[2024-01-24 12:37:09,695] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:37:09,697] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:37:09,697] [INFO] DQC Reference Directory: /var/lib/cwl/stg2058c50f-b1e3-48a8-9c1b-20a6b26efa71/dqc_reference
[2024-01-24 12:37:11,067] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:37:11,068] [INFO] Task started: Prodigal
[2024-01-24 12:37:11,068] [INFO] Running command: gunzip -c /var/lib/cwl/stg92736b61-24a3-4184-a5c5-775fc8602377/GCF_004343075.1_ASM434307v1_genomic.fna.gz | prodigal -d GCF_004343075.1_ASM434307v1_genomic.fna/cds.fna -a GCF_004343075.1_ASM434307v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:37:22,540] [INFO] Task succeeded: Prodigal
[2024-01-24 12:37:22,541] [INFO] Task started: HMMsearch
[2024-01-24 12:37:22,541] [INFO] Running command: hmmsearch --tblout GCF_004343075.1_ASM434307v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2058c50f-b1e3-48a8-9c1b-20a6b26efa71/dqc_reference/reference_markers.hmm GCF_004343075.1_ASM434307v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:37:22,823] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:37:22,825] [INFO] Found 6/6 markers.
[2024-01-24 12:37:22,864] [INFO] Query marker FASTA was written to GCF_004343075.1_ASM434307v1_genomic.fna/markers.fasta
[2024-01-24 12:37:22,864] [INFO] Task started: Blastn
[2024-01-24 12:37:22,865] [INFO] Running command: blastn -query GCF_004343075.1_ASM434307v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2058c50f-b1e3-48a8-9c1b-20a6b26efa71/dqc_reference/reference_markers.fasta -out GCF_004343075.1_ASM434307v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:37:23,841] [INFO] Task succeeded: Blastn
[2024-01-24 12:37:23,845] [INFO] Selected 14 target genomes.
[2024-01-24 12:37:23,846] [INFO] Target genome list was writen to GCF_004343075.1_ASM434307v1_genomic.fna/target_genomes.txt
[2024-01-24 12:37:23,854] [INFO] Task started: fastANI
[2024-01-24 12:37:23,855] [INFO] Running command: fastANI --query /var/lib/cwl/stg92736b61-24a3-4184-a5c5-775fc8602377/GCF_004343075.1_ASM434307v1_genomic.fna.gz --refList GCF_004343075.1_ASM434307v1_genomic.fna/target_genomes.txt --output GCF_004343075.1_ASM434307v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:37:35,397] [INFO] Task succeeded: fastANI
[2024-01-24 12:37:35,398] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2058c50f-b1e3-48a8-9c1b-20a6b26efa71/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:37:35,398] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2058c50f-b1e3-48a8-9c1b-20a6b26efa71/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:37:35,410] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:37:35,410] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:37:35,410] [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
Rhodovulum marinum	strain=DSM 18063	GCA_004343075.1	320662	320662	type	True	100.0	1291	1295	95	conclusive
Rhodovulum euryhalinum	strain=DSM 4868	GCA_004342445.1	35805	35805	type	True	85.4259	907	1295	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	84.7625	835	1295	95	below_threshold
Rhodovulum steppense	strain=DSM 21153	GCA_004339675.1	540251	540251	type	True	84.3244	855	1295	95	below_threshold
Rhodovulum strictum	strain=DSM 11289	GCA_009649175.1	58314	58314	type	True	83.837	795	1295	95	below_threshold
Rhodovulum adriaticum	strain=DSM 2781	GCA_004345735.1	35804	35804	type	True	82.4961	719	1295	95	below_threshold
Rhodovulum adriaticum	strain=DSM 2781	GCA_016583705.1	35804	35804	type	True	82.4927	716	1295	95	below_threshold
Rhodovulum visakhapatnamense	strain=JA181	GCA_004365965.1	364297	364297	type	True	82.153	791	1295	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	79.0668	483	1295	95	below_threshold
Paracoccus binzhouensis	strain=wg1	GCA_016446475.1	2796149	2796149	type	True	79.0411	493	1295	95	below_threshold
Salipiger marinus	strain=DSM 26424	GCA_900100085.1	555512	555512	type	True	78.7555	528	1295	95	below_threshold
Pseudooceanicola onchidii	strain=XY-99	GCA_004959925.1	2562279	2562279	type	True	78.6167	433	1295	95	below_threshold
Palleronia sediminis	strain=SS33	GCA_004358695.1	2547833	2547833	type	True	78.3296	440	1295	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	78.1072	380	1295	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:37:35,412] [INFO] DFAST Taxonomy check result was written to GCF_004343075.1_ASM434307v1_genomic.fna/tc_result.tsv
