[2023-06-13 12:39:39,389] [INFO] DFAST_QC pipeline started.
[2023-06-13 12:39:39,392] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 12:39:39,392] [INFO] DQC Reference Directory: /var/lib/cwl/stgf5e3de51-eab7-41dc-8747-bd70d334cda6/dqc_reference
[2023-06-13 12:39:41,031] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 12:39:41,032] [INFO] Task started: Prodigal
[2023-06-13 12:39:41,032] [INFO] Running command: gunzip -c /var/lib/cwl/stg841ca942-037a-4198-99e8-9e9690cde45e/GCA_022448445.1_ASM2244844v1_genomic.fna.gz | prodigal -d GCA_022448445.1_ASM2244844v1_genomic.fna/cds.fna -a GCA_022448445.1_ASM2244844v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 12:39:51,332] [INFO] Task succeeded: Prodigal
[2023-06-13 12:39:51,334] [INFO] Task started: HMMsearch
[2023-06-13 12:39:51,334] [INFO] Running command: hmmsearch --tblout GCA_022448445.1_ASM2244844v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf5e3de51-eab7-41dc-8747-bd70d334cda6/dqc_reference/reference_markers.hmm GCA_022448445.1_ASM2244844v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 12:39:51,606] [INFO] Task succeeded: HMMsearch
[2023-06-13 12:39:51,608] [INFO] Found 6/6 markers.
[2023-06-13 12:39:51,650] [INFO] Query marker FASTA was written to GCA_022448445.1_ASM2244844v1_genomic.fna/markers.fasta
[2023-06-13 12:39:51,650] [INFO] Task started: Blastn
[2023-06-13 12:39:51,650] [INFO] Running command: blastn -query GCA_022448445.1_ASM2244844v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf5e3de51-eab7-41dc-8747-bd70d334cda6/dqc_reference/reference_markers.fasta -out GCA_022448445.1_ASM2244844v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 12:39:52,339] [INFO] Task succeeded: Blastn
[2023-06-13 12:39:52,343] [INFO] Selected 17 target genomes.
[2023-06-13 12:39:52,344] [INFO] Target genome list was writen to GCA_022448445.1_ASM2244844v1_genomic.fna/target_genomes.txt
[2023-06-13 12:39:52,346] [INFO] Task started: fastANI
[2023-06-13 12:39:52,346] [INFO] Running command: fastANI --query /var/lib/cwl/stg841ca942-037a-4198-99e8-9e9690cde45e/GCA_022448445.1_ASM2244844v1_genomic.fna.gz --refList GCA_022448445.1_ASM2244844v1_genomic.fna/target_genomes.txt --output GCA_022448445.1_ASM2244844v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 12:40:05,401] [INFO] Task succeeded: fastANI
[2023-06-13 12:40:05,401] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf5e3de51-eab7-41dc-8747-bd70d334cda6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 12:40:05,401] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf5e3de51-eab7-41dc-8747-bd70d334cda6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 12:40:05,410] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2023-06-13 12:40:05,410] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-13 12:40:05,410] [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 macleodii	strain=ATCC 27126	GCA_000172635.2	28108	28108	type	True	97.7938	1288	1460	95	conclusive
Alteromonas abrolhosensis	strain=PEL67E	GCA_001953635.1	1892904	1892904	type	True	90.4504	1171	1460	95	below_threshold
Alteromonas portus	strain=HB161718	GCA_005117025.1	2565549	2565549	type	True	88.4737	1045	1460	95	below_threshold
Alteromonas gracilis	strain=9a2	GCA_002993325.1	1479524	1479524	type	True	83.8216	901	1460	95	below_threshold
Alteromonas mediterranea	strain=DE	GCA_000020585.3	314275	314275	type	True	83.7572	915	1460	95	below_threshold
Alteromonas australica	strain=H 17	GCA_000730385.1	589873	589873	type	True	80.55	409	1460	95	below_threshold
Alteromonas oceanisediminis	strain=SM 2104	GCA_018474025.1	2836180	2836180	type	True	78.7368	92	1460	95	below_threshold
Psychrosphaera ytuae	strain=MTZ26	GCA_017638545.1	2820710	2820710	type	True	77.5935	52	1460	95	below_threshold
