[2024-01-24 14:14:37,194] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:14:37,198] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:14:37,199] [INFO] DQC Reference Directory: /var/lib/cwl/stg4e0a3430-feec-405a-94f2-d2d55b440acf/dqc_reference
[2024-01-24 14:14:38,904] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:14:38,907] [INFO] Task started: Prodigal
[2024-01-24 14:14:38,907] [INFO] Running command: gunzip -c /var/lib/cwl/stgb614a8f9-7c6a-4f7c-ab44-ba18e92adfbb/GCF_004360155.1_ASM436015v1_genomic.fna.gz | prodigal -d GCF_004360155.1_ASM436015v1_genomic.fna/cds.fna -a GCF_004360155.1_ASM436015v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:14:48,746] [INFO] Task succeeded: Prodigal
[2024-01-24 14:14:48,747] [INFO] Task started: HMMsearch
[2024-01-24 14:14:48,747] [INFO] Running command: hmmsearch --tblout GCF_004360155.1_ASM436015v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4e0a3430-feec-405a-94f2-d2d55b440acf/dqc_reference/reference_markers.hmm GCF_004360155.1_ASM436015v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:14:49,210] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:14:49,212] [INFO] Found 6/6 markers.
[2024-01-24 14:14:49,262] [INFO] Query marker FASTA was written to GCF_004360155.1_ASM436015v1_genomic.fna/markers.fasta
[2024-01-24 14:14:49,262] [INFO] Task started: Blastn
[2024-01-24 14:14:49,263] [INFO] Running command: blastn -query GCF_004360155.1_ASM436015v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4e0a3430-feec-405a-94f2-d2d55b440acf/dqc_reference/reference_markers.fasta -out GCF_004360155.1_ASM436015v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:14:52,795] [INFO] Task succeeded: Blastn
[2024-01-24 14:14:52,799] [INFO] Selected 18 target genomes.
[2024-01-24 14:14:52,799] [INFO] Target genome list was writen to GCF_004360155.1_ASM436015v1_genomic.fna/target_genomes.txt
[2024-01-24 14:14:52,823] [INFO] Task started: fastANI
[2024-01-24 14:14:52,823] [INFO] Running command: fastANI --query /var/lib/cwl/stgb614a8f9-7c6a-4f7c-ab44-ba18e92adfbb/GCF_004360155.1_ASM436015v1_genomic.fna.gz --refList GCF_004360155.1_ASM436015v1_genomic.fna/target_genomes.txt --output GCF_004360155.1_ASM436015v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:15:06,455] [INFO] Task succeeded: fastANI
[2024-01-24 14:15:06,456] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4e0a3430-feec-405a-94f2-d2d55b440acf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:15:06,456] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4e0a3430-feec-405a-94f2-d2d55b440acf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:15:06,468] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:15:06,468] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:15:06,468] [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
Paraglaciecola marina	strain=D3211	GCA_004360155.1	2500157	2500157	type	True	100.0	1511	1514	95	conclusive
Paraglaciecola aquimarina	strain=GGW-M5	GCA_021532655.1	1235557	1235557	type	True	78.5322	275	1514	95	below_threshold
Paraglaciecola psychrophila	strain=170	GCA_000347635.1	326544	326544	type	True	78.2854	249	1514	95	below_threshold
Paraglaciecola arctica	strain=BSs20135	GCA_000314995.1	1128911	1128911	type	True	78.2421	329	1514	95	below_threshold
Paraglaciecola psychrophila	strain=170	GCA_000315075.1	326544	326544	type	True	78.1689	254	1514	95	below_threshold
Paraglaciecola hydrolytica	strain=S66	GCA_001565895.1	1799789	1799789	type	True	77.6834	181	1514	95	below_threshold
Glaciecola nitratireducens	strain=FR1064	GCA_000226565.1	300231	300231	type	True	77.4498	67	1514	95	below_threshold
Aliiglaciecola lipolytica	strain=E3	GCA_000314975.1	477689	477689	type	True	77.4141	108	1514	95	below_threshold
Alteromonas lipolytica	strain=JW12	GCA_001758465.1	1856405	1856405	type	True	77.3915	69	1514	95	below_threshold
Alteromonas naphthalenivorans	strain=SN2	GCA_000213655.1	715451	715451	type	True	77.1498	91	1514	95	below_threshold
Paraneptunicella aestuarii	strain=NBU2194	GCA_019900845.1	2831148	2831148	type	True	76.6181	66	1514	95	below_threshold
Pseudoalteromonas espejiana	strain=NBRC 102222	GCA_007989585.1	28107	28107	type	True	76.5895	58	1514	95	below_threshold
Pseudoalteromonas espejiana	strain=ATCC 29659	GCA_002221525.1	28107	28107	type	True	76.5311	63	1514	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:15:06,470] [INFO] DFAST Taxonomy check result was written to GCF_004360155.1_ASM436015v1_genomic.fna/tc_result.tsv
