[2024-01-24 13:09:34,052] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:09:34,054] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:09:34,054] [INFO] DQC Reference Directory: /var/lib/cwl/stg9dc50331-6697-43f5-bf3d-59ad26a74c7a/dqc_reference
[2024-01-24 13:09:35,384] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:09:35,385] [INFO] Task started: Prodigal
[2024-01-24 13:09:35,385] [INFO] Running command: gunzip -c /var/lib/cwl/stg33be4b78-39b0-4351-a151-ee3b871d7de2/GCF_000447205.1_ABySS_v1.3.3_genomic.fna.gz | prodigal -d GCF_000447205.1_ABySS_v1.3.3_genomic.fna/cds.fna -a GCF_000447205.1_ABySS_v1.3.3_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:09:48,733] [INFO] Task succeeded: Prodigal
[2024-01-24 13:09:48,734] [INFO] Task started: HMMsearch
[2024-01-24 13:09:48,734] [INFO] Running command: hmmsearch --tblout GCF_000447205.1_ABySS_v1.3.3_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9dc50331-6697-43f5-bf3d-59ad26a74c7a/dqc_reference/reference_markers.hmm GCF_000447205.1_ABySS_v1.3.3_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:09:49,016] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:09:49,017] [INFO] Found 6/6 markers.
[2024-01-24 13:09:49,065] [INFO] Query marker FASTA was written to GCF_000447205.1_ABySS_v1.3.3_genomic.fna/markers.fasta
[2024-01-24 13:09:49,065] [INFO] Task started: Blastn
[2024-01-24 13:09:49,066] [INFO] Running command: blastn -query GCF_000447205.1_ABySS_v1.3.3_genomic.fna/markers.fasta -db /var/lib/cwl/stg9dc50331-6697-43f5-bf3d-59ad26a74c7a/dqc_reference/reference_markers.fasta -out GCF_000447205.1_ABySS_v1.3.3_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:09:50,055] [INFO] Task succeeded: Blastn
[2024-01-24 13:09:50,058] [INFO] Selected 18 target genomes.
[2024-01-24 13:09:50,058] [INFO] Target genome list was writen to GCF_000447205.1_ABySS_v1.3.3_genomic.fna/target_genomes.txt
[2024-01-24 13:09:50,066] [INFO] Task started: fastANI
[2024-01-24 13:09:50,066] [INFO] Running command: fastANI --query /var/lib/cwl/stg33be4b78-39b0-4351-a151-ee3b871d7de2/GCF_000447205.1_ABySS_v1.3.3_genomic.fna.gz --refList GCF_000447205.1_ABySS_v1.3.3_genomic.fna/target_genomes.txt --output GCF_000447205.1_ABySS_v1.3.3_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:10:06,816] [INFO] Task succeeded: fastANI
[2024-01-24 13:10:06,817] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9dc50331-6697-43f5-bf3d-59ad26a74c7a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:10:06,817] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9dc50331-6697-43f5-bf3d-59ad26a74c7a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:10:06,832] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:10:06,832] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:10:06,832] [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
Sphingobium ummariense	strain=RL-3	GCA_000447205.1	420994	420994	type	True	100.0	1497	1516	95	conclusive
Sphingobium indicum	strain=B90A	GCA_000264945.2	332055	332055	type	True	84.3104	770	1516	95	below_threshold
Sphingobium baderi	strain=LL03	GCA_000445145.1	1332080	1332080	type	True	83.5152	660	1516	95	below_threshold
Sphingobium fuliginis	strain=DSM 18781	GCA_004152845.1	336203	336203	type	True	83.426	777	1516	95	below_threshold
Sphingobium baderi	strain=LL03	GCA_001046655.1	1332080	1332080	type	True	83.3456	645	1516	95	below_threshold
Sphingobium fuliginis	strain=CCM 7327	GCA_014636045.1	336203	336203	type	True	83.3322	771	1516	95	below_threshold
Sphingobium cloacae	strain=JCM 10874	GCA_002355855.1	120107	120107	type	True	83.1551	675	1516	95	below_threshold
Sphingobium wenxiniae	strain=JZ-1	GCA_014205735.1	595605	595605	type	True	83.0733	647	1516	95	below_threshold
Sphingobium wenxiniae	strain=CGMCC 1.7748	GCA_007830065.1	595605	595605	type	True	83.0477	652	1516	95	below_threshold
Sphingobium cloacae	strain=NBRC 102517	GCA_001591285.1	120107	120107	type	True	83.0118	653	1516	95	below_threshold
Sphingobium amiense	strain=DSM 16289	GCA_003967075.1	135719	135719	type	True	82.8205	736	1516	95	below_threshold
Sphingobium chungbukense	strain=DJ77	GCA_001005725.1	56193	56193	type	True	82.5845	759	1516	95	below_threshold
Sphingobium bisphenolivorans	strain=YL23	GCA_000412635.1	1335760	1335760	type	True	82.422	653	1516	95	below_threshold
Sphingomonas changnyeongensis	strain=C33	GCA_009913435.1	2698679	2698679	type	True	78.539	389	1516	95	below_threshold
Sphingomonas aracearum	strain=WZY 27	GCA_003345355.1	2283317	2283317	type	True	78.4561	388	1516	95	below_threshold
Sphingomonas profundi	strain=LMO-1	GCA_009739515.1	2681549	2681549	type	True	78.4515	441	1516	95	below_threshold
Sphingomonas citri	strain=RRHST34	GCA_019429485.1	2862499	2862499	type	True	78.1982	436	1516	95	below_threshold