Shewanella nanhaiensis	strain=NR704-98	GCA_019457885.1	2864872	2864872	type	True	76.1113	52	1460	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 12:40:05,412] [INFO] DFAST Taxonomy check result was written to GCA_022448445.1_ASM2244844v1_genomic.fna/tc_result.tsv
[2023-06-13 12:40:05,413] [INFO] ===== Taxonomy check completed =====
[2023-06-13 12:40:05,413] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 12:40:05,413] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf5e3de51-eab7-41dc-8747-bd70d334cda6/dqc_reference/checkm_data
[2023-06-13 12:40:05,414] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 12:40:05,459] [INFO] Task started: CheckM
[2023-06-13 12:40:05,460] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022448445.1_ASM2244844v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022448445.1_ASM2244844v1_genomic.fna/checkm_input GCA_022448445.1_ASM2244844v1_genomic.fna/checkm_result
[2023-06-13 12:40:39,924] [INFO] Task succeeded: CheckM
[2023-06-13 12:40:39,925] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-13 12:40:39,947] [INFO] ===== Completeness check finished =====
[2023-06-13 12:40:39,947] [INFO] ===== Start GTDB Search =====
[2023-06-13 12:40:39,947] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022448445.1_ASM2244844v1_genomic.fna/markers.fasta)
[2023-06-13 12:40:39,947] [INFO] Task started: Blastn
[2023-06-13 12:40:39,947] [INFO] Running command: blastn -query GCA_022448445.1_ASM2244844v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf5e3de51-eab7-41dc-8747-bd70d334cda6/dqc_reference/reference_markers_gtdb.fasta -out GCA_022448445.1_ASM2244844v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 12:40:40,804] [INFO] Task succeeded: Blastn
[2023-06-13 12:40:40,810] [INFO] Selected 8 target genomes.
[2023-06-13 12:40:40,810] [INFO] Target genome list was writen to GCA_022448445.1_ASM2244844v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 12:40:40,811] [INFO] Task started: fastANI
[2023-06-13 12:40:40,811] [INFO] Running command: fastANI --query /var/lib/cwl/stg841ca942-037a-4198-99e8-9e9690cde45e/GCA_022448445.1_ASM2244844v1_genomic.fna.gz --refList GCA_022448445.1_ASM2244844v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022448445.1_ASM2244844v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 12:40:49,070] [INFO] Task succeeded: fastANI
[2023-06-13 12:40:49,078] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 12:40:49,078] [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_000172635.2	s__Alteromonas macleodii	97.7938	1288	1460	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	97.79	96.10	0.88	0.76	56	conclusive
GCF_000808575.1	s__Alteromonas marina	92.5838	1092	1460	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	97.44	97.44	0.91	0.91	2	-
GCF_001953635.1	s__Alteromonas abrolhosensis	90.4504	1171	1460	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	98.27	97.25	0.92	0.89	10	-
GCF_005117025.1	s__Alteromonas portus	88.476	1046	1460	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	86.3674	789	1460	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_903772925.1	s__Alteromonas macleodii_A	85.4505	1000	1460	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	84.7179	1042	1460	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	99.20	99.20	0.96	0.96	2	-
GCF_000020585.3	s__Alteromonas mediterranea	83.7572	915	1460	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	98.15	97.41	0.86	0.82	24	-
--------------------------------------------------------------------------------
[2023-06-13 12:40:49,080] [INFO] GTDB search result was written to GCA_022448445.1_ASM2244844v1_genomic.fna/result_gtdb.tsv
[2023-06-13 12:40:49,081] [INFO] ===== GTDB Search completed =====
[2023-06-13 12:40:49,084] [INFO] DFAST_QC result json was written to GCA_022448445.1_ASM2244844v1_genomic.fna/dqc_result.json
[2023-06-13 12:40:49,084] [INFO] DFAST_QC completed!
[2023-06-13 12:40:49,084] [INFO] Total running time: 0h1m10s