[2024-01-24 14:15:06,471] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:15:06,471] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:15:06,471] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4e0a3430-feec-405a-94f2-d2d55b440acf/dqc_reference/checkm_data
[2024-01-24 14:15:06,472] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:15:06,517] [INFO] Task started: CheckM
[2024-01-24 14:15:06,518] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004360155.1_ASM436015v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004360155.1_ASM436015v1_genomic.fna/checkm_input GCF_004360155.1_ASM436015v1_genomic.fna/checkm_result
[2024-01-24 14:15:40,862] [INFO] Task succeeded: CheckM
[2024-01-24 14:15:40,864] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:15:40,886] [INFO] ===== Completeness check finished =====
[2024-01-24 14:15:40,887] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:15:40,887] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004360155.1_ASM436015v1_genomic.fna/markers.fasta)
[2024-01-24 14:15:40,888] [INFO] Task started: Blastn
[2024-01-24 14:15:40,888] [INFO] Running command: blastn -query GCF_004360155.1_ASM436015v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4e0a3430-feec-405a-94f2-d2d55b440acf/dqc_reference/reference_markers_gtdb.fasta -out GCF_004360155.1_ASM436015v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:15:41,977] [INFO] Task succeeded: Blastn
[2024-01-24 14:15:41,981] [INFO] Selected 17 target genomes.
[2024-01-24 14:15:41,981] [INFO] Target genome list was writen to GCF_004360155.1_ASM436015v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:15:41,993] [INFO] Task started: fastANI
[2024-01-24 14:15:41,994] [INFO] Running command: fastANI --query /var/lib/cwl/stgb614a8f9-7c6a-4f7c-ab44-ba18e92adfbb/GCF_004360155.1_ASM436015v1_genomic.fna.gz --refList GCF_004360155.1_ASM436015v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004360155.1_ASM436015v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:15:56,969] [INFO] Task succeeded: fastANI
[2024-01-24 14:15:57,028] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:15:57,028] [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_004360155.1	s__Paraglaciecola sp004360155	100.0	1511	1514	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Paraglaciecola	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_018861065.1	s__Paraglaciecola arctica_B	78.5524	290	1514	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Paraglaciecola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009796765.1	s__Paraglaciecola sp009796765	78.5339	308	1514	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Paraglaciecola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003232445.1	s__Paraglaciecola arctica_A	78.5116	188	1514	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Paraglaciecola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002835935.1	s__Paraglaciecola sp002835935	78.3146	265	1514	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Paraglaciecola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000347635.1	s__Paraglaciecola psychrophila	78.3008	248	1514	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Paraglaciecola	95.0	99.98	99.98	1.00	1.00	2	-
GCF_000314995.1	s__Paraglaciecola arctica	78.2306	330	1514	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Paraglaciecola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001758465.1	s__Alteromonas lipolytica	77.4119	70	1514	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	99.99	99.99	1.00	1.00	2	-
GCA_001562115.1	s__Alteromonas stellipolaris	77.3614	91	1514	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	99.45	98.97	0.97	0.94	8	-
GCF_000213655.1	s__Alteromonas naphthalenivorans	77.1223	92	1514	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	97.31	95.95	0.86	0.84	6	-
GCF_018100795.1	s__Alteromonas sp018100795	76.9387	98	1514	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014077505.1	s__Cognaticolwellia sp014077505	76.7446	63	1514	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:15:57,030] [INFO] GTDB search result was written to GCF_004360155.1_ASM436015v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:15:57,031] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:15:57,035] [INFO] DFAST_QC result json was written to GCF_004360155.1_ASM436015v1_genomic.fna/dqc_result.json
[2024-01-24 14:15:57,035] [INFO] DFAST_QC completed!
[2024-01-24 14:15:57,035] [INFO] Total running time: 0h1m20s