2024-01-24 12:44:28,868] [INFO] Task started: Blastn
[2024-01-24 12:44:28,868] [INFO] Running command: blastn -query GCF_007995055.1_ASM799505v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7e45fa20-867f-4038-86a0-c0f458a71929/dqc_reference/reference_markers.fasta -out GCF_007995055.1_ASM799505v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:44:29,862] [INFO] Task succeeded: Blastn
[2024-01-24 12:44:29,866] [INFO] Selected 21 target genomes.
[2024-01-24 12:44:29,867] [INFO] Target genome list was writen to GCF_007995055.1_ASM799505v1_genomic.fna/target_genomes.txt
[2024-01-24 12:44:29,933] [INFO] Task started: fastANI
[2024-01-24 12:44:29,933] [INFO] Running command: fastANI --query /var/lib/cwl/stg2117443c-bae3-42f7-aff1-ea65a3c9b36a/GCF_007995055.1_ASM799505v1_genomic.fna.gz --refList GCF_007995055.1_ASM799505v1_genomic.fna/target_genomes.txt --output GCF_007995055.1_ASM799505v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:44:45,362] [INFO] Task succeeded: fastANI
[2024-01-24 12:44:45,363] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7e45fa20-867f-4038-86a0-c0f458a71929/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:44:45,364] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7e45fa20-867f-4038-86a0-c0f458a71929/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:44:45,383] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:44:45,383] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:44:45,384] [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
Sphingosinicella ginsenosidimutans	strain=BS-11	GCA_007995055.1	1176539	1176539	type	True	100.0	1011	1013	95	conclusive
Sphingomonas parva	strain=17J27-24	GCA_004564275.1	2555898	2555898	type	True	79.8168	509	1013	95	below_threshold
Sphingosinicella humi	strain=QZX222	GCA_003129465.1	2068657	2068657	type	True	79.6947	493	1013	95	below_threshold
Sphingomonas oleivorans	strain=FW-11	GCA_003050615.1	1735121	1735121	type	True	78.9772	354	1013	95	below_threshold
Sphingomonas deserti	strain=GL-C-18	GCA_003012735.1	2116704	2116704	type	True	78.8874	492	1013	95	below_threshold
Sphingomonas changnyeongensis	strain=C33	GCA_009913435.1	2698679	2698679	type	True	78.8246	364	1013	95	below_threshold
Sphingomonas flavalba	strain=ZLT-5	GCA_004796535.1	2559804	2559804	type	True	78.7784	385	1013	95	below_threshold
Rhizorhabdus dicambivorans	strain=Ndbn-20	GCA_002355275.1	1850238	1850238	type	True	78.7529	412	1013	95	below_threshold
Sphingomonas mesophila	strain=SYSUP0001	GCA_003499275.1	2303576	2303576	type	True	78.6865	319	1013	95	below_threshold
Sphingomonas oligoaromativorans	strain=DSM 102246	GCA_011762195.1	575322	575322	type	True	78.6474	401	1013	95	below_threshold
Sphingomonas ginsengisoli An et al. 2013	strain=KACC 16858	GCA_009363895.1	363835	363835	type	True	78.5994	348	1013	95	below_threshold
Sphingomonas colocasiae	strain=JCM 31229	GCA_019880585.1	1848973	1848973	type	True	78.4742	442	1013	95	below_threshold
Sphingomonas morindae	strain=NBD5	GCA_023822065.1	1541170	1541170	type	True	78.3803	400	1013	95	below_threshold
Sphingomonas formosensis	strain=CC-Nfb-2	GCA_009755815.1	861534	861534	type	True	78.3216	417	1013	95	below_threshold
Sphingosinithalassobacter tenebrarum	strain=zrk23	GCA_011057975.1	2711215	2711215	type	True	78.2935	356	1013	95	below_threshold
Sphingomonas glacialis	strain=CGMCC 1.8957	GCA_014653575.1	658225	658225	type	True	78.2268	354	1013	95	below_threshold
Sphingomonas folli	strain=RHCKR7	GCA_019429525.1	2862497	2862497	type	True	78.1862	415	1013	95	below_threshold
Sphingomonas aracearum	strain=WZY 27	GCA_003345355.1	2283317	2283317	type	True	78.048	334	1013	95	below_threshold
Sphingobium cloacae	strain=JCM 10874	GCA_002355855.1	120107	120107	type	True	77.8452	306	1013	95	below_threshold
Novosphingobium aerophilum	strain=4Y4	GCA_014230305.1	2839843	2839843	type	True	77.7221	277	1013	95	below_threshold
Sphingomonas prati	strain=DSM 103336	GCA_014199405.1	1843237	1843237	type	True	77.6511	319	1013	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:44:45,385] [INFO] DFAST Taxonomy check result was written to GCF_007995055.1_ASM799505v1_genomic.fna/tc_result.tsv
[2024-01-24 12:44:45,386] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:44:45,386] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:44:45,386] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7e45fa20-867f-4038-86a0-c0f458a71929/dqc_reference/checkm_data
