[2024-01-24 14:47:08,410] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:47:08,417] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:47:08,418] [INFO] DQC Reference Directory: /var/lib/cwl/stg576268b1-0eb9-4d4a-aaf5-215fd36e6cf8/dqc_reference
[2024-01-24 14:47:09,842] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:47:09,843] [INFO] Task started: Prodigal
[2024-01-24 14:47:09,844] [INFO] Running command: gunzip -c /var/lib/cwl/stge30c653c-f52f-4f97-8002-b08694f3eccf/GCF_011602085.1_ASM1160208v1_genomic.fna.gz | prodigal -d GCF_011602085.1_ASM1160208v1_genomic.fna/cds.fna -a GCF_011602085.1_ASM1160208v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:47:25,709] [INFO] Task succeeded: Prodigal
[2024-01-24 14:47:25,709] [INFO] Task started: HMMsearch
[2024-01-24 14:47:25,709] [INFO] Running command: hmmsearch --tblout GCF_011602085.1_ASM1160208v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg576268b1-0eb9-4d4a-aaf5-215fd36e6cf8/dqc_reference/reference_markers.hmm GCF_011602085.1_ASM1160208v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:47:26,069] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:47:26,070] [INFO] Found 6/6 markers.
[2024-01-24 14:47:26,123] [INFO] Query marker FASTA was written to GCF_011602085.1_ASM1160208v1_genomic.fna/markers.fasta
[2024-01-24 14:47:26,124] [INFO] Task started: Blastn
[2024-01-24 14:47:26,124] [INFO] Running command: blastn -query GCF_011602085.1_ASM1160208v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg576268b1-0eb9-4d4a-aaf5-215fd36e6cf8/dqc_reference/reference_markers.fasta -out GCF_011602085.1_ASM1160208v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:47:26,874] [INFO] Task succeeded: Blastn
[2024-01-24 14:47:26,878] [INFO] Selected 18 target genomes.
[2024-01-24 14:47:26,878] [INFO] Target genome list was writen to GCF_011602085.1_ASM1160208v1_genomic.fna/target_genomes.txt
[2024-01-24 14:47:26,885] [INFO] Task started: fastANI
[2024-01-24 14:47:26,885] [INFO] Running command: fastANI --query /var/lib/cwl/stge30c653c-f52f-4f97-8002-b08694f3eccf/GCF_011602085.1_ASM1160208v1_genomic.fna.gz --refList GCF_011602085.1_ASM1160208v1_genomic.fna/target_genomes.txt --output GCF_011602085.1_ASM1160208v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:47:41,343] [INFO] Task succeeded: fastANI
[2024-01-24 14:47:41,344] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg576268b1-0eb9-4d4a-aaf5-215fd36e6cf8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:47:41,344] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg576268b1-0eb9-4d4a-aaf5-215fd36e6cf8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:47:41,354] [INFO] Found 11 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 14:47:41,355] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:47:41,355] [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
Pseudoteredinibacter isoporae	strain=LMG 25246	GCA_011602085.1	570281	570281	type	True	100.0	1617	1618	95	conclusive
Pseudoteredinibacter isoporae	strain=DSM 22368	GCA_014207695.1	570281	570281	type	True	99.997	1612	1618	95	conclusive
Pseudoteredinibacter isoporae	strain=DSM 22368	GCA_011683895.1	570281	570281	type	True	99.9874	1607	1618	95	conclusive
Aestuariicella hydrocarbonica	strain=JCM 30134	GCA_011602365.1	1470433	1470433	type	True	77.2684	107	1618	95	below_threshold
Aestuariicella albida	strain=HHU G3-2	GCA_018863235.1	2842452	2842452	type	True	77.0985	107	1618	95	below_threshold
Agaribacterium haliotis	strain=feces2	GCA_002312815.1	2013869	2013869	type	True	77.075	59	1618	95	below_threshold
Microbulbifer mangrovi	strain=DD-13	GCA_002009015.1	927787	927787	type	True	76.7027	62	1618	95	below_threshold
Pseudomaricurvus alcaniphilus	strain=MEBiC06469	GCA_011440395.1	1166482	1166482	type	True	76.4782	79	1618	95	below_threshold
Simiduia agarivorans	strain=DSM 21679	GCA_000420285.1	447471	447471	type	True	76.3816	82	1618	95	below_threshold
Microbulbifer celer	strain=KCTC 12973	GCA_020991125.1	435905	435905	type	True	76.3009	63	1618	95	below_threshold
Microbulbifer harenosus	strain=HB161719	GCA_005771435.1	2576840	2576840	type	True	75.8997	59	1618	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:47:41,357] [INFO] DFAST Taxonomy check result was written to GCF_011602085.1_ASM1160208v1_genomic.fna/tc_result.tsv
[2024-01-24 14:47:41,357] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:47:41,358] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:47:41,358] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg576268b1-0eb9-4d4a-aaf5-215fd36e6cf8/dqc_reference/checkm_data
