[2024-01-25 18:00:50,756] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:00:50,757] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:00:50,757] [INFO] DQC Reference Directory: /var/lib/cwl/stg6c8b6c8a-4397-4e0f-a38f-37df84d76f77/dqc_reference
[2024-01-25 18:00:51,921] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:00:51,922] [INFO] Task started: Prodigal
[2024-01-25 18:00:51,922] [INFO] Running command: gunzip -c /var/lib/cwl/stgf61a7dec-a007-4f32-8e9f-73d98ac5d02e/GCF_010500865.1_ASM1050086v1_genomic.fna.gz | prodigal -d GCF_010500865.1_ASM1050086v1_genomic.fna/cds.fna -a GCF_010500865.1_ASM1050086v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:01:00,372] [INFO] Task succeeded: Prodigal
[2024-01-25 18:01:00,372] [INFO] Task started: HMMsearch
[2024-01-25 18:01:00,372] [INFO] Running command: hmmsearch --tblout GCF_010500865.1_ASM1050086v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6c8b6c8a-4397-4e0f-a38f-37df84d76f77/dqc_reference/reference_markers.hmm GCF_010500865.1_ASM1050086v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:01:00,637] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:01:00,638] [INFO] Found 6/6 markers.
[2024-01-25 18:01:00,673] [INFO] Query marker FASTA was written to GCF_010500865.1_ASM1050086v1_genomic.fna/markers.fasta
[2024-01-25 18:01:00,673] [INFO] Task started: Blastn
[2024-01-25 18:01:00,673] [INFO] Running command: blastn -query GCF_010500865.1_ASM1050086v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6c8b6c8a-4397-4e0f-a38f-37df84d76f77/dqc_reference/reference_markers.fasta -out GCF_010500865.1_ASM1050086v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:01:01,339] [INFO] Task succeeded: Blastn
[2024-01-25 18:01:01,341] [INFO] Selected 14 target genomes.
[2024-01-25 18:01:01,342] [INFO] Target genome list was writen to GCF_010500865.1_ASM1050086v1_genomic.fna/target_genomes.txt
[2024-01-25 18:01:01,357] [INFO] Task started: fastANI
[2024-01-25 18:01:01,357] [INFO] Running command: fastANI --query /var/lib/cwl/stgf61a7dec-a007-4f32-8e9f-73d98ac5d02e/GCF_010500865.1_ASM1050086v1_genomic.fna.gz --refList GCF_010500865.1_ASM1050086v1_genomic.fna/target_genomes.txt --output GCF_010500865.1_ASM1050086v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:01:12,418] [INFO] Task succeeded: fastANI
[2024-01-25 18:01:12,418] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6c8b6c8a-4397-4e0f-a38f-37df84d76f77/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:01:12,419] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6c8b6c8a-4397-4e0f-a38f-37df84d76f77/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:01:12,425] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:01:12,426] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:01:12,426] [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 profundi	strain=345S023	GCA_010500865.1	2696062	2696062	type	True	100.0	1414	1417	95	conclusive
Alteromonas australica	strain=H 17	GCA_000730385.1	589873	589873	type	True	81.4416	545	1417	95	below_threshold
Alteromonas naphthalenivorans	strain=SN2	GCA_000213655.1	715451	715451	type	True	79.716	434	1417	95	below_threshold
Alteromonas abrolhosensis	strain=PEL67E	GCA_001953635.1	1892904	1892904	type	True	79.6971	375	1417	95	below_threshold
Alteromonas gracilis	strain=9a2	GCA_002993325.1	1479524	1479524	type	True	79.6757	353	1417	95	below_threshold
Alteromonas macleodii	strain=ATCC 27126	GCA_000172635.2	28108	28108	type	True	79.4816	362	1417	95	below_threshold
Alteromonas portus	strain=HB161718	GCA_005117025.1	2565549	2565549	type	True	79.2536	357	1417	95	below_threshold
Alteromonas hispanica	strain=LMG 22958	GCA_010500915.1	315421	315421	type	True	79.1833	314	1417	95	below_threshold
Alteromonas lipotrueae	strain=MD_652	GCA_019249215.1	2803814	2803814	type	True	78.9332	408	1417	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:01:12,427] [INFO] DFAST Taxonomy check result was written to GCF_010500865.1_ASM1050086v1_genomic.fna/tc_result.tsv
[2024-01-25 18:01:12,428] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:01:12,428] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:01:12,428] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6c8b6c8a-4397-4e0f-a38f-37df84d76f77/dqc_reference/checkm_data
[2024-01-25 18:01:12,429] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:01:12,472] [INFO] Task started: CheckM
[2024-01-25 18:01:12,472] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_010500865.1_ASM1050086v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_010500865.1_ASM1050086v1_genomic.fna/checkm_input GCF_010500865.1_ASM1050086v1_genomic.fna/checkm_result
[2024-01-25 18:01:41,165] [INFO] Task succeeded: CheckM
[2024-01-25 18:01:41,166] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:01:41,203] [INFO] ===== Completeness check finished =====
[2024-01-25 18:01:41,203] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:01:41,203] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_010500865.1_ASM1050086v1_genomic.fna/markers.fasta)
[2024-01-25 18:01:41,204] [INFO] Task started: Blastn
[2024-01-25 18:01:41,204] [INFO] Running command: blastn -query GCF_010500865.1_ASM1050086v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6c8b6c8a-4397-4e0f-a38f-37df84d76f77/dqc_reference/reference_markers_gtdb.fasta -out GCF_010500865.1_ASM1050086v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:01:42,364] [INFO] Task succeeded: Blastn
[2024-01-25 18:01:42,367] [INFO] Selected 17 target genomes.