[2024-01-24 12:44:45,387] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:44:45,421] [INFO] Task started: CheckM
[2024-01-24 12:44:45,422] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007995055.1_ASM799505v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007995055.1_ASM799505v1_genomic.fna/checkm_input GCF_007995055.1_ASM799505v1_genomic.fna/checkm_result
[2024-01-24 12:45:25,477] [INFO] Task succeeded: CheckM
[2024-01-24 12:45:25,478] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:45:25,502] [INFO] ===== Completeness check finished =====
[2024-01-24 12:45:25,503] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:45:25,503] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007995055.1_ASM799505v1_genomic.fna/markers.fasta)
[2024-01-24 12:45:25,503] [INFO] Task started: Blastn
[2024-01-24 12:45:25,504] [INFO] Running command: blastn -query GCF_007995055.1_ASM799505v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7e45fa20-867f-4038-86a0-c0f458a71929/dqc_reference/reference_markers_gtdb.fasta -out GCF_007995055.1_ASM799505v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:45:27,340] [INFO] Task succeeded: Blastn
[2024-01-24 12:45:27,343] [INFO] Selected 12 target genomes.
[2024-01-24 12:45:27,343] [INFO] Target genome list was writen to GCF_007995055.1_ASM799505v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:45:27,385] [INFO] Task started: fastANI
[2024-01-24 12:45:27,385] [INFO] Running command: fastANI --query /var/lib/cwl/stg2117443c-bae3-42f7-aff1-ea65a3c9b36a/GCF_007995055.1_ASM799505v1_genomic.fna.gz --refList GCF_007995055.1_ASM799505v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007995055.1_ASM799505v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:45:36,725] [INFO] Task succeeded: fastANI
[2024-01-24 12:45:36,735] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:45:36,735] [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_007995055.1	s__Allosphingosinicella ginsenosidimutans	100.0	1012	1013	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Allosphingosinicella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_019239785.1	s__Allosphingosinicella sp019239785	80.7296	505	1013	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Allosphingosinicella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005883305.1	s__Allosphingosinicella sp005883305	80.6168	562	1013	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Allosphingosinicella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900177405.1	s__Allosphingosinicella indica	80.203	477	1013	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Allosphingosinicella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003347635.1	s__Allosphingosinicella sp003347635	80.1843	604	1013	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Allosphingosinicella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004564275.1	s__Allosphingosinicella parva	79.7849	512	1013	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Allosphingosinicella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019232625.1	s__Allosphingosinicella sp019232625	79.567	512	1013	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Allosphingosinicella	95.0	99.90	99.89	0.98	0.97	3	-
GCA_019239415.1	s__Allosphingosinicella sp019239415	79.5403	483	1013	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Allosphingosinicella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004151485.1	s__Allosphingosinicella sp004151485	79.5161	526	1013	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Allosphingosinicella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004341505.2	s__Sphingomonas sp004341505	78.523	338	1013	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	95.45	95.45	0.78	0.78	2	-
GCF_009755815.1	s__Sphingomonas_M formosensis	78.3286	416	1013	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_M	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011057975.1	s__Sphingomonas sp011057975	78.3005	356	1013	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:45:36,737] [INFO] GTDB search result was written to GCF_007995055.1_ASM799505v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:45:36,737] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:45:36,741] [INFO] DFAST_QC result json was written to GCF_007995055.1_ASM799505v1_genomic.fna/dqc_result.json
[2024-01-24 12:45:36,741] [INFO] DFAST_QC completed!
[2024-01-24 12:45:36,741] [INFO] Total running time: 0h1m18s