[2023-06-19 15:01:21,571] [INFO] DFAST_QC pipeline started.
[2023-06-19 15:01:21,594] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 15:01:21,594] [INFO] DQC Reference Directory: /var/lib/cwl/stg2c2d3cd0-e78a-49ee-90a7-25517897670b/dqc_reference
[2023-06-19 15:01:22,794] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 15:01:22,795] [INFO] Task started: Prodigal
[2023-06-19 15:01:22,795] [INFO] Running command: gunzip -c /var/lib/cwl/stgf4972a97-bcc5-4b9e-ad1b-2eeec8467281/GCA_018335735.1_ASM1833573v1_genomic.fna.gz | prodigal -d GCA_018335735.1_ASM1833573v1_genomic.fna/cds.fna -a GCA_018335735.1_ASM1833573v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 15:01:30,240] [INFO] Task succeeded: Prodigal
[2023-06-19 15:01:30,241] [INFO] Task started: HMMsearch
[2023-06-19 15:01:30,241] [INFO] Running command: hmmsearch --tblout GCA_018335735.1_ASM1833573v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2c2d3cd0-e78a-49ee-90a7-25517897670b/dqc_reference/reference_markers.hmm GCA_018335735.1_ASM1833573v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 15:01:30,480] [INFO] Task succeeded: HMMsearch
[2023-06-19 15:01:30,481] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgf4972a97-bcc5-4b9e-ad1b-2eeec8467281/GCA_018335735.1_ASM1833573v1_genomic.fna.gz]
[2023-06-19 15:01:30,511] [INFO] Query marker FASTA was written to GCA_018335735.1_ASM1833573v1_genomic.fna/markers.fasta
[2023-06-19 15:01:30,511] [INFO] Task started: Blastn
[2023-06-19 15:01:30,511] [INFO] Running command: blastn -query GCA_018335735.1_ASM1833573v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2c2d3cd0-e78a-49ee-90a7-25517897670b/dqc_reference/reference_markers.fasta -out GCA_018335735.1_ASM1833573v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 15:01:31,188] [INFO] Task succeeded: Blastn
[2023-06-19 15:01:31,192] [INFO] Selected 15 target genomes.
[2023-06-19 15:01:31,193] [INFO] Target genome list was writen to GCA_018335735.1_ASM1833573v1_genomic.fna/target_genomes.txt
[2023-06-19 15:01:31,196] [INFO] Task started: fastANI
[2023-06-19 15:01:31,197] [INFO] Running command: fastANI --query /var/lib/cwl/stgf4972a97-bcc5-4b9e-ad1b-2eeec8467281/GCA_018335735.1_ASM1833573v1_genomic.fna.gz --refList GCA_018335735.1_ASM1833573v1_genomic.fna/target_genomes.txt --output GCA_018335735.1_ASM1833573v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 15:01:40,989] [INFO] Task succeeded: fastANI
[2023-06-19 15:01:40,990] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2c2d3cd0-e78a-49ee-90a7-25517897670b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 15:01:40,990] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2c2d3cd0-e78a-49ee-90a7-25517897670b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 15:01:41,003] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 15:01:41,003] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-19 15:01:41,003] [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
Roseovarius mucosus	strain=DSM 17069	GCA_000768555.3	215743	215743	type	True	87.913	518	763	95	below_threshold
Roseovarius azorensis	strain=DSM 100674	GCA_900109455.1	1287727	1287727	type	True	80.5984	340	763	95	below_threshold
Roseovarius tolerans	strain=DSM 11457	GCA_900109855.1	74031	74031	type	True	80.2473	336	763	95	below_threshold
Roseovarius lutimaris	strain=DSM 28463	GCA_900115165.1	1005928	1005928	type	True	79.5994	308	763	95	below_threshold
Roseovarius marisflavi	strain=DSM 29327	GCA_900142625.1	1054996	1054996	type	True	79.3295	293	763	95	below_threshold
Roseovarius gaetbuli	strain=CECT 8370	GCA_900172365.1	1356575	1356575	type	True	79.1505	305	763	95	below_threshold
Roseovarius nitratireducens	strain=TFZ	GCA_002925845.1	2044597	2044597	type	True	79.0727	239	763	95	below_threshold
Roseovarius nubinhibens	strain=ISM	GCA_000152625.1	314263	314263	type	True	78.8424	217	763	95	below_threshold
Roseovarius aestuarii	strain=KCTC 22174	GCA_019966515.1	475083	475083	type	True	77.7323	156	763	95	below_threshold
Salipiger marinus	strain=DSM 26424	GCA_900100085.1	555512	555512	type	True	77.4765	184	763	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	77.3707	133	763	95	below_threshold