[2024-01-25 18:01:42,367] [INFO] Target genome list was writen to GCF_010500865.1_ASM1050086v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:01:42,383] [INFO] Task started: fastANI
[2024-01-25 18:01:42,383] [INFO] Running command: fastANI --query /var/lib/cwl/stgf61a7dec-a007-4f32-8e9f-73d98ac5d02e/GCF_010500865.1_ASM1050086v1_genomic.fna.gz --refList GCF_010500865.1_ASM1050086v1_genomic.fna/target_genomes_gtdb.txt --output GCF_010500865.1_ASM1050086v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:01:57,463] [INFO] Task succeeded: fastANI
[2024-01-25 18:01:57,474] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:01:57,475] [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_010500865.1	s__Alteromonas profundi	100.0	1414	1417	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000730385.1	s__Alteromonas australica	81.4498	544	1417	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	98.80	98.45	0.91	0.74	29	-
GCF_016405965.1	s__Alteromonas sp016405965	79.7206	355	1417	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000213655.1	s__Alteromonas naphthalenivorans	79.6977	436	1417	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	97.31	95.95	0.86	0.84	6	-
GCF_001953635.1	s__Alteromonas abrolhosensis	79.6839	374	1417	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	98.27	97.25	0.92	0.89	10	-
GCF_002993325.1	s__Alteromonas gracilis	79.676	353	1417	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	96.94	96.21	0.87	0.84	4	-
GCF_001885075.1	s__Alteromonas sp001885075	79.6316	336	1417	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	79.6131	372	1417	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	97.44	97.44	0.91	0.91	2	-
GCF_903772925.1	s__Alteromonas macleodii_A	79.5673	362	1417	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000172635.2	s__Alteromonas macleodii	79.4748	363	1417	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	97.79	96.10	0.88	0.76	56	-
GCF_003443615.1	s__Alteromonas sp003443615	79.4722	378	1417	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	100.00	100.00	1.00	1.00	2	-
GCA_001562115.1	s__Alteromonas stellipolaris	79.4351	410	1417	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	99.45	98.97	0.97	0.94	8	-
GCF_009811415.1	s__Alteromonas sp009811415	79.3052	343	1417	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018100795.1	s__Alteromonas sp018100795	79.2736	400	1417	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000597705.1	s__Alteromonas sp000597705	79.27	372	1417	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	99.20	99.20	0.96	0.96	2	-
GCF_005117025.1	s__Alteromonas portus	79.2536	357	1417	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902506055.1	s__Alteromonas lipotrueae	79.1779	401	1417	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	99.66	99.49	0.97	0.95	4	-
--------------------------------------------------------------------------------
[2024-01-25 18:01:57,477] [INFO] GTDB search result was written to GCF_010500865.1_ASM1050086v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:01:57,478] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:01:57,483] [INFO] DFAST_QC result json was written to GCF_010500865.1_ASM1050086v1_genomic.fna/dqc_result.json
[2024-01-25 18:01:57,484] [INFO] DFAST_QC completed!
[2024-01-25 18:01:57,484] [INFO] Total running time: 0h1m7s