[2024-01-24 13:28:28,988] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:28:28,990] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:28:28,990] [INFO] DQC Reference Directory: /var/lib/cwl/stgb87708dd-8e46-44fd-91af-e38ef355a176/dqc_reference
[2024-01-24 13:28:30,278] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:28:30,279] [INFO] Task started: Prodigal
[2024-01-24 13:28:30,280] [INFO] Running command: gunzip -c /var/lib/cwl/stg5f741a90-1ecf-45a2-861a-166f32bd6a36/GCF_014164585.1_ASM1416458v1_genomic.fna.gz | prodigal -d GCF_014164585.1_ASM1416458v1_genomic.fna/cds.fna -a GCF_014164585.1_ASM1416458v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:28:42,659] [INFO] Task succeeded: Prodigal
[2024-01-24 13:28:42,660] [INFO] Task started: HMMsearch
[2024-01-24 13:28:42,660] [INFO] Running command: hmmsearch --tblout GCF_014164585.1_ASM1416458v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb87708dd-8e46-44fd-91af-e38ef355a176/dqc_reference/reference_markers.hmm GCF_014164585.1_ASM1416458v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:28:42,994] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:28:42,996] [INFO] Found 6/6 markers.
[2024-01-24 13:28:43,052] [INFO] Query marker FASTA was written to GCF_014164585.1_ASM1416458v1_genomic.fna/markers.fasta
[2024-01-24 13:28:43,052] [INFO] Task started: Blastn
[2024-01-24 13:28:43,052] [INFO] Running command: blastn -query GCF_014164585.1_ASM1416458v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb87708dd-8e46-44fd-91af-e38ef355a176/dqc_reference/reference_markers.fasta -out GCF_014164585.1_ASM1416458v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:28:43,803] [INFO] Task succeeded: Blastn
[2024-01-24 13:28:43,806] [INFO] Selected 23 target genomes.
[2024-01-24 13:28:43,806] [INFO] Target genome list was writen to GCF_014164585.1_ASM1416458v1_genomic.fna/target_genomes.txt
[2024-01-24 13:28:43,817] [INFO] Task started: fastANI
[2024-01-24 13:28:43,817] [INFO] Running command: fastANI --query /var/lib/cwl/stg5f741a90-1ecf-45a2-861a-166f32bd6a36/GCF_014164585.1_ASM1416458v1_genomic.fna.gz --refList GCF_014164585.1_ASM1416458v1_genomic.fna/target_genomes.txt --output GCF_014164585.1_ASM1416458v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:28:58,440] [INFO] Task succeeded: fastANI
[2024-01-24 13:28:58,441] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb87708dd-8e46-44fd-91af-e38ef355a176/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:28:58,441] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb87708dd-8e46-44fd-91af-e38ef355a176/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:28:58,452] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:28:58,452] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:28:58,453] [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
Oceanospirillum beijerinckii	strain=DSM 7166	GCA_000422425.1	64976	64976	type	True	82.2177	608	1794	95	below_threshold
Oceanospirillum sanctuarii	strain=AK56	GCA_002150805.1	1434821	1434821	type	True	79.4688	374	1794	95	below_threshold
Oceanospirillum linum	strain=ATCC 11336	GCA_001995095.2	966	966	type	True	78.7607	300	1794	95	below_threshold
Oceanospirillum multiglobuliferum	strain=ATCC 33336	GCA_002059185.1	64969	64969	type	True	78.5065	204	1794	95	below_threshold
Oceanospirillum multiglobuliferum	strain=ATCC 33336	GCA_900167095.1	64969	64969	type	True	78.4229	209	1794	95	below_threshold
Oceanospirillum maris	strain=DSM 6286	GCA_000422865.1	64977	64977	type	True	78.3359	239	1794	95	below_threshold
Amphritea japonica	strain=ATCC BAA-1530	GCA_016592435.1	452627	452627	type	True	77.3455	76	1794	95	below_threshold
Amphritea japonica	strain=JCM 14782	GCA_024347275.1	452627	452627	type	True	77.247	80	1794	95	below_threshold
Marinobacterium jannaschii	strain=DSM 6295	GCA_000620085.1	64970	64970	type	True	76.8528	108	1794	95	below_threshold
Marinospirillum celere	strain=DSM 18438	GCA_900112235.1	1122252	1122252	type	True	76.6381	64	1794	95	below_threshold
Oceanobacter mangrovi	strain=SM2-42	GCA_019740315.1	2862510	2862510	type	True	76.517	85	1794	95	below_threshold
Endozoicomonas numazuensis	strain=DSM 25634	GCA_000722635.1	1137799	1137799	type	True	76.4895	52	1794	95	below_threshold