Sphingomonas hylomeconis	strain=CCTCC AB 2013304	GCA_025370105.1	1395958	1395958	type	True	78.1141	381	1516	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:10:06,834] [INFO] DFAST Taxonomy check result was written to GCF_000447205.1_ABySS_v1.3.3_genomic.fna/tc_result.tsv
[2024-01-24 13:10:06,835] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:10:06,835] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:10:06,836] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9dc50331-6697-43f5-bf3d-59ad26a74c7a/dqc_reference/checkm_data
[2024-01-24 13:10:06,837] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:10:06,882] [INFO] Task started: CheckM
[2024-01-24 13:10:06,882] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000447205.1_ABySS_v1.3.3_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000447205.1_ABySS_v1.3.3_genomic.fna/checkm_input GCF_000447205.1_ABySS_v1.3.3_genomic.fna/checkm_result
[2024-01-24 13:10:46,325] [INFO] Task succeeded: CheckM
[2024-01-24 13:10:46,326] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:10:46,343] [INFO] ===== Completeness check finished =====
[2024-01-24 13:10:46,343] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:10:46,344] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000447205.1_ABySS_v1.3.3_genomic.fna/markers.fasta)
[2024-01-24 13:10:46,344] [INFO] Task started: Blastn
[2024-01-24 13:10:46,344] [INFO] Running command: blastn -query GCF_000447205.1_ABySS_v1.3.3_genomic.fna/markers.fasta -db /var/lib/cwl/stg9dc50331-6697-43f5-bf3d-59ad26a74c7a/dqc_reference/reference_markers_gtdb.fasta -out GCF_000447205.1_ABySS_v1.3.3_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:10:48,136] [INFO] Task succeeded: Blastn
[2024-01-24 13:10:48,139] [INFO] Selected 17 target genomes.
[2024-01-24 13:10:48,140] [INFO] Target genome list was writen to GCF_000447205.1_ABySS_v1.3.3_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:10:48,150] [INFO] Task started: fastANI
[2024-01-24 13:10:48,150] [INFO] Running command: fastANI --query /var/lib/cwl/stg33be4b78-39b0-4351-a151-ee3b871d7de2/GCF_000447205.1_ABySS_v1.3.3_genomic.fna.gz --refList GCF_000447205.1_ABySS_v1.3.3_genomic.fna/target_genomes_gtdb.txt --output GCF_000447205.1_ABySS_v1.3.3_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:11:05,572] [INFO] Task succeeded: fastANI
[2024-01-24 13:11:05,586] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:11:05,587] [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_000447205.1	s__Sphingobium ummariense	100.0	1496	1516	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_000264945.2	s__Sphingobium indicum	84.3223	770	1516	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	98.64	97.75	0.82	0.64	8	-
GCF_001563265.1	s__Sphingobium sp001563265	83.6249	800	1516	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	98.38	97.84	0.74	0.68	3	-
GCF_004152845.1	s__Sphingobium fuliginis	83.4109	779	1516	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	98.53	97.80	0.87	0.78	14	-
GCF_002355855.1	s__Sphingobium cloacae	83.1779	671	1516	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_007830065.1	s__Sphingobium wenxiniae	83.0501	650	1516	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	99.17	98.76	0.86	0.79	4	-
GCF_003967075.1	s__Sphingobium amiense	82.7965	736	1516	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	99.99	99.99	1.00	1.00	2	-
GCA_002457415.1	s__Sphingobium sp002457415	82.7002	656	1516	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013911745.1	s__Sphingobium sp013911745	82.6145	588	1516	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013375535.1	s__Sphingobium sp013375535	82.5976	733	1516	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001005725.1	s__Sphingobium chungbukense	82.5706	761	1516	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	97.77	97.77	0.72	0.72	2	-
GCF_008692605.1	s__Sphingobium estronivorans	82.4426	649	1516	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000412635.1	s__Sphingobium bisphenolivorans	82.4136	654	1516	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900100475.1	s__Sphingobium faniae	82.2696	640	1516	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001456115.1	s__Sphingobium baderi_A	82.2206	650	1516	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014873695.1	s__Sphingobium sp014873695	82.1624	738	1516	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013375555.1	s__Sphingobium sp013375555	82.1138	697	1516	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:11:05,588] [INFO] GTDB search result was written to GCF_000447205.1_ABySS_v1.3.3_genomic.fna/result_gtdb.tsv
[2024-01-24 13:11:05,589] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:11:05,593] [INFO] DFAST_QC result json was written to GCF_000447205.1_ABySS_v1.3.3_genomic.fna/dqc_result.json
[2024-01-24 13:11:05,593] [INFO] DFAST_QC completed!
[2024-01-24 13:11:05,593] [INFO] Total running time: 0h1m32s