[2024-01-25 18:57:50,483] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:57:50,489] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:57:50,489] [INFO] DQC Reference Directory: /var/lib/cwl/stg95c0a364-ee88-4436-8c6d-06da47c70d16/dqc_reference
[2024-01-25 18:57:51,616] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:57:51,617] [INFO] Task started: Prodigal
[2024-01-25 18:57:51,617] [INFO] Running command: gunzip -c /var/lib/cwl/stg6db187be-e7fb-4ade-9ac4-82d49ed8b432/GCF_010500895.1_ASM1050089v1_genomic.fna.gz | prodigal -d GCF_010500895.1_ASM1050089v1_genomic.fna/cds.fna -a GCF_010500895.1_ASM1050089v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:57:59,933] [INFO] Task succeeded: Prodigal
[2024-01-25 18:57:59,933] [INFO] Task started: HMMsearch
[2024-01-25 18:57:59,933] [INFO] Running command: hmmsearch --tblout GCF_010500895.1_ASM1050089v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg95c0a364-ee88-4436-8c6d-06da47c70d16/dqc_reference/reference_markers.hmm GCF_010500895.1_ASM1050089v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:58:00,207] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:58:00,208] [INFO] Found 6/6 markers.
[2024-01-25 18:58:00,239] [INFO] Query marker FASTA was written to GCF_010500895.1_ASM1050089v1_genomic.fna/markers.fasta
[2024-01-25 18:58:00,239] [INFO] Task started: Blastn
[2024-01-25 18:58:00,240] [INFO] Running command: blastn -query GCF_010500895.1_ASM1050089v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg95c0a364-ee88-4436-8c6d-06da47c70d16/dqc_reference/reference_markers.fasta -out GCF_010500895.1_ASM1050089v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:58:00,929] [INFO] Task succeeded: Blastn
[2024-01-25 18:58:00,932] [INFO] Selected 21 target genomes.
[2024-01-25 18:58:00,933] [INFO] Target genome list was writen to GCF_010500895.1_ASM1050089v1_genomic.fna/target_genomes.txt
[2024-01-25 18:58:00,944] [INFO] Task started: fastANI
[2024-01-25 18:58:00,945] [INFO] Running command: fastANI --query /var/lib/cwl/stg6db187be-e7fb-4ade-9ac4-82d49ed8b432/GCF_010500895.1_ASM1050089v1_genomic.fna.gz --refList GCF_010500895.1_ASM1050089v1_genomic.fna/target_genomes.txt --output GCF_010500895.1_ASM1050089v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:58:17,108] [INFO] Task succeeded: fastANI
[2024-01-25 18:58:17,109] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg95c0a364-ee88-4436-8c6d-06da47c70d16/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:58:17,109] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg95c0a364-ee88-4436-8c6d-06da47c70d16/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:58:17,116] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:58:17,116] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:58:17,116] [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
Alteromonas genovensis	strain=LMG 24078	GCA_010500895.1	471225	471225	type	True	100.0	1339	1339	95	conclusive
Alteromonas hispanica	strain=LMG 22958	GCA_010500915.1	315421	315421	type	True	82.341	763	1339	95	below_threshold
Alteromonas mediterranea	strain=DE	GCA_000020585.3	314275	314275	type	True	79.7984	432	1339	95	below_threshold
Alteromonas portus	strain=HB161718	GCA_005117025.1	2565549	2565549	type	True	79.5838	434	1339	95	below_threshold
Alteromonas macleodii	strain=ATCC 27126	GCA_000172635.2	28108	28108	type	True	79.4956	450	1339	95	below_threshold
Alteromonas abrolhosensis	strain=PEL67E	GCA_001953635.1	1892904	1892904	type	True	79.3242	453	1339	95	below_threshold
Alteromonas alba	strain=190	GCA_002993365.1	2079529	2079529	type	True	78.4773	119	1339	95	below_threshold
Alteromonas halophila	strain=KCTC 22164	GCA_014651815.1	516698	516698	type	True	78.3023	156	1339	95	below_threshold
Alteromonas oceani	strain=S35	GCA_003731635.1	2071609	2071609	type	True	78.2751	126	1339	95	below_threshold
Paraglaciecola arctica	strain=BSs20135	GCA_000314995.1	1128911	1128911	type	True	76.8851	72	1339	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:58:17,118] [INFO] DFAST Taxonomy check result was written to GCF_010500895.1_ASM1050089v1_genomic.fna/tc_result.tsv
[2024-01-25 18:58:17,119] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:58:17,119] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:58:17,119] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg95c0a364-ee88-4436-8c6d-06da47c70d16/dqc_reference/checkm_data