[2024-01-24 12:37:35,412] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:37:35,412] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:37:35,413] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2058c50f-b1e3-48a8-9c1b-20a6b26efa71/dqc_reference/checkm_data
[2024-01-24 12:37:35,414] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:37:35,453] [INFO] Task started: CheckM
[2024-01-24 12:37:35,453] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004343075.1_ASM434307v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004343075.1_ASM434307v1_genomic.fna/checkm_input GCF_004343075.1_ASM434307v1_genomic.fna/checkm_result
[2024-01-24 12:38:13,294] [INFO] Task succeeded: CheckM
[2024-01-24 12:38:13,296] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:38:13,319] [INFO] ===== Completeness check finished =====
[2024-01-24 12:38:13,320] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:38:13,320] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004343075.1_ASM434307v1_genomic.fna/markers.fasta)
[2024-01-24 12:38:13,320] [INFO] Task started: Blastn
[2024-01-24 12:38:13,321] [INFO] Running command: blastn -query GCF_004343075.1_ASM434307v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2058c50f-b1e3-48a8-9c1b-20a6b26efa71/dqc_reference/reference_markers_gtdb.fasta -out GCF_004343075.1_ASM434307v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:38:15,173] [INFO] Task succeeded: Blastn
[2024-01-24 12:38:15,178] [INFO] Selected 13 target genomes.
[2024-01-24 12:38:15,178] [INFO] Target genome list was writen to GCF_004343075.1_ASM434307v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:38:15,186] [INFO] Task started: fastANI
[2024-01-24 12:38:15,187] [INFO] Running command: fastANI --query /var/lib/cwl/stg92736b61-24a3-4184-a5c5-775fc8602377/GCF_004343075.1_ASM434307v1_genomic.fna.gz --refList GCF_004343075.1_ASM434307v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004343075.1_ASM434307v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:38:26,190] [INFO] Task succeeded: fastANI
[2024-01-24 12:38:26,201] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:38:26,202] [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_004343075.1	s__Rhodovulum marinum	100.0	1291	1295	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_004342445.1	s__Rhodovulum euryhalinum	85.4142	908	1295	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004339675.1	s__Rhodovulum steppense	84.3285	855	1295	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142935.1	s__Rhodovulum sp900142935	84.1692	883	1295	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011048875.1	s__Rhodovulum sp011048875	84.1007	593	1295	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009649175.1	s__Rhodovulum strictum	83.8517	793	1295	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004345735.1	s__Rhodovulum adriaticum	82.4478	724	1295	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	99.99	99.99	0.99	0.99	2	-
GCF_004365965.1	s__Rhodovulum visakhapatnamense	82.1119	795	1295	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	98.55	98.44	0.90	0.89	5	-
GCF_004343505.1	s__Rhodovulum bhavnagarense	81.8975	622	1295	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003053725.1	s__Rhodovulum kholense	81.7719	786	1295	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	98.27	98.27	0.96	0.96	2	-
GCF_002073975.1	s__Rhodovulum sp002073975	80.9678	748	1295	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004799285.1	s__Gemmobacter_D aestuarii	78.8996	495	1295	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002834145.1	s__Roseovarius salinarum	78.8656	449	1295	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:38:26,203] [INFO] GTDB search result was written to GCF_004343075.1_ASM434307v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:38:26,204] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:38:26,209] [INFO] DFAST_QC result json was written to GCF_004343075.1_ASM434307v1_genomic.fna/dqc_result.json
[2024-01-24 12:38:26,209] [INFO] DFAST_QC completed!
[2024-01-24 12:38:26,209] [INFO] Total running time: 0h1m17s