Pseudooceanicola onchidii	strain=XY-99	GCA_004959925.1	2562279	2562279	type	True	77.073	110	763	95	below_threshold
Pseudophaeobacter flagellatus	strain=MA21411-1	GCA_021228235.1	2899119	2899119	type	True	76.6541	104	763	95	below_threshold
Palleronia rufa	strain=MOLA 401	GCA_000743715.1	1530186	1530186	type	True	76.5749	82	763	95	below_threshold
Zongyanglinia marina	strain=DSW4-44	GCA_005771405.1	2578117	2578117	type	True	75.9702	61	763	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-19 15:01:41,005] [INFO] DFAST Taxonomy check result was written to GCA_018335735.1_ASM1833573v1_genomic.fna/tc_result.tsv
[2023-06-19 15:01:41,007] [INFO] ===== Taxonomy check completed =====
[2023-06-19 15:01:41,007] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 15:01:41,007] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2c2d3cd0-e78a-49ee-90a7-25517897670b/dqc_reference/checkm_data
[2023-06-19 15:01:41,008] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 15:01:41,044] [INFO] Task started: CheckM
[2023-06-19 15:01:41,044] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018335735.1_ASM1833573v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018335735.1_ASM1833573v1_genomic.fna/checkm_input GCA_018335735.1_ASM1833573v1_genomic.fna/checkm_result
[2023-06-19 15:02:08,967] [INFO] Task succeeded: CheckM
[2023-06-19 15:02:08,969] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 68.75%
Contamintation: 10.23%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 15:02:09,001] [INFO] ===== Completeness check finished =====
[2023-06-19 15:02:09,001] [INFO] ===== Start GTDB Search =====
[2023-06-19 15:02:09,002] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018335735.1_ASM1833573v1_genomic.fna/markers.fasta)
[2023-06-19 15:02:09,002] [INFO] Task started: Blastn
[2023-06-19 15:02:09,002] [INFO] Running command: blastn -query GCA_018335735.1_ASM1833573v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2c2d3cd0-e78a-49ee-90a7-25517897670b/dqc_reference/reference_markers_gtdb.fasta -out GCA_018335735.1_ASM1833573v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 15:02:10,082] [INFO] Task succeeded: Blastn
[2023-06-19 15:02:10,087] [INFO] Selected 5 target genomes.
[2023-06-19 15:02:10,088] [INFO] Target genome list was writen to GCA_018335735.1_ASM1833573v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 15:02:10,093] [INFO] Task started: fastANI
[2023-06-19 15:02:10,093] [INFO] Running command: fastANI --query /var/lib/cwl/stgf4972a97-bcc5-4b9e-ad1b-2eeec8467281/GCA_018335735.1_ASM1833573v1_genomic.fna.gz --refList GCA_018335735.1_ASM1833573v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018335735.1_ASM1833573v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 15:02:14,409] [INFO] Task succeeded: fastANI
[2023-06-19 15:02:14,421] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 15:02:14,421] [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_002080415.1	s__Roseovarius mucosus_A	96.1115	605	763	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	97.86	96.11	0.91	0.79	6	conclusive
GCF_000768555.3	s__Roseovarius mucosus	87.913	518	763	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	96.95	96.93	0.91	0.89	3	-
GCA_018066915.1	s__Roseovarius sp018066915	87.5964	479	763	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	99.88	99.88	0.93	0.93	2	-
GCF_000152845.1	s__Roseovarius sp000152845	85.6098	495	763	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	97.99	97.99	0.83	0.83	2	-
GCF_000744325.1	s__Roseovarius sp000744325	83.8437	458	763	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-19 15:02:14,425] [INFO] GTDB search result was written to GCA_018335735.1_ASM1833573v1_genomic.fna/result_gtdb.tsv
[2023-06-19 15:02:14,428] [INFO] ===== GTDB Search completed =====
[2023-06-19 15:02:14,435] [INFO] DFAST_QC result json was written to GCA_018335735.1_ASM1833573v1_genomic.fna/dqc_result.json
[2023-06-19 15:02:14,435] [INFO] DFAST_QC completed!
[2023-06-19 15:02:14,435] [INFO] Total running time: 0h0m53s