[2023-06-29 06:34:22,387] [INFO] DFAST_QC pipeline started.
[2023-06-29 06:34:22,390] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 06:34:22,390] [INFO] DQC Reference Directory: /var/lib/cwl/stg627d99f7-0c1c-4ac7-91d9-c051c92444df/dqc_reference
[2023-06-29 06:34:24,284] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 06:34:24,285] [INFO] Task started: Prodigal
[2023-06-29 06:34:24,285] [INFO] Running command: gunzip -c /var/lib/cwl/stg639bdc8e-db2d-4c8d-8067-e2cd4585b73b/GCA_020628265.1_ASM2062826v1_genomic.fna.gz | prodigal -d GCA_020628265.1_ASM2062826v1_genomic.fna/cds.fna -a GCA_020628265.1_ASM2062826v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 06:34:30,123] [INFO] Task succeeded: Prodigal
[2023-06-29 06:34:30,124] [INFO] Task started: HMMsearch
[2023-06-29 06:34:30,124] [INFO] Running command: hmmsearch --tblout GCA_020628265.1_ASM2062826v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg627d99f7-0c1c-4ac7-91d9-c051c92444df/dqc_reference/reference_markers.hmm GCA_020628265.1_ASM2062826v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 06:34:30,325] [INFO] Task succeeded: HMMsearch
[2023-06-29 06:34:30,327] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg639bdc8e-db2d-4c8d-8067-e2cd4585b73b/GCA_020628265.1_ASM2062826v1_genomic.fna.gz]
[2023-06-29 06:34:30,355] [INFO] Query marker FASTA was written to GCA_020628265.1_ASM2062826v1_genomic.fna/markers.fasta
[2023-06-29 06:34:30,355] [INFO] Task started: Blastn
[2023-06-29 06:34:30,355] [INFO] Running command: blastn -query GCA_020628265.1_ASM2062826v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg627d99f7-0c1c-4ac7-91d9-c051c92444df/dqc_reference/reference_markers.fasta -out GCA_020628265.1_ASM2062826v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 06:34:31,066] [INFO] Task succeeded: Blastn
[2023-06-29 06:34:31,071] [INFO] Selected 19 target genomes.
[2023-06-29 06:34:31,072] [INFO] Target genome list was writen to GCA_020628265.1_ASM2062826v1_genomic.fna/target_genomes.txt
[2023-06-29 06:34:31,076] [INFO] Task started: fastANI
[2023-06-29 06:34:31,076] [INFO] Running command: fastANI --query /var/lib/cwl/stg639bdc8e-db2d-4c8d-8067-e2cd4585b73b/GCA_020628265.1_ASM2062826v1_genomic.fna.gz --refList GCA_020628265.1_ASM2062826v1_genomic.fna/target_genomes.txt --output GCA_020628265.1_ASM2062826v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 06:34:41,807] [INFO] Task succeeded: fastANI
[2023-06-29 06:34:41,807] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg627d99f7-0c1c-4ac7-91d9-c051c92444df/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 06:34:41,808] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg627d99f7-0c1c-4ac7-91d9-c051c92444df/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 06:34:41,823] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 06:34:41,823] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 06:34:41,823] [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
Pseudooctadecabacter jejudonensis	strain=CECT 8397	GCA_900172275.1	1391910	1391910	type	True	79.6793	335	569	95	below_threshold
Thalassorhabdomicrobium marinisediminis	strain=BH-SD16	GCA_003072065.1	2170577	2170577	type	True	78.744	247	569	95	below_threshold
Salibaculum griseiflavum	strain=WDS4C29	GCA_003129565.1	1914409	1914409	type	True	77.6774	194	569	95	below_threshold
Octadecabacter temperatus	strain=SB1	GCA_001187845.1	1458307	1458307	type	True	77.5717	163	569	95	below_threshold
Octadecabacter temperatus	strain=DSM 26878	GCA_900142425.1	1458307	1458307	type	True	77.5673	164	569	95	below_threshold
Roseovarius bejariae	strain=A21	GCA_009669325.1	2576383	2576383	type	True	77.4855	115	569	95	below_threshold
Octadecabacter ascidiaceicola	strain=CECT 8868	GCA_900185015.1	1655543	1655543	type	True	77.4612	188	569	95	below_threshold
Sulfitobacter indolifex	strain=DSM 14862	GCA_022788655.1	225422	225422	type	True	77.3966	107	569	95	below_threshold
Roseovarius pacificus	strain=CGMCC 1.7083	GCA_014645335.1	337701	337701	type	True	77.2886	120	569	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	77.2522	104	569	95	below_threshold
Phaeobacter piscinae	strain=P14	GCA_002407245.1	1580596	1580596	type	True	77.1293	110	569	95	below_threshold
Roseovarius nubinhibens	strain=ISM	GCA_000152625.1	314263	314263	type	True	77.1173	118	569	95	below_threshold
Phaeobacter gallaeciensis	strain=DSM 26640	GCA_000819625.1	60890	60890	type	True	77.1063	103	569	95	below_threshold
Phaeobacter gallaeciensis	strain=DSM 26640	GCA_000511385.1	60890	60890	type	True	77.0828	105	569	95	below_threshold
Pelagivirga sediminicola	strain=BH-SD19	GCA_003072125.1	2170575	2170575	type	True	77.0072	103	569	95	below_threshold
Paracoccus zeaxanthinifaciens	strain=ATCC 21588	GCA_000420145.1	187400	187400	type	True	76.7837	83	569	95	below_threshold
Paracoccus nototheniae	strain=I-41R45	GCA_004335005.1	2489002	2489002	type	True	76.7154	83	569	95	below_threshold
Palleronia rufa	strain=MOLA 401	GCA_000743715.1	1530186	1530186	type	True	76.5475	83	569	95	below_threshold
Paracoccus mutanolyticus	strain=RSP-02	GCA_003285265.1	1499308	1499308	type	True	76.4248	70	569	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 06:34:41,825] [INFO] DFAST Taxonomy check result was written to GCA_020628265.1_ASM2062826v1_genomic.fna/tc_result.tsv