[2024-01-25 18:58:17,120] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:58:17,159] [INFO] Task started: CheckM
[2024-01-25 18:58:17,160] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_010500895.1_ASM1050089v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_010500895.1_ASM1050089v1_genomic.fna/checkm_input GCF_010500895.1_ASM1050089v1_genomic.fna/checkm_result
[2024-01-25 18:58:45,431] [INFO] Task succeeded: CheckM
[2024-01-25 18:58:45,432] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:58:45,449] [INFO] ===== Completeness check finished =====
[2024-01-25 18:58:45,449] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:58:45,450] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_010500895.1_ASM1050089v1_genomic.fna/markers.fasta)
[2024-01-25 18:58:45,450] [INFO] Task started: Blastn
[2024-01-25 18:58:45,450] [INFO] Running command: blastn -query GCF_010500895.1_ASM1050089v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg95c0a364-ee88-4436-8c6d-06da47c70d16/dqc_reference/reference_markers_gtdb.fasta -out GCF_010500895.1_ASM1050089v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:58:46,536] [INFO] Task succeeded: Blastn
[2024-01-25 18:58:46,539] [INFO] Selected 14 target genomes.
[2024-01-25 18:58:46,539] [INFO] Target genome list was writen to GCF_010500895.1_ASM1050089v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:58:46,557] [INFO] Task started: fastANI
[2024-01-25 18:58:46,557] [INFO] Running command: fastANI --query /var/lib/cwl/stg6db187be-e7fb-4ade-9ac4-82d49ed8b432/GCF_010500895.1_ASM1050089v1_genomic.fna.gz --refList GCF_010500895.1_ASM1050089v1_genomic.fna/target_genomes_gtdb.txt --output GCF_010500895.1_ASM1050089v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:58:58,096] [INFO] Task succeeded: fastANI
[2024-01-25 18:58:58,105] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:58:58,105] [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_010500895.1	s__Alteromonas genovensis	100.0	1339	1339	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	98.09	98.06	0.82	0.81	3	conclusive
GCF_000753865.1	s__Alteromonas sp000753865	94.6121	1192	1339	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_010500915.1	s__Alteromonas hispanica	82.3381	764	1339	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	97.81	97.72	0.82	0.79	5	-
GCA_002691625.1	s__Alteromonas sp002691625	81.3795	119	1339	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	99.62	99.31	0.91	0.90	3	-
GCF_000597705.1	s__Alteromonas sp000597705	79.5885	447	1339	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	99.20	99.20	0.96	0.96	2	-
GCF_903772925.1	s__Alteromonas macleodii_A	79.5741	462	1339	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005117025.1	s__Alteromonas portus	79.5719	435	1339	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001885075.1	s__Alteromonas sp001885075	79.5258	383	1339	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000808575.1	s__Alteromonas marina	79.5234	466	1339	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	97.44	97.44	0.91	0.91	2	-
GCF_000172635.2	s__Alteromonas macleodii	79.4904	450	1339	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	97.79	96.10	0.88	0.76	56	-
GCF_000730385.1	s__Alteromonas australica	79.3647	345	1339	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	98.80	98.45	0.91	0.74	29	-
GCF_016756315.1	s__Alteromonas sp009811495	79.3247	415	1339	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	98.33	96.67	0.93	0.86	3	-
GCF_006538345.1	s__Alteromonas sp006538345	78.5786	212	1339	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_009796765.1	s__Paraglaciecola sp009796765	77.8087	72	1339	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Paraglaciecola	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:58:58,107] [INFO] GTDB search result was written to GCF_010500895.1_ASM1050089v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:58:58,108] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:58:58,111] [INFO] DFAST_QC result json was written to GCF_010500895.1_ASM1050089v1_genomic.fna/dqc_result.json
[2024-01-25 18:58:58,111] [INFO] DFAST_QC completed!
[2024-01-25 18:58:58,111] [INFO] Total running time: 0h1m8s