[2024-01-24 12:16:08,616] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:16:08,618] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:16:08,618] [INFO] DQC Reference Directory: /var/lib/cwl/stg9fa712d1-e581-4029-964c-129ab6a60561/dqc_reference
[2024-01-24 12:16:09,900] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:16:09,901] [INFO] Task started: Prodigal
[2024-01-24 12:16:09,901] [INFO] Running command: gunzip -c /var/lib/cwl/stgf4838184-d1af-467e-acf3-7f3f20af7eed/GCF_019249215.1_ASM1924921v1_genomic.fna.gz | prodigal -d GCF_019249215.1_ASM1924921v1_genomic.fna/cds.fna -a GCF_019249215.1_ASM1924921v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:16:20,477] [INFO] Task succeeded: Prodigal
[2024-01-24 12:16:20,478] [INFO] Task started: HMMsearch
[2024-01-24 12:16:20,478] [INFO] Running command: hmmsearch --tblout GCF_019249215.1_ASM1924921v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9fa712d1-e581-4029-964c-129ab6a60561/dqc_reference/reference_markers.hmm GCF_019249215.1_ASM1924921v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:16:20,790] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:16:20,792] [INFO] Found 6/6 markers.
[2024-01-24 12:16:20,838] [INFO] Query marker FASTA was written to GCF_019249215.1_ASM1924921v1_genomic.fna/markers.fasta
[2024-01-24 12:16:20,839] [INFO] Task started: Blastn
[2024-01-24 12:16:20,839] [INFO] Running command: blastn -query GCF_019249215.1_ASM1924921v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9fa712d1-e581-4029-964c-129ab6a60561/dqc_reference/reference_markers.fasta -out GCF_019249215.1_ASM1924921v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:16:21,618] [INFO] Task succeeded: Blastn
[2024-01-24 12:16:21,622] [INFO] Selected 17 target genomes.
[2024-01-24 12:16:21,622] [INFO] Target genome list was writen to GCF_019249215.1_ASM1924921v1_genomic.fna/target_genomes.txt
[2024-01-24 12:16:21,629] [INFO] Task started: fastANI
[2024-01-24 12:16:21,629] [INFO] Running command: fastANI --query /var/lib/cwl/stgf4838184-d1af-467e-acf3-7f3f20af7eed/GCF_019249215.1_ASM1924921v1_genomic.fna.gz --refList GCF_019249215.1_ASM1924921v1_genomic.fna/target_genomes.txt --output GCF_019249215.1_ASM1924921v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:16:35,140] [INFO] Task succeeded: fastANI
[2024-01-24 12:16:35,141] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9fa712d1-e581-4029-964c-129ab6a60561/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:16:35,141] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9fa712d1-e581-4029-964c-129ab6a60561/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:16:35,152] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:16:35,152] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:16:35,152] [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 lipotrueae	strain=MD_652	GCA_019249215.1	2803814	2803814	type	True	100.0	1561	1563	95	conclusive
Alteromonas naphthalenivorans	strain=SN2	GCA_000213655.1	715451	715451	type	True	92.9154	1298	1563	95	below_threshold
Alteromonas australica	strain=H 17	GCA_000730385.1	589873	589873	type	True	80.3527	459	1563	95	below_threshold
Alteromonas mediterranea	strain=DE	GCA_000020585.3	314275	314275	type	True	79.3533	415	1563	95	below_threshold
Alteromonas profundi	strain=345S023	GCA_010500865.1	2696062	2696062	type	True	79.0707	416	1563	95	below_threshold
Alteromonas gracilis	strain=9a2	GCA_002993325.1	1479524	1479524	type	True	79.0213	398	1563	95	below_threshold
Alteromonas macleodii	strain=ATCC 27126	GCA_000172635.2	28108	28108	type	True	79.0171	399	1563	95	below_threshold
Alteromonas portus	strain=HB161718	GCA_005117025.1	2565549	2565549	type	True	78.9938	404	1563	95	below_threshold
Alteromonas abrolhosensis	strain=PEL67E	GCA_001953635.1	1892904	1892904	type	True	78.9148	421	1563	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:16:35,154] [INFO] DFAST Taxonomy check result was written to GCF_019249215.1_ASM1924921v1_genomic.fna/tc_result.tsv
[2024-01-24 12:16:35,155] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:16:35,155] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:16:35,156] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9fa712d1-e581-4029-964c-129ab6a60561/dqc_reference/checkm_data
[2024-01-24 12:16:35,157] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:16:35,208] [INFO] Task started: CheckM
[2024-01-24 12:16:35,209] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019249215.1_ASM1924921v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019249215.1_ASM1924921v1_genomic.fna/checkm_input GCF_019249215.1_ASM1924921v1_genomic.fna/checkm_result
[2024-01-24 12:17:11,132] [INFO] Task succeeded: CheckM
[2024-01-24 12:17:11,133] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:17:11,157] [INFO] ===== Completeness check finished =====
[2024-01-24 12:17:11,158] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:17:11,158] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019249215.1_ASM1924921v1_genomic.fna/markers.fasta)
[2024-01-24 12:17:11,159] [INFO] Task started: Blastn
[2024-01-24 12:17:11,159] [INFO] Running command: blastn -query GCF_019249215.1_ASM1924921v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9fa712d1-e581-4029-964c-129ab6a60561/dqc_reference/reference_markers_gtdb.fasta -out GCF_019249215.1_ASM1924921v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:17:12,283] [INFO] Task succeeded: Blastn
[2024-01-24 12:17:12,287] [INFO] Selected 8 target genomes.
[2024-01-24 12:17:12,287] [INFO] Target genome list was writen to GCF_019249215.1_ASM1924921v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:17:12,294] [INFO] Task started: fastANI
[2024-01-24 12:17:12,295] [INFO] Running command: fastANI --query /var/lib/cwl/stgf4838184-d1af-467e-acf3-7f3f20af7eed/GCF_019249215.1_ASM1924921v1_genomic.fna.gz --refList GCF_019249215.1_ASM1924921v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019249215.1_ASM1924921v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:17:20,339] [INFO] Task succeeded: fastANI
[2024-01-24 12:17:20,351] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:17:20,351] [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_902506055.1	s__Alteromonas lipotrueae	99.4427	1503	1563	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	99.66	99.49	0.97	0.95	4	conclusive
GCF_000213655.1	s__Alteromonas naphthalenivorans	92.9492	1295	1563	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	89.7259	1284	1563	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001562115.1	s__Alteromonas stellipolaris	89.6501	1334	1563	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	99.45	98.97	0.97	0.94	8	-
GCF_000730385.1	s__Alteromonas australica	80.3597	457	1563	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	79.1689	376	1563	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010500865.1	s__Alteromonas profundi	79.0816	415	1563	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002993325.1	s__Alteromonas gracilis	79.006	398	1563	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	96.94	96.21	0.87	0.84	4	-
--------------------------------------------------------------------------------
[2024-01-24 12:17:20,353] [INFO] GTDB search result was written to GCF_019249215.1_ASM1924921v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:17:20,354] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:17:20,357] [INFO] DFAST_QC result json was written to GCF_019249215.1_ASM1924921v1_genomic.fna/dqc_result.json
[2024-01-24 12:17:20,357] [INFO] DFAST_QC completed!
[2024-01-24 12:17:20,357] [INFO] Total running time: 0h1m12s