[2023-06-29 06:34:41,826] [INFO] ===== Taxonomy check completed =====
[2023-06-29 06:34:41,826] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 06:34:41,826] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg627d99f7-0c1c-4ac7-91d9-c051c92444df/dqc_reference/checkm_data
[2023-06-29 06:34:41,827] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 06:34:41,850] [INFO] Task started: CheckM
[2023-06-29 06:34:41,850] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_020628265.1_ASM2062826v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_020628265.1_ASM2062826v1_genomic.fna/checkm_input GCA_020628265.1_ASM2062826v1_genomic.fna/checkm_result
[2023-06-29 06:35:05,199] [INFO] Task succeeded: CheckM
[2023-06-29 06:35:05,201] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 49.54%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-29 06:35:05,224] [INFO] ===== Completeness check finished =====
[2023-06-29 06:35:05,224] [INFO] ===== Start GTDB Search =====
[2023-06-29 06:35:05,225] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_020628265.1_ASM2062826v1_genomic.fna/markers.fasta)
[2023-06-29 06:35:05,225] [INFO] Task started: Blastn
[2023-06-29 06:35:05,225] [INFO] Running command: blastn -query GCA_020628265.1_ASM2062826v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg627d99f7-0c1c-4ac7-91d9-c051c92444df/dqc_reference/reference_markers_gtdb.fasta -out GCA_020628265.1_ASM2062826v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 06:35:06,229] [INFO] Task succeeded: Blastn
[2023-06-29 06:35:06,234] [INFO] Selected 17 target genomes.
[2023-06-29 06:35:06,234] [INFO] Target genome list was writen to GCA_020628265.1_ASM2062826v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 06:35:06,241] [INFO] Task started: fastANI
[2023-06-29 06:35:06,241] [INFO] Running command: fastANI --query /var/lib/cwl/stg639bdc8e-db2d-4c8d-8067-e2cd4585b73b/GCA_020628265.1_ASM2062826v1_genomic.fna.gz --refList GCA_020628265.1_ASM2062826v1_genomic.fna/target_genomes_gtdb.txt --output GCA_020628265.1_ASM2062826v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 06:35:16,416] [INFO] Task succeeded: fastANI
[2023-06-29 06:35:16,435] [INFO] Found 17 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 06:35:16,435] [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_900172275.1	s__Pseudooctadecabacter jejudonensis	79.6793	335	569	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooctadecabacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003072065.1	s__Thalassorhabdomicrobium marinisediminis	78.744	247	569	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassorhabdomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018608045.1	s__Octadecabacter sp018608045	77.713	171	569	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Octadecabacter	95.0	98.68	98.68	0.85	0.85	2	-
GCF_003129565.1	s__Salibaculum griseiflavum	77.6774	194	569	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001187845.1	s__Octadecabacter temperatus	77.5911	162	569	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Octadecabacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_009669325.1	s__Roseovarius bejariae	77.4855	115	569	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900185015.1	s__Octadecabacter ascidiaceicola	77.4612	188	569	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Octadecabacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004799325.1	s__Thalassobius vesicularis	77.4552	137	569	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000220565.1	s__Pseudooceanicola sp000220565	77.1448	112	569	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001969365.1	s__Tateyamaria omphalii_A	77.1401	153	569	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tateyamaria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002407245.1	s__Phaeobacter piscinae	77.1293	110	569	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Phaeobacter	95.0	97.42	96.04	0.93	0.90	10	-
GCA_003533975.1	s__Octadecabacter sp003533975	77.1068	121	569	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Octadecabacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000511385.1	s__Phaeobacter gallaeciensis	77.0828	105	569	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Phaeobacter	95.0	99.42	98.01	0.98	0.96	8	-
GCF_001679925.1	s__Leisingera sp001679925	77.0426	125	569	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003072125.1	s__Roseovarius sediminicola	77.0072	103	569	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000420145.1	s__Paracoccus zeaxanthinifaciens	76.7837	83	569	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003651245.1	s__Roseovarius spongiae	76.5758	107	569	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 06:35:16,437] [INFO] GTDB search result was written to GCA_020628265.1_ASM2062826v1_genomic.fna/result_gtdb.tsv
[2023-06-29 06:35:16,437] [INFO] ===== GTDB Search completed =====
[2023-06-29 06:35:16,443] [INFO] DFAST_QC result json was written to GCA_020628265.1_ASM2062826v1_genomic.fna/dqc_result.json
[2023-06-29 06:35:16,444] [INFO] DFAST_QC completed!
[2023-06-29 06:35:16,444] [INFO] Total running time: 0h0m54s