[2023-06-16 20:34:59,275] [INFO] DFAST_QC pipeline started.
[2023-06-16 20:34:59,277] [INFO] DFAST_QC version: 0.5.7
[2023-06-16 20:34:59,277] [INFO] DQC Reference Directory: /var/lib/cwl/stgf817f405-4bf3-4285-80f6-5200cd4d71c2/dqc_reference
[2023-06-16 20:35:00,472] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-16 20:35:00,473] [INFO] Task started: Prodigal
[2023-06-16 20:35:00,473] [INFO] Running command: gunzip -c /var/lib/cwl/stgdf1e5127-77da-44dc-ab90-c24c76d46e5f/GCA_003521985.1_ASM352198v1_genomic.fna.gz | prodigal -d GCA_003521985.1_ASM352198v1_genomic.fna/cds.fna -a GCA_003521985.1_ASM352198v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-16 20:35:05,251] [INFO] Task succeeded: Prodigal
[2023-06-16 20:35:05,252] [INFO] Task started: HMMsearch
[2023-06-16 20:35:05,252] [INFO] Running command: hmmsearch --tblout GCA_003521985.1_ASM352198v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf817f405-4bf3-4285-80f6-5200cd4d71c2/dqc_reference/reference_markers.hmm GCA_003521985.1_ASM352198v1_genomic.fna/protein.faa > /dev/null
[2023-06-16 20:35:05,410] [INFO] Task succeeded: HMMsearch
[2023-06-16 20:35:05,411] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgdf1e5127-77da-44dc-ab90-c24c76d46e5f/GCA_003521985.1_ASM352198v1_genomic.fna.gz]
[2023-06-16 20:35:05,443] [INFO] Query marker FASTA was written to GCA_003521985.1_ASM352198v1_genomic.fna/markers.fasta
[2023-06-16 20:35:05,444] [INFO] Task started: Blastn
[2023-06-16 20:35:05,444] [INFO] Running command: blastn -query GCA_003521985.1_ASM352198v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf817f405-4bf3-4285-80f6-5200cd4d71c2/dqc_reference/reference_markers.fasta -out GCA_003521985.1_ASM352198v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-16 20:35:05,983] [INFO] Task succeeded: Blastn
[2023-06-16 20:35:05,987] [INFO] Selected 12 target genomes.
[2023-06-16 20:35:05,987] [INFO] Target genome list was writen to GCA_003521985.1_ASM352198v1_genomic.fna/target_genomes.txt
[2023-06-16 20:35:05,989] [INFO] Task started: fastANI
[2023-06-16 20:35:05,989] [INFO] Running command: fastANI --query /var/lib/cwl/stgdf1e5127-77da-44dc-ab90-c24c76d46e5f/GCA_003521985.1_ASM352198v1_genomic.fna.gz --refList GCA_003521985.1_ASM352198v1_genomic.fna/target_genomes.txt --output GCA_003521985.1_ASM352198v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-16 20:35:14,702] [INFO] Task succeeded: fastANI
[2023-06-16 20:35:14,703] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf817f405-4bf3-4285-80f6-5200cd4d71c2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-16 20:35:14,703] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf817f405-4bf3-4285-80f6-5200cd4d71c2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-16 20:35:14,710] [INFO] Found 5 fastANI hits (1 hits with ANI > threshold)
[2023-06-16 20:35:14,710] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-16 20:35:14,710] [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	98.1931	581	644	95	conclusive
Alteromonas abrolhosensis	strain=PEL67E	GCA_001953635.1	1892904	1892904	type	True	89.644	542	644	95	below_threshold
Alteromonas portus	strain=HB161718	GCA_005117025.1	2565549	2565549	type	True	87.7906	487	644	95	below_threshold
Alteromonas mediterranea	strain=DE	GCA_000020585.3	314275	314275	type	True	84.1751	463	644	95	below_threshold
Alteromonas gracilis	strain=9a2	GCA_002993325.1	1479524	1479524	type	True	83.5193	438	644	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-16 20:35:14,713] [INFO] DFAST Taxonomy check result was written to GCA_003521985.1_ASM352198v1_genomic.fna/tc_result.tsv
[2023-06-16 20:35:14,714] [INFO] ===== Taxonomy check completed =====
[2023-06-16 20:35:14,714] [INFO] ===== Start completeness check using CheckM =====
[2023-06-16 20:35:14,714] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf817f405-4bf3-4285-80f6-5200cd4d71c2/dqc_reference/checkm_data
[2023-06-16 20:35:14,715] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-16 20:35:14,744] [INFO] Task started: CheckM
[2023-06-16 20:35:14,745] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_003521985.1_ASM352198v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_003521985.1_ASM352198v1_genomic.fna/checkm_input GCA_003521985.1_ASM352198v1_genomic.fna/checkm_result
[2023-06-16 20:35:34,720] [INFO] Task succeeded: CheckM
[2023-06-16 20:35:34,721] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 68.27%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-16 20:35:34,742] [INFO] ===== Completeness check finished =====
[2023-06-16 20:35:34,742] [INFO] ===== Start GTDB Search =====
[2023-06-16 20:35:34,742] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_003521985.1_ASM352198v1_genomic.fna/markers.fasta)
[2023-06-16 20:35:34,742] [INFO] Task started: Blastn
[2023-06-16 20:35:34,742] [INFO] Running command: blastn -query GCA_003521985.1_ASM352198v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf817f405-4bf3-4285-80f6-5200cd4d71c2/dqc_reference/reference_markers_gtdb.fasta -out GCA_003521985.1_ASM352198v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-16 20:35:35,298] [INFO] Task succeeded: Blastn
[2023-06-16 20:35:35,302] [INFO] Selected 7 target genomes.
[2023-06-16 20:35:35,302] [INFO] Target genome list was writen to GCA_003521985.1_ASM352198v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-16 20:35:35,303] [INFO] Task started: fastANI
[2023-06-16 20:35:35,303] [INFO] Running command: fastANI --query /var/lib/cwl/stgdf1e5127-77da-44dc-ab90-c24c76d46e5f/GCA_003521985.1_ASM352198v1_genomic.fna.gz --refList GCA_003521985.1_ASM352198v1_genomic.fna/target_genomes_gtdb.txt --output GCA_003521985.1_ASM352198v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-16 20:35:40,656] [INFO] Task succeeded: fastANI
[2023-06-16 20:35:40,664] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-16 20:35:40,664] [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	98.1931	581	644	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	91.9724	511	644	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	89.644	542	644	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	87.7906	487	644	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	85.0481	481	644	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	84.2592	486	644	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	99.20	99.20	0.96	0.96	2	-
GCF_003443615.1	s__Alteromonas sp003443615	84.0569	488	644	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2023-06-16 20:35:40,667] [INFO] GTDB search result was written to GCA_003521985.1_ASM352198v1_genomic.fna/result_gtdb.tsv
[2023-06-16 20:35:40,668] [INFO] ===== GTDB Search completed =====
[2023-06-16 20:35:40,671] [INFO] DFAST_QC result json was written to GCA_003521985.1_ASM352198v1_genomic.fna/dqc_result.json
[2023-06-16 20:35:40,671] [INFO] DFAST_QC completed!
[2023-06-16 20:35:40,671] [INFO] Total running time: 0h0m41s