Marinobacterium profundum	strain=PAMC 27536	GCA_001528745.1	1714300	1714300	type	True	76.1274	51	1794	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:28:58,454] [INFO] DFAST Taxonomy check result was written to GCF_014164585.1_ASM1416458v1_genomic.fna/tc_result.tsv
[2024-01-24 13:28:58,455] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:28:58,455] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:28:58,456] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb87708dd-8e46-44fd-91af-e38ef355a176/dqc_reference/checkm_data
[2024-01-24 13:28:58,458] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:28:58,512] [INFO] Task started: CheckM
[2024-01-24 13:28:58,512] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014164585.1_ASM1416458v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014164585.1_ASM1416458v1_genomic.fna/checkm_input GCF_014164585.1_ASM1416458v1_genomic.fna/checkm_result
[2024-01-24 13:29:41,579] [INFO] Task succeeded: CheckM
[2024-01-24 13:29:41,580] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 8.33%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:29:41,601] [INFO] ===== Completeness check finished =====
[2024-01-24 13:29:41,601] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:29:41,602] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014164585.1_ASM1416458v1_genomic.fna/markers.fasta)
[2024-01-24 13:29:41,602] [INFO] Task started: Blastn
[2024-01-24 13:29:41,602] [INFO] Running command: blastn -query GCF_014164585.1_ASM1416458v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb87708dd-8e46-44fd-91af-e38ef355a176/dqc_reference/reference_markers_gtdb.fasta -out GCF_014164585.1_ASM1416458v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:29:42,786] [INFO] Task succeeded: Blastn
[2024-01-24 13:29:42,790] [INFO] Selected 16 target genomes.
[2024-01-24 13:29:42,790] [INFO] Target genome list was writen to GCF_014164585.1_ASM1416458v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:29:42,803] [INFO] Task started: fastANI
[2024-01-24 13:29:42,803] [INFO] Running command: fastANI --query /var/lib/cwl/stg5f741a90-1ecf-45a2-861a-166f32bd6a36/GCF_014164585.1_ASM1416458v1_genomic.fna.gz --refList GCF_014164585.1_ASM1416458v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014164585.1_ASM1416458v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:29:54,691] [INFO] Task succeeded: fastANI
[2024-01-24 13:29:54,706] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:29:54,706] [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_014164585.1	s__Oceanospirillum sp014164585	100.0	1788	1794	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Oceanospirillum	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000422425.1	s__Oceanospirillum beijerinckii	82.2281	607	1794	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Oceanospirillum	95.0	98.77	98.77	0.90	0.90	2	-
GCF_002150805.1	s__Oceanospirillum sanctuarii	79.4688	374	1794	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Oceanospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001995095.2	s__Oceanospirillum linum	78.7607	300	1794	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Oceanospirillum	95.0	99.99	99.99	0.99	0.99	2	-
GCF_900167095.1	s__Oceanospirillum multiglobuliferum	78.4229	209	1794	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Oceanospirillum	95.0	99.98	99.98	0.99	0.99	2	-
GCF_000422865.1	s__Oceanospirillum maris	78.302	240	1794	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Oceanospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000620085.1	s__Marinobacterium_B jannaschii	76.901	107	1794	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018067325.1	s__Amphritea sp018067325	76.5424	70	1794	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Amphritea	95.0	99.51	99.51	0.92	0.92	2	-
GCF_001528745.1	s__Marinobacterium_A profundum	76.1884	51	1794	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:29:54,708] [INFO] GTDB search result was written to GCF_014164585.1_ASM1416458v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:29:54,708] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:29:54,712] [INFO] DFAST_QC result json was written to GCF_014164585.1_ASM1416458v1_genomic.fna/dqc_result.json
[2024-01-24 13:29:54,712] [INFO] DFAST_QC completed!
[2024-01-24 13:29:54,712] [INFO] Total running time: 0h1m26s