[2024-01-24 14:47:41,359] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:47:41,413] [INFO] Task started: CheckM
[2024-01-24 14:47:41,414] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_011602085.1_ASM1160208v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_011602085.1_ASM1160208v1_genomic.fna/checkm_input GCF_011602085.1_ASM1160208v1_genomic.fna/checkm_result
[2024-01-24 14:48:33,431] [INFO] Task succeeded: CheckM
[2024-01-24 14:48:33,433] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:48:33,456] [INFO] ===== Completeness check finished =====
[2024-01-24 14:48:33,456] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:48:33,457] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_011602085.1_ASM1160208v1_genomic.fna/markers.fasta)
[2024-01-24 14:48:33,457] [INFO] Task started: Blastn
[2024-01-24 14:48:33,457] [INFO] Running command: blastn -query GCF_011602085.1_ASM1160208v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg576268b1-0eb9-4d4a-aaf5-215fd36e6cf8/dqc_reference/reference_markers_gtdb.fasta -out GCF_011602085.1_ASM1160208v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:48:34,626] [INFO] Task succeeded: Blastn
[2024-01-24 14:48:34,631] [INFO] Selected 22 target genomes.
[2024-01-24 14:48:34,631] [INFO] Target genome list was writen to GCF_011602085.1_ASM1160208v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:48:34,649] [INFO] Task started: fastANI
[2024-01-24 14:48:34,649] [INFO] Running command: fastANI --query /var/lib/cwl/stge30c653c-f52f-4f97-8002-b08694f3eccf/GCF_011602085.1_ASM1160208v1_genomic.fna.gz --refList GCF_011602085.1_ASM1160208v1_genomic.fna/target_genomes_gtdb.txt --output GCF_011602085.1_ASM1160208v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:48:50,716] [INFO] Task succeeded: fastANI
[2024-01-24 14:48:50,728] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:48:50,728] [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_011602085.1	s__Pseudoteredinibacter isoporae	100.0	1617	1618	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Pseudoteredinibacter	95.0	100.00	100.00	1.00	0.99	3	conclusive
GCF_011602365.1	s__Pseudomaricurvus hydrocarbonicus	77.2684	107	1618	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Pseudomaricurvus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011683955.1	s__Pseudomaricurvus alkylphenolicus	77.2243	108	1618	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Pseudomaricurvus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002312815.1	s__Agaribacterium haliotis	77.075	59	1618	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Agaribacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018863235.1	s__Pseudomaricurvus sp018863235	77.0708	106	1618	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Pseudomaricurvus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009857815.1	s__Pseudomaricurvus sp009857815	77.0171	98	1618	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Pseudomaricurvus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002707785.1	s__Pseudomaricurvus sp002707785	76.955	94	1618	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Pseudomaricurvus	95.0	99.83	99.83	0.94	0.94	2	-
GCF_004363885.1	s__Cellvibrio sp004363885	76.8322	61	1618	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Cellvibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009903625.1	s__Microbulbifer sp009903625	76.7109	74	1618	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Microbulbifer	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011440395.1	s__Pseudomaricurvus alcaniphilus	76.4581	80	1618	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Pseudomaricurvus	95.0	98.35	98.35	0.88	0.88	2	-
GCF_001639145.1	s__Microbulbifer sp001639145	76.3978	66	1618	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Microbulbifer	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014904735.1	s__Microbulbifer hainanensis	75.9298	58	1618	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Microbulbifer	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005771435.1	s__Microbulbifer harenosus	75.8997	59	1618	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Microbulbifer	95.0	98.17	98.17	0.93	0.93	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:48:50,730] [INFO] GTDB search result was written to GCF_011602085.1_ASM1160208v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:48:50,731] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:48:50,740] [INFO] DFAST_QC result json was written to GCF_011602085.1_ASM1160208v1_genomic.fna/dqc_result.json
[2024-01-24 14:48:50,740] [INFO] DFAST_QC completed!
[2024-01-24 14:48:50,740] [INFO] Total running time: 0h1m42s